Miracle-dz/UniFAR-FTUs huggingface dataset:
A Foundational Large Language Model for Edible Plant Genomes

In recent years, significant progress has been made in the field of plant genomics, demonstrated by the increased use of high-throughput methodologies that allow for the characterization of multiple genome-wide molecular phenotypes. These results have provided valuable insights into plant traits and their underlying genetic mechanisms, especially in well-researched model plant species. Nonetheless, although acquiring and characterizing these molecular phenotypes can offer valuable insights into plant traits, effectively leveraging them to make accurate predictions represents a critical step in crop genomic improvement. We present AgroNT, a novel foundational large language model trained on reference genomes from 48 plant species with a predominant focus on crop species. We show that AgroNT can obtain state-of-the-art predictions for many genomic elements, including polyadenylation sites, splice sites, open chromatin and enhancer regions. Furthermore, AgroNT can be used to predict the strength of promoter sequences and tissue-specific gene expression levels or prioritize functional variants. Using the cassava genome as an example of an understudied species, we perform a large-scale in silico saturation mutagenesis analysis to assess the impact of >10 million mutations on gene expression levels and enhancer elements in the cassava genome, and provide the results as a valuable resource for regulatory causal variant characterization. Furthermore, owing to the lack of comprehensive benchmarks in the context of deep learning-based methods in plant genomic research, we propose the use of the multiple datasets encompassing seven distinct genomic prediction tasks, which have been compiled here, as the Plants Genomic Benchmark (PGB). The pre-trained AgroNT model is now publicly available on Hugging Face at https://huggingface.co/InstaDeepAI/agro-nt for future research purposes.
Analysis of the peptide helicity using an ensemble spectroscopic model with re-calibrated parameters

The α-helix is the fundamental building block of protein structure. Understanding the physical principles that determine how a specific amino acid sequence defines helicity is a key step towards elucidating the sequence-structure relationship. An established method for quantitation of helix content using circular dichroism (CD) relies on the linear spectroscopic model. In this model, the helix length-correction is not applied to each ensemble conformer individually, rather an average value is assumed for all conformers. Here we assess the validity of this approximation and introduce a more physically realistic ensemble-based analysis of the CD signal. We find that the linear model tends to underestimate peptide helicity, with the difference depending on the ensemble composition. Using a CD dataset covering a broad range of helicities, we re-calibrate spectroscopic parameters (helix and coil baselines) and determine helix-coil parameters for a set of alanine-rich peptides. Our results show that the ensemble model can leverage the small spectroscopic differences between peptide conformers, enabling it to extract more information from the experimental data. We show that some previously poorly-defined quantities, such as helix nucleation constant and heat capacity change associated with helix folding, can be reliably determined using ensemble model. Overall, the presented ensemble-based treatment of the CD signal, together with the re-calibrated values of the spectroscopic baseline parameters, provides a coherent framework for the analysis of the peptide helix content.
FACTORS AFFECTING BONE MINERAL DENSITY IN ELITE FEMALE RUNNERS By MAUREEN CARTOON

