Miracle-dz/UniFAR-FTUs huggingface dataset:
Y chromosome sequencing data suggests dual paths of haplogroup N1a1 into Finland

The paternally inherited Y chromosome is highly informative of genetic ancestry, therefore making it useful in studies of population history. In Finland, two Y- chromosomal haplogroups reveal the major substructure of the population: N1a1 (TAT) enriched in the northeast and I1a (M253) in the southwest, suggested to reflect eastern and western ancestry contributions to the population. Yet, beyond these major Y-chromosomal lineages, the distribution of finer-scale Y- chromosomal variation has not been assessed in Finland. Here we provide the most comprehensive Y-chromosomal study among the Finns up to date, exploiting full sequences for 1,802 geographically mapped Finnish Y chromosomes from the FINRISK project. We assessed the distribution of common Y-chromosomal haplogroups (frequency ≥ 1%) throughout 19 Finnish regions, and further compared the autosomal genetic backgrounds of the Y-chromosomal haplogroups. With such high-resolution data, we identified novel sublineages and geographical enrichment patterns among the major Finnish haplogroups N1a1 (64%), I1a (25%), R1a (4.3%), and R1b (4.8%). Most notably, we discovered that haplogroup N1a1 splits into three major lineages within the country. While two of the sublineages followed a northeastern enrichment pattern observed for N1a1 in general, the sublineage N1a1a1a1a1a (CTS2929) (22% of all samples) displayed an enrichment in the southwest. Further, the carriers of this haplogroup showed a high proportion of southwestern autosomal ancestry unlike the other N1a1 sublineages. Collectively, these results point to distinct demographics within haplogroup N1a1, possibly induced by two distinct arrival routes into Finland. Overall, our study suggests a more complex genetic population history for Finns than previously proposed.
Association of Macular Pigment Density with Plasma Omega-3 Fatty Acids : The PIMAVOSA Study

METHODS. The PIMAVOSA study is an observational study of 107 healthy volunteers, aged 20 to 60 years and born in southwest France, without histories of ocular disease. Macular pigment optical density (MPOD) was measured using the two-wavelength autofluorescence method with a modified scanning laser ophthalmoscope. Plasma measurements (lutein, zeaxanthin, and fatty acids) were performed from fasting blood samples collected on the day of the eye examination.
Detecting phenotype-specific tumor microenvironment by merging bulk and single cell expression data to spatial transcriptomics

In addressing the limitations of current multimodal analysis methods that largely ignore phenotypic data, leading to a lack of biological interpretability at the phenotypic level, we developed the Single-Cell and Tissue Phenotype prediction (SCTP), a deep-learning-based multimodal fusion framework. SCTP can simultaneously detect phenotype-specific cells and characterize the tumor microenvironment of pathological tissue by integrating essential information from the bulk sample phenotype, the composition of individual cells, and the spatial distribution of cells. Upon evaluating SCTP’s efficiency and robustness against traditional analytical methods, we developed a specialized model, SCTP-CRC, tailored for colorectal cancer (CRC). This model integrates RNA-seq, scRNA-seq, and spatial transcriptomic data to offer a better understanding of CRC. SCTP-CRC has proven effective in accurately identifying tumor-associated cells and clusters and continuously defines boundary regions as well as the spatial organization of the entire tumor microenvironment. This enables a detailed depiction of cellular communication networks, capturing the dynamic shifts that occur during tumor progression. Furthermore, SCTP-CRC extends to the identification of abnormal sub-regions in the early state of CRC and uncovers potential early-warning signature genes such as MMP2, IGKC, and PIGR. These biomarkers are not only important in recognizing the onset of CRC but may also play a crucial role in differentiating between CRC-derived liver metastases and primary liver tumors. SCTP stands as a transformative framework, offering a deeper understanding of the tumor microenvironment through its ability to quantitatively characterize cancer’s fundamental traits and dissect the intricate molecular and cellular interactions at play. This comprehensive insight supports the early diagnosis and enables personalized treatment strategies, marking a significant stride toward improving patient outcomes and tailoring therapies to individual disease profiles.
Attentional inhibition by alpha power is modulated by faster theta rhythm and audio-visual congruency during natural speech perception

