Table Of Contents Page, PNAS Volume 123, Number 15
This Week in PNAS
Opinion
QnAs
Retrospective
With the death of Charles Weissmann, molecular biology has lost of one of its most
productive, outstanding, and critical representatives. A molecular biologist who became
famous through his ground-breaking discoveries, as well as his scientific ...
Commentaries
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Perspectives
Living shorelines that comprise oyster reefs within a mosaic of multiple coastal habitats
can be a resilient and adaptive coastal protection alternative to conventional engineered
structures. The success of an oyster reef living shoreline depends on the ...
The cerebellum is implicated in nearly every domain of human cognition, yet our understanding
of how this subcortical structure contributes to cognition remains elusive. Efforts
on this front have tended to fall into one of two camps. On one side are ...
Letters
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The cultural construction of “executive function”
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Brief Reports
We exploited co-occurrences between color and other properties of natural scenes to
identify and visualize functionally distinct brain regions. For each voxel in the
Natural Scenes Dataset (NSD), we computed a scaled response-weighted average of the
...
Large cardinal axioms extend the standard set of axioms for mathematics by asserting
that very large infinite sets exist. A prominent line of current research in mathematical
logic is identifying ever stronger principles of this kind; this serves as an ...
Clinical trials and experimental observations have shown that B cells are essential
for development of T cell–mediated organ-specific autoimmunity, although their exact
contribution is not clear. As antigen presentation by B cells is focused on antigens
...
The evolution of reproductive specialization, in which somatic cells forfeit reproduction,
represents a fundamental innovation in complex multicellular life. This specialization
imposes a fitness cost: because somatic cells do not produce offspring, ...
Physical Sciences
Applied Mathematics
This paper presents a bioinspired optimization approach to address a class of inverse
problems involving entropy optimization (EOP) from knowledge of the moments of a distribution
function. In particular, we study the Hausdorff moment problem, where one ...
We present an automated procedure for computing model gradients for partial differential
equation (PDE) solvers built on sparse spectral methods, a broad class of numerical
techniques widely used in the study of fluid dynamics, continuum mechanics, waves,
...
Applied Physical Sciences
Chemputation treats chemical synthesis as the execution of reaction code on programmable
hardware. We show that a Chemputer, equipped with an extensible set of reagents, catalysts,
and process conditions, together with a compiler that maps reaction and ...
Laser-driven control of droplets is important in microfluidics, targeted delivery,
and droplet-based laser–matter interactions, yet propulsion direction and breakup
remain difficult to predict. Here, we demonstrate that an acoustically levitated droplet’s
...
Understanding how grain boundaries mediate fracture remains a critical challenge in
designing ductile, high-performance refractory alloys. Here, we extend the Rice–Thomson
criterion to account for the angle between cracks and the impinging grain ...
Biophysics and Computational Biology
RNA molecules form homotypic clusters in a variety of contexts. mRNAs enriched in
germ granules in Drosophila embryos are a canonical example, with polar granule component (pgc) mRNAs colocalized with other pgc mRNAs, and nanos mRNAs with other nanos ...
In eukaryotic cells, mitochondria form networks that range from highly fused interconnected
structures to fragmented populations of individual organelles that undergo transient
interactions. These structures can be described as temporal networks of ...
How living organisms utilize physical mechanisms to sense their environments and make
informed decisions is an open question at the interface of biology and physics. In
filamentous organisms like fungal hyphae, the decisions are taken by their growing
tip ...
Nonsegmented negative-sense RNA viruses (nsNSVs) rely on a multifunctional RNA-dependent
RNA polymerase (RdRP) complex for transcription and replication. In measles virus
(MeV), the nonstructural protein C has long been implicated in regulating RNA ...
Chemistry
In this work, the stabilization enthalpy of patchy core–shell nanocomplexes is used
to assess their thermodynamic stability. It is defined as the enthalpy of formation
of a hydrated core–shell complex from hydrated (uncoated) core and hydrated shell
...
Chemically complex extracellular matrices define cellular microenvironments and shape
cell behavior across all domains of life. But how has evolution optimized these materials
to ensure the success of multicellular communities? Inspired by the well-...
Ferroelectric anomalous photovoltaic (APV) effect, as a fascinating physical conceptual
phenomenon, holds significant potentials for new optoelectronic device applications.