Introduction: The benefits of regular exercise on skeletal health have been welldocumented in terms of stimulation of bone accrual and bone maintenance. Mediumimpact sports activities such as running have been demonstrated to exert site-specific enhancement of bone mass in the lower appendicular skeleton. However, elite female runners engaged in high intensity training and sports activity may also be at risk of amenorrhea and low bone mineral density (BMD) resulting from inadequate caloric intake. Purpose: To investigate the effect of intensive exercise and maintenance of adequate caloric intake on BMD in a group of elite female runners. Methods: This study represents a secondary assessment of existing data that were obtained between 1994 and 2009. Using dual-energy X-ray absorptiometry, a group of elite runners (n=11) in this study was screened in the Laboratory for Elite Athlete Performance at Georgia State University. This was a longitudinal study in which three sequential measurements of BMD as well as fat and lean tissue body composition of each athlete took place. The average interval between measurements was 1.1 years and 2.6 years respectively. Regional BMD measurements for head, arms, legs, trunk, ribs, pelvis, and spine were assessed, as well as the value for total body BMD. The study participants also received dietary counseling emphasizing daily caloric balance and adequate calcium intake. Results: The average age of the runners increased from 24.59 (±4.41) to 28.14 (±5.94) years over the study. This was accompanied by an increase in body mass (54.98±3.54 to 56.11±4.07 kg), while height remained constant. The average body mass index (BMI) of the subjects increased from 19.34 to 19.71 kg/m, largely due to an increase in total percent body fat (13.97±2.96% to 16.01±4.28%). Average regional and total BMD values increased over the study period and increases were between 2 and 4%. At the baseline, a majority of subjects (n=7) had a BMI>19 kg/m, while a sub-group of runners (n=4) had a BMI˂19 kg/m. Mean trunk, pelvis and spine BMD parameters for the two BMI groups were significantly different (p˂0.05), with reduced BMD values in the lower BMI sub-group. The average T-scores associated with arm BMD were considerably lower than T-scores associated with leg BMD values in the runners. The average Tscores for leg BMD values were almost two standard deviations higher than leg BMD values for a reference population at peak bone mass. Two subjects were osteopenic, resulting in an 18% prevalence rate of osteopenia in the group of runners. Conclusions: The majority of elite runners in this study exhibited a positive trend in BMD parameters. This was reflected as increased total as well as regional BMD values. Increased body mass in addition to the activity of running positively contributed to bone mass via a weight-bearing effect. Increased adipose tissue may also have been a source of endocrine hormones such as estrogen and leptin, which exert a positive effect on bone accrual.
RELAXING SELECTIVE PRESSURES ON DEVELOPMENTALLY COMPLEX INTEGUMENTARY STRUCTURES: FEATHER VANE SYMMETRY EVOLVES IN ADDITION TO BODY MASS AND WING LENGTH AFTER FLIGHT LOSS IN RECENT BIRDS

Feathers are complex integumentary structures with high diversity across species and within plumage and have varied functions (e.g., thermoregulation, flight). Flight is lost in many crown lineages, and frequently occurs in island ‘founding’ or semiaquatic context. Different extant lineages lost flight across at least three orders of magnitude of time (∼79.58 Ma–15 Ka). Flight loss’s effect on sensory capacity, brain size, and skeletomusculature have been studied, but less work exists on relations between flightlessness and feathers. To understand how flight loss affects feather anatomy, we measured 11 feather metrics (e.g., barb length, barb angle) from primaries, tertials, rectrices, and contour feathers on skins of 30 flightless taxa and their phylogenetically closest volant taxa, supplemented with broader sampling of primaries across all orders of volant crown birds. Our sample includes 27 independent losses of flight; the sample contains nearly half the extant flightless species count and matches its ∼3:2 terrestrial:semiaquatic ratio. Vane symmetry increases in flightless lineages, and these patterns are strongest in flight feathers and weakest in coverts. Greatest changes in feathers are in the oldest flightless lineages like penguins, which show robust filaments (rachis, barbs, and barbules) on small feathers, and ratites, which show high interspecific diversity with plumulaceous filaments and/or filament loss. Phylogenetic comparative methods show that some of these microscopic feather traits, such as barb/barbule length and rachis width, are not as dramatically modified upon flight loss as are body mass increase and relative wing and tail fan reduction, whereas the effect on vane symmetry is more easily detected. Upon relaxing selection for flight, feathers do not soon significantly modify many of their flight adaptations, although increased vane symmetry is likely the most detectable shift. Feathers of recently flightless lineages are in many ways like those of their volant relatives. Feather microstructure evolution is often subtle in flightless taxa, except when flight loss is ancient, perhaps because developmental constraints act upon feathers and/or selection for novel feather morphologies is not strong. Changes in skeletomusculature of the flight apparatus are likely more evident in recently flightless taxa and may be a more reliable way to detect flight loss in fossils, with increased vane symmetry as potentially a microscopic signal. Finally, we see an intriguing, reversed pattern in feather evolution after flight loss from the pattern proposed in popular developmental models of feathers, with the later stages of feather development (asymmetric displacement of barb loci) being lost more readily, while early stages of development (e.g., differentiated barb ridges on follicle collar) are only lost after many millions of years of flightlessness.
Allosteric Modulation of YAP/TAZ-TEAD Interaction by Palmitoylation and Small Molecule Inhibitors