Audio-visual processing is an essential aspect of human communication, however the mechanisms that underlie attention and processing in the auditory and visual domains are still limited. In order to understand how the brain attends to and processes information while ignoring irrelevant information, we employed a complex audio-visual paradigm to understand how the brain monitors and integrates audio-visual information in congruent and incongruent conditions. In three conditions, participants watched a Ted Talk presentation while listening to 1) congruent audio in both ears, 2) congruent audio in one ear and incongruent in the other (attending to congruent) or 3) congruent audio in one ear and incongruent audio in the other (attending to the incongruent). In order to investigate correlates of attention and audio-visual processing, we developed a novel method of detecting audio-visual congruency in the fluctuation rhythms of alpha power during each condition. Employing this method, we found that higher frequency alpha power fluctuation, falling in the delta-theta range, corresponded regionally to the side of attention, suggesting a novel mechanism of processing in that alpha-band activity may act as a temporal filter or attentional mechanism during audio-visual attention.
KoRV-related retroviruses in diverse Australian and African rodent species

The koala retrovirus (KoRV) is a key contributor to the ongoing decline of Australia’s koala population. KoRV has only been found in koalas and its enigmatic origins, as well as that of its close relative, the gibbon ape leukemia virus (GALV), have been a source of enduring debate. Bats and rodents are each proposed as major reservoirs of interspecies transmission with ongoing efforts to identify additional animal hosts of KoRV-related retroviruses. In this study we identified nine rodent species as novel hosts of KoRV-related retroviruses. Included among these hosts are two African rodents, revealing the first appearance of this clade beyond the Australian and Southeast Asian region. One of these African rodents, Mastomys natalensis, carries an endogenous KoRV-related retrovirus that is fully intact and potentially still infectious. Our findings suggest that rodents are the major carriers of KoRV-related retroviruses, with a potential point of origin in Southeast Asia.
SMOS soil moisture product validation in croplands

The comparison of concurrent SMOS‐retrieved data with ground measurements over four SMOS nodes in PRA showed a slightly θv underestimation by the SMOS‐MIRAS product, with a bias of ‐ 0.02 m3m−3, and a standard deviation of the differences of ± 0.06 m3m−3, which yields a RMSE of ± 0.06 m3m−3. The RMSE value is close to meet the mission’s goal of ± 0.04 m3m−3 [6]. Even though the slight underestimation, SMOS‐MIRAS seems able to follow the temporal evolution of ground SM in this area of croplands. Additionally, experimental transects were carried out within the parcels where permanent SM stations are located in the PRA. The good correlation obtained between the ground θv measurements within the node and the means of the station data suggest the possibility of using temporal series of adjusted station values to continue the validation of SMOS‐retrieved data in a future study. SMOS SOIL MOISTURE PRODUCT VALIDATION IN CROPLANDS
The importance of stereochemistry in the disorder-order continuum of protein-protein interactions

Intrinsically disordered proteins can bind via the formation of highly disordered protein complexes without the formation of 3D-structure. Most naturally occurring proteins are “left-handed” or levorotatory (L), made up only of L-amino acids, imprinting molecular structure and communication with stereochemistry. In contrast, their mirror image “right-handed” or dextrorotatory (D) amino acids are rare in Nature. Whether disordered protein complexes are truly independent of 3D-topology and thus of chiral constraints is not clear. To test the chiral constraints of disordered protein-protein interactions, a set of interacting protein pairs covering the disorder-order continuum was chosen as representative examples. By observing both the natural ligands and their stereochemical mirror images in free and bound states, we discovered that chirality was inconsequential in a fully disordered complex. However, if the interaction relied on the ligand undergoing coupled folding and binding, correct stereochemistry was essential. Between these extremes, binding could be observed for the D-ligand with a strength that correlated with the amount of disorder in the final complex. These findings have important implications for our understanding of protein-protein interactions, the molecular processes leading to complex formation, the use of D-peptides in drug discovery, and the chemistry of protein evolution of the first living entities on Earth.
Geologically storing carbon: learning from the Otway Project Experience.