However, due to the lack of knowledge on the origin and underlying mechanism of ...
Earth, Atmospheric, and Planetary Sciences
During the Eocene–Oligocene Transition ( 34.4 to 33.7 Ma), major climatic and tectonic changes initiated Earth’s current icehouse
climate. Plate motion intensified mountain building, reduced atmospheric CO2, and triggered global cooling. Crucially, the ...
Accurate subseasonal to seasonal (S2S) weather forecasts are critical for managing
risks to society, yet improving forecast skill remains challenging. Ensemble forecasting
mitigates atmospheric chaos but is limited by computational cost and by declining
...
Rocks release subtle geochemical warning signals before breaking. These signals, coming
from naturally occurring nuclides (e.g., radon, helium, argon, and thoron), have often
been reported before earthquakes, volcanic eruptions, landslides, and rock and ...
Environmental Sciences
Alluvial rivers have long been described by hydraulic geometry theory, which links
equilibrium channel dimensions to flow discharge. Yet natural rivers are inherently
dynamic, with planforms evolving over time and widths fluctuating around an equilibrium
...
Social Sciences
Demography
Human aging is marked by a steady rise in the risk of dying with age–a process demographers
call senescence. Over the past century, life expectancy has risen dramatically, but
is this because we are aging slower, or simply starting it later? Vaupel ...
Accelerated global population aging challenges conventional economic growth paths.
Yet, the mechanisms underlying the transition from the age-based demographic dividend,
derived from a favorable age support ratio (ASR), to a skill-based dividend, driven
...
Political Sciences
Qualitative studies on local police collaborations with federal immigration enforcement
authorities reveal risks to the well-being of noncitizens, particularly the undocumented,
and their families and communities. Yet statistical evidence of these ...
Psychological and Cognitive Sciences
We often share personal memories with others, but the social function of episodic
memory retrieval is not clear. In two experiments (N1 = 50, N2 = 125), run in two different labs, in different countries with different languages,
and using naturalistic as ...
Many college students experience introductory physics as psychologically threatening.
In a preregistered RCT, we applied the biopsychosocial model of challenge-threat to
describe patterns of threat in introductory physics and test whether a 5-d ...
Prosocial and antisocial behaviors can reflect the actor’s positive or negative feelings
toward a specific person and their broader disposition toward others’ welfare. Observers’
inferences about these motives shape what they learn about the actor’s ...
Everyday cognition depends on the brain’s capacity to shift between sensing the external
world and constructing it from memory. To achieve this, large-scale cortical systems
must flexibly integrate incoming sensory signals with internally generated ...
Social Sciences
Does more schooling cause higher lifetime earnings? Social scientists have long sought
to determine the economic returns to schooling given its importance to individual
life chances and public policy. Prior estimates are limited by unobserved confounding
...
Sustainability Science
To mitigate the potential impacts of wildfire, communities across the United States
are engaging in collaborative wildfire risk mitigation planning. Planning involves
identifying a set of goals, developing management strategies to achieve those goals,
and ...
Biological Sciences
Applied Biological Sciences
The hinge ligament of bivalves exhibits remarkable flexibility and compressive strength
due to its composite structure of aragonite nanofibers embedded in an organic matrix.
While these nanofibers are crucial for shell mechanics, the molecular mechanisms ...
Developing safe, reversible, and nonhormonal male contraceptives has been hindered
by the lack of defined biological windows that can be transiently interrupted without
compromising long-term fertility. Here, we tested whether meiotic prophase I can serve
...
Infestation of potato by the potato tuber moth (Phthorimaea operculella) varies markedly among cultivars, yet the chemical and molecular mechanisms underlying
this variation remain poorly understood. Here, we combine field surveys, chemical
ecology, ...
Engineered extracellular vesicles (EVs) are a class of nonviral delivery vectors for
RNA-based vaccines and gene therapies. A specialized form of engineered EVs, known
as enveloped protein nanocages (EPNs), has been developed to enhance cargo loading
and ...
Biochemistry
In this work, the stabilization enthalpy of patchy core–shell nanocomplexes is used
to assess their thermodynamic stability. It is defined as the enthalpy of formation
of a hydrated core–shell complex from hydrated (uncoated) core and hydrated shell
...