The Hippo signaling pathway is a highly conserved signaling network that plays a central role in regulating cellular growth, proliferation, and organ size. This pathway consists of a kinase cascade that integrates various upstream signals to control the activation or inactivation of YAP/TAZ proteins. Phosphorylated YAP/TAZ is sequestered in the cytoplasm; however, when the Hippo pathway is deactivated, they translocate into the nucleus, where they associate with TEAD transcription factors. This partnership is instrumental in regulating the transcription of pro-growth and anti-apoptotic genes. Thus, in many cancers, aberrantly hyperactivated YAP/TAZ promotes oncogenesis by contributing to cancer cell proliferation, metastasis, and therapy resistance. Because YAP and TAZ exert their oncogenic effects by binding with TEAD, it is critical to understand this key interaction to develop cancer therapeutics. Previous research has indicated that TEAD undergoes an auto-palmitoylation at a conserved cysteine, and small molecules that inhibit TEAD palmitoylation disrupt effective YAP/TAZ binding. However, how exactly palmitoylation contributes to YAP/TAZ-TEAD interactions and how the TEAD palmitoylation inhibitors disrupt this interaction remains unknown. Utilizing molecular dynamics simulations, our investigation not only provides a detailed atomistic insight into the YAP/TAZ-TEAD dynamics but also unveils that the inhibitor studied influences YAP and TAZ binding to TEAD in distinct manners. This discovery holds significant implications for the design and deployment of future molecular interventions targeting this interaction.
Augmentation of J waves and electrical storms in patients with early repolarization.

To the Editor: Early repolarization, consisting of an elevation of the QRS–ST junction (J point), QRS notching or slurring (J wave), and a tall, symmetric T wave, is generally considered to be benign.1 On the basis of preclinical experimental evidence, it has been suggested that some forms of early repolarization seen in the clinic may not be benign, especially when associated with the occasional appearance of J waves or ST-segment elevation.2 Sporadic case reports and basic electrophysiological research have suggested a critical role of the J wave in the pathogenesis of idiopathic ventricular fibrillation.3,4 Clinical evidence in support of .
Tectonic interpretation of the connectivity of a multiscale fracture system in limestone

This paper studies the statistics and tectonism of a multiscale natural fracture system in limestone. The fracture network exhibits a self‐similar characteristic with a correlation between its power law length exponent a and fractal dimension D, i.e., a ≈ D + 1. Contradicting the scale‐invariant connectivity of idealized self‐similar systems, the percolation state of trace patterns mapped at different scales and localities of the study area varies significantly, from well to poorly connected. A tectonic interpretation based on a polyphase fracture network evolution history is proposed to explain this discrepancy. We present data to suggest that the driving force for fracture formation may be dissipated at the end of a tectonic event when the system becomes connected. However, the “effective” connectivity can successively be reduced by cementation of early fractures and reestablished by subsequent cracking, rendering a variable “apparent” connectivity that can be significantly above the percolation threshold.
Climate and human influences on historical fire regimes (AD 1400–1900) in the eastern Great Basin (USA)