Carbon capture and geological storage (CCS) is presently the only way that we can make deep cuts in emissions from fossil fuel-based, large-scale sources of CO2 such as power stations and industrial plants. But if this technology is to be acceptable to the community, it is essential that it is credibly demonstrated by world-class scientists and engineers in an open and transparent manner at a commercially significant scale. The aim of the Otway Project was to do just this. Geologically Storing Carbon provides a detailed account of the CO2CRC Otway Project, one of the most comprehensive demonstrations of the deep geological storage or geosequestration of carbon dioxide undertaken anywhere. This book of 18 comprehensive chapters written by leading experts in the field is concerned with outstanding science, but it is not just a collection of scientific papers – it is about 'learning by doing'. For example, it explains how the project was organised, managed, funded and constructed, as well as the approach taken to community issues, regulations and approvals. It also describes how to understand the site: Are the rocks mechanically suitable? Will the CO2 leak? Is there enough storage capacity? Is monitoring effective? This is the book for geologists, engineers, regulators, project developers, industry, communities or anyone who wants to better understand how a carbon storage project really 'works'. It is also for people concerned with obtaining an in-depth appreciation of one of the key technology options for decreasing greenhouse emissions to the atmosphere.
Lifespan reference curves for harmonizing multi-site regional brain white matter metrics from diffusion MRI

Age-related white matter (WM) microstructure maturation and decline occur throughout the human lifespan, complementing the process of gray matter development and degeneration. Here, we create normative lifespan reference curves for global and regional WM microstructure by harmonizing diffusion MRI (dMRI)-derived data from ten public datasets (N = 40,898 subjects; age: 3-95 years; 47.6% male). We tested three harmonization methods on regional diffusion tensor imaging (DTI) based fractional anisotropy (FA), a metric of WM microstructure, extracted using the ENIGMA-DTI pipeline. ComBat-GAM harmonization provided multi-study trajectories most consistent with known WM maturation peaks. Lifespan FA reference curves were validated with test-retest data and used to assess the effect of the ApoE4 risk factor for dementia in WM across the lifespan. We found significant associations between ApoE4 and FA in WM regions associated with neurodegenerative disease even in healthy individuals across the lifespan, with regional age-by-genotype interactions. Our lifespan reference curves and tools to harmonize new dMRI data to the curves are publicly available as eHarmonize (https://github.com/ahzhu/eharmonize).
Forest fire vulnerability map using remote sensing data, GIS and AHP analysis (Case study: Zarivar Lake surrounding area)

Fire has an important role in destruction and negative side effects on forest ecosystem. The main aim of this study was to determine the main factors influencing the fire on set in Zarivar Lake forest area using remote sensing data, Geographic Information System (GIS) and Analytical Hierarchy Process (AHP) analysis. Vegetation density map derived from SPOT-HRG image data with 71.38% accuracy and 0.695 Kappa coefficients. The results of AHP analysis on destructive fire factors indicated that temperature and human-made factors had maximum influence on fire occurrence in the study area. Based on AHP analysis, final vulnerability map of study area was produced in Arc Map environment with 5 vulnerability areas. The results indicated that 78.03% of burned areas in 2009 and 2010 occurred in very high, high and moderate vulnerability area of final fire vulnerability map. So, this map can be used in forest management of Zarivar Lake area in dry season.
Single-cell Masked Autoencoder: An Accurate and Interpretable Automated Immunophenotyper