Envenomation by sicariid spiders such as the brown recluse can cause loxoscelism,
a syndrome involving localized dermonecrosis and/or systemic effects like hemolysis.
The causative venom toxins are unusual interfacial phospholipase D enzymes that cyclize
...
Heat shock proteins 70 (Hsp70) represent a ubiquitous and conserved family of molecular
chaperones involved in a variety of cellular processes. The conformational cycles
of several Hsp70 chaperones, driven by ATP binding and hydrolysis, and regulated by
...
The root-like holdfast of the tunicate Halocynthia roretzi provides strong underwater adhesion. However, the biological processing and biochemical
composition underlying its adhesive remain largely unknown. Here, we identify a nanocondensate-based
...
The Arg/N-degron pathway of Saccharomyces cerevisiae is mediated by two interacting E3 ubiquitin ligases, Ubr1 and Ufd4. We show here
that the mitotic checkpoint kinase Chk1 bears a C-degron that can be recognized by
both Ubr1 and Ufd4. Ubr1 is an E3 that ...
In organisms ranging from Archaea to humans, a subset of genes encoding tRNAs contain
introns. Upon splicing, the tRNA exons are joined and the released free introns are
rapidly degraded. Although tRNAs introns were previously considered to be “junk” ...
Biophysics and Computational Biology
RNA molecules form homotypic clusters in a variety of contexts. mRNAs enriched in
germ granules in Drosophila embryos are a canonical example, with polar granule component (pgc) mRNAs colocalized with other pgc mRNAs, and nanos mRNAs with other nanos ...
While it is well known that ion binding can stabilize RNA structure, little is known
about how transient/probabilistic ionic interactions facilitate biologically relevant
conformational rearrangements. To address this, we developed a theoretical model ...
Neurotransmitter release requires the precise localization and assembly of the SNARE
machinery at presynaptic release sites. Although liquid–liquid phase separation of
active zone scaffolds is known to organize these sites, the mechanism for the specific
...
Malaria is a leading cause of disease in developing countries. The licensed malaria
vaccine RTS,S/AS01 confers partial protection in part due to the elicitation of circumsporozoite
protein (CSP) antibodies, of which those to the CSP repeat and junctional ...
Inferring protein production kinetics in dividing cells is complicated by protein
inheritance from the mother cell. For instance, fluorescence measurements commonly
used to assess gene activation may reflect not only newly produced proteins but also
those ...
Temperature-sensitive transient receptor potential melastatin subfamily 4 (TRPM4)
ion channels convert intracellular calcium increases into membrane depolarization,
thereby linking these two powerful cellular signaling pathways in diverse physiological
...
De novo design of membrane proteins (MPs) is a rapidly growing field with transformative
potential for synthetic biology. Yet, progress has lagged behind that of soluble proteins,
largely due to limited understanding of the fundamental principles ...
The chemokine system, comprising a network of chemokines and their receptors, orchestrates
leukocyte migration and plays a central role in immune surveillance and inflammation.
Targeting this system has emerged as a promising strategy in cancer ...
PIEZO channels are critical for sensory mechanotransduction. While MyoD-family inhibitor
proteins were identified as PIEZO1 auxiliary subunits, their broader regulatory roles,
particularly in sensory cells, remained unclear. Here, we demonstrate native ...
Human glycoprotein hormones such as thyroid-stimulating hormone (TSH) and follicle-stimulating
hormone (FSH) belong to a broader family of cystine-knot hormones (CKHs), all of which
act through leucine-rich-repeat (LRR)-containing G protein–coupled ...
Many protein–protein interactions (PPIs) are mediated by the binding of short linear
motifs (SLiMs) to peptide recognition domains (PRDs). Here, we describe PrePPI-SLiM,
a proteome-scale computational pipeline that leverages data from the Eukaryotic ...
Cell Biology
In eukaryotic cells, mitochondria form networks that range from highly fused interconnected
structures to fragmented populations of individual organelles that undergo transient
interactions. These structures can be described as temporal networks of ...
Most plant tissues are symplasms in which cells are connected by plasmodesmata, membrane-lined
cytosplasmic bridges that enable diffusive and/or advective cell-to-cell movements
of components of the cytosol. Current models assume that hydrodynamic radius ...