High fire activity in western North America is associated with drought. Drought and fire prevail under negative El Niño Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO) phases in the Southwest and with positive phases in the Northwest. Here, I infer climate effects on historic fire patterns in the geographically intermediate, eastern Great Basin and seek out evidence of human influence on reconstructed fire regimes. Surface fire chronologies were constructed for 10 sites using tree-ring-based fire scars. Regional (67) and local (247) fire years and no-fire (187) years were identified from 1400 to 1900 CE. I compared fire chronologies with indices of the Palmer Drought Severity Index (PDSI), ENSO, and PDO. Regionally, fires were significantly more common during drought and were associated with negative ENSO and positive-to-negative PDO transitions while no-fire years were associated with positive ENSO and negative-to-positive PDO transitions. Conditions were significantly wetter 2 years prior to regional fire years and drier 4 years prior to no-fire years, providing evidence that fires were historically fuel limited. Local fire years occurred under a broad range of climate conditions. Most sites showed either persistent late or bimodal (early and late) fire seasonality patterns. These patterns are distinct from the mid-season peak observed for modern lightning-caused fires, suggesting a human influence on historical ignition patterns. Results demonstrate that climate was an important synchronizer of fire at the regional scale and that locally fire regimes were the product of climate-regulated fuels and some combination of human and lightning ignition patterns.
Smallholder cattle production systems in Metekel zone, northwest Ethiopia

A cross-sectional survey was conducted in Metekel zone, Benishangul Gumuz National Regional State, Northwest of Ethiopia to assess livestock production system, productive and reproductive performance of cattle and identify constraints to livestock. Stratified random sampling technique was used to select 160 farming households and administer a pre-tested and structured questionnaire. The study showed that mixed crop-livestock production system was the dominant farming system in the study area. The average landholding per household was 2.12±0.15 ha. The average livestock holding per household was 13.99±1.08 cattle, 11.37±1.37 goats, 6.14±1.06 sheep, 1.13±0.09 mule, 1.50±0.14 donkey, and 8.45±0.54 chickens, respectively. The major feed resources were natural pasture, crop residue, conserved hay from natural pasture, stubble grazing, and non-conventional feeds. The average milk productions per cow per day during wet and dry seasons were 1.78±0.97 and 0.88±0.56 liters, respectively. Average age at first calving, calving interval and lactation length were reported to be 46.06±13.99, 23.38±13.95 and 9.81±3.91 months, respectively. Respondents revealed feed shortage, disease prevalence mainly bovine trypanosomiasis, lack of capital, water and labor scarcity as major livestock constraints in that order of importance. Thus, intervention options should aim to alleviate the prevailing constraints to smallholder livestock production in the area. Key words:
Thermal evolution Cooling of the Žiar Mountains basement (Inner Western Carpathians, Slovakia) constrained by fission track data

Thermal evolution of the Žiar Mts was studied using zircon and apatite fission track (ZFT and AFT) thermochronology applied to basement and sedimentary rocks. Basement samples from the Tatric Unit of the Inner Western Carpathians (IWC) yielded cooling ZFT ages in the range from 109± 5.9 to 92.1± 5.3 Ma and apparent AFT ages between 33.7± 2.7 and 24.4± 1.7 Ma. Paleogene sediments of the Central Carpathian Paleogene Basin (CCPB) yielded apparent AFT ages of 73.2± 2.7 and 49.6± 1.8 Ma. ZFT data show that during early Late Cretaceous thrusting the crystalline basement was buried by a nappe pile to crustal depths with temperatures between 210 and 310 °C, where the crystalline core was metamorphosed at anchizonal conditions. AFT data revealed a complex thermal evolution, implying that after nappe stacking and metamorphism the basement was exhumed to the surface and that it was buried beneath a thick pile of sediments of the CCPB. The CCPB was inverted and the basement finally exhumed in the Late Oligocene to Early Miocene. The AFT system in the basement and CCPB samples record also a distinct, Middle Miocene thermal event, related to the increased heat flow induced by upwelling of hot mantle material and related volcanic activity. Our data support the hypothesis that the study area was part of a large CCPB basin and contradict the widely accepted assumption that the Variscan crystalline core of the Žiar Mts lacks an Alpine metamorphic overprint.
Experience Effects in R & D Alliances 1011