High-throughput single-cell cytometry data are crucial for understanding immune system’s involvement in diseases and responses to treatment. Traditional methods for annotating cytometry data, specifically manual gating and clustering , face challenges in scalability, robustness, and accuracy. In this study, we propose a single-cell masked autoencoder (scMAE), which offers an automated solution for immunophenotyping tasks including cell type annotation. The scMAE model is designed to uphold user-defined cell type definitions, thereby facilitating easier interpretation and cross-study comparisons. The scMAE model operates on a pre-train and fine-tune approach. In the pre-training phase, scMAE employs Masked Single-cell Modelling (MScM) to learn relationships between protein markers in immune cells solely based on protein expression, without relying on prior information such as cell identity and cell type-specific marker proteins. Subsequently, the pre-trained scMAE
Approximate String Matching with Compressed Indexes

A compressed full-text self-index for a text T is a data structure requiring reduced space and able to search for patterns P in T . It can also reproduce any substring of T , thus actually replacing T . Despite the recent explosion of interest on compressed indexes, there has not been much progress on functionalities beyond the basic exact search. In this paper we focus on indexed approximate string matching (ASM), which is of great interest, say, in bioinformatics. We study ASM algorithms for Lempel-Ziv compressed indexes and for compressed suffix trees/arrays. Most compressed self-indexes belong to one of these classes. We start by adapting the classical method of partitioning into exact search to self-indexes, and optimize it over a representative of either class of self-index. Then, we show that a LempelZiv index can be seen as an extension of the classical q-samples index. We give new insights on this type of index, which can be of independent interest, and then apply them to a LempelZiv index. Finally, we improve hierarchical verification, a successful technique for sequential searching, so as to extend the matches of pattern pieces to the left or right. Most compressed suffix trees/arrays support the required bidirectionality, thus enabling the implementation of the improved technique. In turn, the improved verification largely reduces the accesses to the text, which are expensive in self-indexes. We show experimentally that our algorithms are competitive and provide useful space-time tradeoffs compared to classical indexes. Algorithms 2009, 2 1106
Behaviour of dry stack concrete masonry blocks under eccentric compression

As part of a research project on dry stack concrete masonry (DSCM) walling system, a series of tests have been carried out on the concrete masonry blocks. Blocks containing one, two and three holes were tested. Three-high stack bonded prisms have primarily been tested. Three levels of eccentricities (e = t/6, t/3 and 5t/6 where t is the gross thickness of the block in the direction of eccentricity) have been considered. This paper describes the failure and deformation behaviour of these concrete blocks under vertical and eccentric compression and the results are related to other published works where possible.
Fast and Flexible String Matching by Combining Bit-parallelism and Suux Automata

The most important features of a string matching algorithm are its eeciency and its exibility. EEciency has traditionally received more attention, while exibility in the search pattern is becoming a more and more important issue. Most classical string matching algorithms are aimed at quickly nding an exact pattern in a text, being Knuth-Morris-Pratt (KMP) and the Boyer-Moore (BM) family the most famous ones. A recent development uses deterministic \suux automata" to design new optimal string matching algorithms, e.g. BDM and TurboBDM. Flexibility has been addressed quite separately by the use of \bit-parallelism", which simulates automata in their nondeterministic form by using bits and exploiting the intrinsic parallelism inside the computer word, e.g. the Shift-Or algorithm. Those algorithms are extended to handle classes of characters and errors in the pattern and/or in the text, their drawback being their inability to skip text characters. In this paper we merge bit-parallelism and suux automata, so that a nondetermin-istic suux automaton is simulated using bit-parallelism. The resulting algorithm, called BNDM, obtains the best from both worlds. It is much simpler to implement than BDM and nearly as simple as Shift-Or. It inherits from Shift-Or the ability to handle exible patterns and from BDM the ability to skip characters. BNDM is 30%-40% faster than BDM and up to 7 times faster than Shift-Or. When compared to the fastest existing algorithms on exact patterns (which belong to the BM family), BNDM is from 20% slower to 3 times faster, depending on the alphabet size. With respect to exible pattern searching, BNDM is by far the fastest technique to deal with classes of characters and is competitive to search allowing errors. In particular, BNDM seems very adequate for computational biology applications, since it is the fastest algorithm to search on DNA sequences and exible searching is an important problem in that area. As a theoretical development related to exible pattern matching, we introduce a new automaton to recognize suuxes of patterns with classes of characters. To the best of our knowledge, this automaton has not been studied before. Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for proot or direct commercial advantage and that copies show this notice on the rst page or initial screen of a display along with the full citation. Copyrights …
Social Sustainability of Natural Resource Management Activities: A Research in Dry Zone of West Bengal