Invasion plasticity allows malignant cells to toggle between collective, mesenchymal,
and amoeboid phenotypes while traversing extracellular matrix (ECM) barriers. Current
dogma holds that collective and mesenchymal invasion programs trigger the ...
Iridosomes, the guanine crystal-forming organelles of pigment-producing iridophores,
are among the most versatile, visually striking yet mechanistically uncharacterized
organelles in vertebrate biology. Lysosome-related organelles (LROs) support cell
type–...
The small GTPase Rac is an essential regulator of cell shape, migration, macropinocytosis,
and phagocytosis. We found that expression of constitutively active RacG12V is sufficient to cause a few migratory cells called border cells to cannibalize ...
Developmental Biology
Adult stem cells maintain tissue homeostasis, yet are themselves vulnerable to loss.
One common mechanism to replace lost stem cells is dedifferentiation, in which progeny
revert to stem cell identity. It is a paradox how stem cells and progeny retain the
...
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Zygotic genome activation (ZGA) marks the first transcriptional milestone and establishes
embryonic totipotency. Although pioneer factors have been reported to initiate this
process, how chromatin is primed for the totipotent state, allowing the binding ...
Ecology
Parental care enhances offspring survival and growth but often entails a trade-off
in which caregivers temporarily suppress their own reproduction to invest in existing
young. In vertebrates, these parental reproductive cycles are controlled by offspring-...
Environmental Sciences
China is the largest emitter of cropland gaseous reactive nitrogen (Ngr, including
NH3, N2O, and NOx), which greatly affects regional air quality, climate change, and human
health. Despite the substantial spatial and temporal variations in cropland Ngr ...
Evolution
Ancestral state reconstruction (ASR) is a foundational tool in comparative biology,
offering insights into the evolutionary history of lineages. With each new evolutionary
model, our ability to estimate ancestral states with increased biological realism
...
While sex chromosome systems show frequent evolutionary transitions in some clades,
in many others they show long-term stability. Previous explanations of this stasis
rely on evolutionary dynamics peculiar to sex chromosomes, such as the accumulation
of ...
Probabilistic models such as the sequentially Markovian coalescent have long provided
a powerful framework for population genetic inference, enabling reconstruction of
demographic history and ancestral relationships from genomic data. However, these
...
Genetics
Repetitive DNA sequences can adopt alternative (i.e., non-B) DNA structures, which
represent an endogenous source of genetic instability. Z-DNA, a non-B-DNA structure,
has been implicated in the development of age-related genetic disorders such as cancer
...
Translational fusion of two separate genes into a compound sequence encoding a fusion
protein is a key evolutionary mechanism which underpins the emergence of new protein
activities, families, and architectures. In biotechnology, gene fusion is a valuable
...
Circulating hormones, that mediate communications across organs to maintain physiological
balance, are commonly detected and quantified using enzyme-linked immunosorbent assays
(ELISAs). However, while ELISA is well suited for organisms where sample blood ...
Mitochondria are central to energy metabolism and cellular signaling, and mutations
in mitochondrial DNA (mtDNA) can disrupt these processes and contribute to human disease.
However, progress in defining how mtDNA variation influences adaptation, ...
Immunology and Inflammation
Bacterial sepsis remains a devastating clinical problem. Here, we describe a protective
role for the recently discovered acid-sensitive, proton-activated chloride channel,
PACC1 (PAC/ASOR/TMEM206), during sepsis. Initially, we found PACC1 was enriched in
...
Bladder cancer remains a significant therapeutic challenge due to its marked heterogeneity
and capacity for immune evasion. Here, we employ spatial metabolomics and spatial
transcriptomics to systematically characterize and visualize the metabolic and ...
Receptor-interacting protein kinase 1 (RIPK1) is a key regulator of cell death and
inflammation, with its activation modulated by diverse posttranslational modifications.
While ubiquitination of RIPK1 at lysine 376 (K376) has been shown to inhibit ...
Microbial-derived short-chain fatty acids regulate a variety of pathways in the healthy
colonic mucosa. In particular, butyrate serves as the primary energy source for colonocytes
and regulates gene transcription by stabilizing the transcription factor ...