Focusing on the link between prior alliance experience and firm benefits from R&D collaborations, this paper explores whether firms learn to manage their alliances. While prior experience should increase collaborative benefits from the current alliance, I expect these returns: (1) to be most beneficial when alliance activities are more uncertain; and (2) to diminish at high levels of experience. Results from a sample of 464 R&D alliances in the telecom equipment industry generally match these expectations. The positive benefits of prior experience in complex alliances suggest that a broader set of alliance management processes allows the firm to manage situations of ambiguity more readily. The lack of cumulative benefits from prior experience appears to be partly due to knowledge depreciating over time, since only recent experience has a positive impact on collaborative returns. Overall, these results provide empirical evidence of the effect of prior experience on collaborative benefits, both directly and conditionally on alliance characteristics, and have implications for learning to manage organizations more generally. Copyright  2005 John Wiley & Sons, Ltd.
Co‐variability of tropical cyclones in the North Atlantic and the eastern North Pacific

In the Western Hemisphere, tropical cyclones (TCs) can form and develop in both the tropical North Atlantic (NA) and eastern North Pacific (ENP) Oceans, which are separated by the narrow landmass of Central America. Here it is shown that TC activity in the NA varies out‐of‐phase with that in the ENP on both interannual and multidecadal timescales. That is, when TC activity in the NA increases (decreases), TC activity in the ENP decreases (increases). Our analyses show that both vertical wind shear and convective instability contribute to the out‐of‐phase relationship, whereas relative humidity and vorticity variations at the lower troposphere do not seem to cause the relationship. The paper also discusses its association with the Pacific and Atlantic sea surface temperatures. An implication is that seasonal hurricane outlook can be improved by considering the NA and ENP together. It is hoped that this article will stimulate more research regarding TC activity in both the NA and ENP.
Assessment of groundwater quality in wells within the Bombali district, Sierra Leone

This study assessed the quality of 60 groundwater wells within the Bombali District of Sierra Leone. Water samples from the wells were analysed for physical (temperature, turbidity, conductivity, total dissolved solids and salinity), chemical (pH, nitrate-nitrogen, sulphate, calcium, ammonia, fluoride, aluminium, iron, copper and manganese) parameters using potable water testing kit; and bacteriological (faecal and non-faecal coliforms) qualities. Results show that 73% of the samples had turbidity values below the WHO, ICMR and United USPHS standards of 5 NTU. The electrical conductivity ( m S/cm) of 5% of the whole samples exceeded the WHO guideline value, 8% of the entire samples had values higher than the WHO, ICMR and USPHS recommended concentration. In terms of iron, 25% of all the samples had values in excess of WHO, ICMR and USPHS recommended value of 0.3mg/l. For manganese, 12% of the entire samples had values more than the WHO and ICMR standards. On the other hand, more water samples (22%) had manganese values above USPHS guideline value. For bacteriological quality, 28% of the wells were polluted by faecal and non-faecal coliforms. 60% and 40% of the entire samples had faecal and non-faecal coliforms respectively above the WHO standard. Remedial measures recommended include regular monitoring of the physico-chemical and bacteriological quality of water yield from these wells as well as teaching of the communities' basic sanitation and hygiene practices.
Multitrees: enriching and reusing hierarchical structure

This paper introduces multitrees, a new type of structure for representing information. Multitrees are a class of directed acyclic graphs (DAGs) with the unusual property that they have large easily identifiable substructures that are trees. These subtrees have a natural semantic interpretation providing alternate hierarchical contexts for information, as well as providing a natural model for hierarchical reuse. The numerous trees found within multitrees also afford familiar, tree-based graphical interactions.
Study of total seed storage protein in indigenous Brassica species based on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE)

Genetic diversity was studied in 234 accessions of locally collected Brassica species for total seed protein content through sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). These accessions were collected from different locations of Pakistan. After the study of these accessions on SDS-PAGE, 28 reproducible bands were used for cluster analysis and with the help of these bands, genetic diversity were estimated. Out of 28, four major bands were observed. Dendogram was constructed and the accessions were divided into two main groups comprising 11 clusters. The results obtained from these clusters showed minimum genetic diversity in these accessions on SDS-PAGE level. Due to low genetic diversity on SDS-PAGE level, it is suggested that two dimensional (2D)-electrophoresis can be used for protein study.