Abstract Watershed-based development and management of natural resources has been the strategy for growth and sustainability of agriculture in arid, semi-arid and dry regions in India. Large public investments have made for the purpose in the last 40 years with little tangible results. In view of the importance of natural resources management programs for development of dry regions in India, a research was undertaken to assess the social sustainability of project. Indicators were constructed to assess the social sustainability in treated watershed TSJ/7 located in Bankura district of west Bengal. Majority of the farmers (69.15 percent) showed medium level of participation. Non-participation was higher in monitoring evaluation and post project maintenance phase. Farmers from a medium socio-economic status showed a slightly better involvement in decision-making (index score 61.64) than lower socio-economic category farmers (index score 56.98). Overall, the project was able to achieve a medium level of social sustainability (index score 49.17).
Effect of Spring Precipitation on Summer Precipitation in Eastern China: Role of Soil Moisture

AbstractThe relation of spring (March–May) to summer (July–August) precipitation in eastern China is examined using observed data. It is found that when spring precipitation from the lower and middle reaches of the Yangtze River valley to northern China (the YRNC region) is higher (lower), more (less) summer precipitation occurs in northeastern China and the lower and middle reaches of the Yangtze River valley, and less (more) in southeastern China. The analysis of physical mechanism showed that higher (lower) spring precipitation in the YRNC region is closely related to wet (dry) spring soil moisture, which decreases (increases) the surface temperature and sensible heat flux in late spring. Because the memory of spring soil moisture in the YRNC region reaches about 2.4 months, the surface thermal anomaly lasts into the subsequent summer, resulting in a weak (strong) East Asian summer monsoon. A weak East Asian summer monsoon corresponds to an anomalous anticyclone and a cyclone over southeastern and nort.
ИНСУЛИНСКА РЕЗИСТЕНЦИЈА И МЕТАБОЛИЧЕН СИНДРОМ КАЈ ХЕПАТИТИС Ц ВИРУС СЕРОНЕГАТИВНИ ХЕРОИНСКИ ЗАВИСНИЦИ

Initial studies on impaired glucose-insulin homeostasis in heroin dependents have not defined the impact of concomitant hepatitis C infection (HCV), which has been strongly associated with the development of insulin resistance and metabolic syndrome (MS). The aim of our study was to evaluate the association of heroin dependence with glucose-insulin homeostasis disturbances and MS in heroin dependents with HCV seronegativity. Materials and methods: The study was prospective and cross-sectional, including 160 heroin dependents compared to a control group of 60 participants.MS was diagnosed using International Diabetes Federation criteria. The homeostatic model assessment for insulin resistance (HOMA-IR) and pancreatic β -cell function (HOMA-%B) were used for assessing insulin resistance and β -cell function of pancreas. Results: MS was detected in 9.32% of heroin addicts. Heroin dependents with MS compared to dependents without MS were older, had higher BMI, waist circumference and significantly higher systolic and diastolic blood pressure, increased triglycerides (F=8.233, df=2, p<0.001), apoB (F=8.154, df=2, p=0.001), and reduced HDL-C (F=25.926, df=2, p<0.001) and apoA-I (F=16.406, df=2, p<0.001), significantly increased inuslinemia (F=4.928, df=2, p<0.05), insulin resistance-HOMA-IR (F=4,928, df=2, p<0,05) and insignificantly increased pancreatic β -cell function (194.66 ±224.05) (F=2.461, df=2, p>0.05). Conclusions: Insulin resistance and МS, independent of HCV, was also registered in heroin dependence. Timely recognition will enable more successful treatment of comorbidities and illicit drug dependence. Abstract