The tumor necrosis factor (TNF) receptor 1 (TNF-R1) plays critical roles in inflammatory
response and autoimmune diseases. The underlying mechanisms on posttranslational regulation
of TNF-R1 and its functional significance remain enigmatic. In this study, ...
Tumor heterogeneity poses a major challenge to tumor therapy due to the expression
of unique, poorly recognized immunogenic proteins driven by environmental stress.
The broad antigenic repertoire of cell-based vaccines, particularly their inclusion
of ...
Anti-programmed cell death 1 (PD-1) antibody therapy is now widely used in various
cancers. However, the role of the antibody Fc region in PD-1 directed immunotherapy
is not well understood. Preclinical studies commonly use species-mismatched rat anti-...
Medical Sciences
Sepsis-induced myocardial dysfunction strongly contributes to high mortality in patients
with sepsis by exacerbating systemic organ failure; however, the onset and molecular
mechanisms driving this vicious cycle remain unclear. Here, we revealed that DRP1-...
Plasma cell-free DNA (cfDNA), originating from multiple organs, holds significant
potential for noninvasive diagnostics and prognostics. Current cfDNA methylation assays
primarily focus on single clinical indications by targeting specific genomic loci.
In ...
Targeted protein degradation (TPD) has emerged as a promising therapeutic strategy;
however, most TPD technologies employ either the ubiquitin–proteasome system or the
lysosomal degradation system. Here, we report the development of midnolin-based ...
Ewing sarcoma is driven by chromosomal translocations that fuse a FET RNA-binding
protein to an ETS transcription factor, most commonly generating the EWS-FLI1 fusion
oncoprotein. EWS-FLI1 engages GGAA microsatellite repeats to form de novo enhancers
that ...
Microbiology
Chemically complex extracellular matrices define cellular microenvironments and shape
cell behavior across all domains of life. But how has evolution optimized these materials
to ensure the success of multicellular communities? Inspired by the well-...
Nonsegmented negative-sense RNA viruses (nsNSVs) rely on a multifunctional RNA-dependent
RNA polymerase (RdRP) complex for transcription and replication. In measles virus
(MeV), the nonstructural protein C has long been implicated in regulating RNA ...
Hypovirulence-associated mycoviruses can be frequently isolated in nature despite
their likely compromised ecological fitness, but how their fungal hosts survive in
natural environments remains largely unresolved. The discovery of more mycoviruses
...
Light is one of the most pervasive physical cues in aquatic environments, yet its
impact on nonphototrophic pathogens remains largely unexplored. Here, we show that
a strain of cholera bacterium Vibrio cholerae directly couples illumination to motility ...
Infections by Gram-negative pathogens like Salmonella and Shigella rely on type III secretion system (T3SS) effectors. While the opportunistic pathogen
Chromobacterium violaceum encodes a crucial T3SS (Cpi-1/-1a), its full effector repertoire remains ...
The immune mechanisms responsible for protection and pathogenesis in pneumoviral infection
are not well defined. We demonstrated that pharmacological activation of the hypoxic
inducible factor (HIF) signaling axis using daprodustat limited viral ...
Antagonistic systems of bacteria are often tightly regulated. The human gut Bacteroidales
harbor three distinct antagonistic type VI secretion systems (T6SS), one of which
is present only in Bacteroides fragilis, known as the GA3 T6SS. Although this is ...
As crucial ecosystem engineers in global drylands, desert cyanobacteria regulate biogeochemical
cycling and contribute to the stabilization of arid soils. These extremophiles frequently
exploit nocturnal dew deposition to resume metabolism, activate ...
Control of schistosomiasis, a neglected tropical disease caused by infection with
Schistosoma spp., remains reliant on a single chemotherapy, praziquantel (PZQ). This strategy presents
a risk to global health should PZQ-resistant schistosomes establish in ...
Activation of the Toll, Immunodeficiency (IMD), Jun-kinase (JNK), and Signal Transducer
and Activator of Transcription (STAT) innate immune signaling pathways limits Plasmodium infection in Anopheles gambiae. Hemocytes (mosquito immune cells) restrict ...
Coronaviruses pose a serious threat to public health, driving the need for antiviral
therapeutics and vaccines. Therefore, it is paramount to understand how this family
of viruses evades cellular antiviral responses and establishes productive infection.
...
Neuroscience
The hippocampus supports episodic memory by binding spatial and semantic information,
yet how this information is simultaneously organized along its long axis remains debated.
Gradient accounts propose a continuous shift in representational scale, from ...
Myo7a, a gene mutated in Usher syndrome and nonsyndromic deafness, encodes an unconventional
myosin essential for hair cell function. Our previous work revealed that cochlear
hair cells express distinct Myo7a isoforms with unique spatial and cell type–...
The subplate (SP) is a transient fetal brain compartment supporting neuronal migration,
axonal ingrowth, and early cortical activity, yet the dynamics of its regional development
remain poorly understood in vivo. Using T2-weighted fetal MRI of 68 ...
Behavioral flexibility relies on transient neural dynamics that govern cortical state
transitions. However, whether humans can deliberately learn to control such state
transitions and generalize trained neural dynamics beyond contexts remains unclear.
...
In many species, chemosensory cues convey important information about reproductive
status, but their role in shaping social interactions among women is less understood.
Here, we combined functional neuroimaging with behavioral measures to test how ...
Microexons of 3 to 27 nucleotides selectively regulated in the vertebrate nervous
system have attracted attention as new elements for modifying the function of neuronal
proteins. Protein tyrosine phosphatase δ (PTPRD) is one of presynaptic hubs for ...
Dopamine critically modulates prefrontal circuits underlying cognitive control, but
how D1-type (D1R) and D2-type (D2R) receptors influence abstract decision coding is
unclear. We recorded single-neuron activity in two monkeys performing a number ...
Astrocytes and tanycytes play essential roles in hypothalamic metabolic sensing, yet
how glial–glial communication translates metabolic cues into neuronal activity remains
poorly understood. We previously demonstrated that tanycytes release lactate and ...
Pharmacology
The opioid epidemic has led to a devastating loss of life nationwide. Of those dependent
on opioids, many individuals desire to quit or reduce use, but their efforts are often
unsuccessful given the powerful reinforcing properties associated with opioid ...
Pharmacological reversal of abnormal promoter DNA hypermethylation at tumor suppressor
genes (TSGs) is a key therapeutic paradigm for cancer management. However, the clinical
efficacy of currently approved nucleoside analog hypomethylating agents (HMAs) ...
Physiology
Up to a third of the global population is afflicted by metabolic dysfunction-associated
steatotic liver disease with excessive triglyceride accumulation in the liver. Prolonged
fasting rapidly causes hepatic steatosis via excessive influx of free fatty ...
Plant Biology
The capacity of trees to withstand intensifying hot drought events depends on the
coordination between hydraulic safety and leaf thermoregulation, yet the limits of
this coordination under chronic stress remain poorly understood. Here, we show that
5 y of ...
Plants in the family Solanaceae produce steroidal glycoalkaloids (SGAs), specialized metabolites that are toxic to
consumers while providing protection against herbivores. The Colorado potato beetle
(CPB) is a major foliar pest of potatoes, and the wild ...
Plants secrete a variety of proteases as a defense response during infection by microbial
pathogens. However, the relationship between their catalytic activities and antimicrobial
functions remains largely unknown. Particularly, few biologically relevant ...
Chromalveolate algae such as diatoms, haptophytes, and dinoflagellates are main contributors
to oceanic primary production, sustaining marine ecosystems and global carbon cycles
while synthesizing a striking array of acetylated carotenoids like ...
The Flowering Locus C (FLC) gene is a flowering repressor in annual plants, but its function in perennial woody
species remains less understood. Here, we explored the role of BpFLC in Betula platyphylla using a genotype that flowers after 5 to 6 y of ...
Population Biology
Human aging is marked by a steady rise in the risk of dying with age–a process demographers
call senescence. Over the past century, life expectancy has risen dramatically, but
is this because we are aging slower, or simply starting it later? Vaupel ...
Psychological and Cognitive Sciences
Everyday cognition depends on the brain’s capacity to shift between sensing the external
world and constructing it from memory. To achieve this, large-scale cortical systems
must flexibly integrate incoming sensory signals with internally generated ...
Systems Biology
Genome-scale metabolic models (GEMs) have become essential tools for understanding
human metabolism. Here, we introduce Human2, a consensus human GEM with enhanced precision
and biological relevance, which leverages large language models (LLMs) and GitHub
...
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