Miracle-dz/UniFAR-FTUs huggingface dataset:
Selection on ancestral genetic variation fuels parallel ecotype formation in bottlenose dolphins

What are the mechanisms that allow species to extend their ranges and adapt to the novel environmental conditions they find in the newly available habitat? The study of parallel adaptation of pairs of populations to similar environments can provide great insights into this question. Here, we test for parallel evolution driven by niche specialization in a highly social marine mammal, the common bottlenose dolphin, Tursiops truncatus, and investigate the origins of the genetic variation driving local adaptation. Coastal ecotypes of common bottlenose dolphins have recurrently emerged in multiple regions of the world from pelagic ecotype populations, when novel habitat became available. Analyzing the whole genomes of 57 individuals using comparative population genomics approaches, we found that coastal ecotype evolution was relatively independent between the Atlantic and Pacific, but related between different regions within the Atlantic. We show that parallel adaptation to coastal habitat was facilitated by repeated selection on ancient alleles present as standing genetic variation in the pelagic populations. Genes under parallel adaptation to coastal habitats have roles in cognitive abilities and feeding. Therefore, parallel adaptation in long-lived social species may be driven by a combination of ecological opportunities, selection acting on ancient variants, and stable behavioural transmission of ecological specialisations. Tried and tested genetic variation that has been subject to repeated bouts of selection, may promote linked adaptive variants with minimal pleiotropic effects, thereby facilitating their persistence at low frequency in source populations and enabling parallel evolution.
Spatially resolved optical monitoring of spinal cord blood flow with a minimally invasive, multi-level epidural probe

Spinal cord ischemia leads to iatrogenic injury in multiple surgical fields, and the ability to immediately identify onset and anatomic origin of ischemia is critical to its management. Current clinical monitoring, however, does not directly measure spinal cord blood flow, resulting in poor sensitivity/specificity, delayed alerts, and delayed intervention. We have developed an epidural device employing diffuse correlation spectroscopy (DCS) to monitor spinal cord ischemia continuously at multiple positions. We investigate the ability of this device to localize spinal cord ischemia in a porcine model and validate DCS versus Laser Doppler Flowmetry (LDF). Specifically, we demonstrate continuous (>0.1Hz) spatially resolved (3 locations) monitoring of spinal cord blood flow in a purely ischemic model with an epidural DCS probe. Changes in blood flow measured by DCS and LDF were highly correlated (r=0.83). Spinal cord blood flow measured by DCS caudal to aortic occlusion decreased 62%, with a sensitivity of 0.87 and specificity of 0.91 for detection of a 25% decrease in flow. This technology may enable early identification and critically important localization of spinal cord ischemia.
Design to Data for mutants of β-glucosidase B from Paenibacillus polymyxa: I45K, A357S, I20A, I20V, and I20E

The relatively small size and scope of most current datasets of biophysical mutation effects in enzymes limit the ability to develop data-driven algorithms enabling accurate generative modeling tools for designing novel enzyme function. Here, the Michaelis-Menten constants (kcat, KM, and kcat/KM) and thermal stability (TM) of five new mutations of β-glucosidase B from Paenibacillus polymyxa (BglB) are characterized. Foldit software was used to create molecular models of the mutants, for which synthetic genes were constructed and the corresponding proteins produced and purified from E. coli. It was found that mutations that disrupted pre-existing hydrogen bonds near the active site had reduced expression in contrast to mutations at the same site that did not affect native hydrogen bonding. This is consistent with previous results showing the relationship between hydrogen bonding and enzyme functionality. These mutants contribute to a growing data set of >100 mutants that have been characterized for expression, kinetic, and thermal properties
Sex Differences in the Human Brain Transcriptome of Cases With Schizophrenia

While schizophrenia differs between males and females in age of onset, symptomatology and the course of the disease, the molecular mechanisms underlying these differences remain uncharacterized. In order to address questions about the sex-specific effects of schizophrenia, we performed a large-scale transcriptome analysis of RNA-seq data from 437 controls and 341 cases from two distinct cohorts from the CommonMind Consortium. Analysis across the cohorts identifies a reproducible gene expression signature of schizophrenia that is highly concordant with previous work. Differential expression across sex is reproducible across cohorts and identifies X- and Y-linked genes, as well as those involved in dosage compensation. Intriguingly, the sex expression signature is also enriched for genes involved in neurexin family protein binding and synaptic organization. Differential expression analysis testing a sex-by-diagnosis interaction effect did not identify any genome-wide signature after multiple testing corrections. Gene coexpression network analysis was performed to reduce dimensionality and elucidate interactions among genes. We found enrichment of co-expression modules for sex-by-diagnosis differential expression signatures, which were highly reproducible across the two cohorts and involve a number of diverse pathways, including neural nucleus development, neuron projection morphogenesis, and regulation of neural precursor cell proliferation. Overall, our results indicate that the effect size of sex differences in schizophrenia gene expression signatures is small and underscore the challenge of identifying robust sex-by-diagnosis signatures, which will require future analyses in larger cohorts.
Inference of Extended Finite State Machines

In this AFP entry, we provide a formal implementation of a state-merging technique to infer extended finite state machines (EFSMs), complete with output and update functions, from black-box traces. In particular, we define the subsumption in context relation as a means of determining whether one transition is able to account for the behaviour of another. Building on this, we define the direct subsumption relation, which lifts the subsumption in context relation to EFSM level such that we can use it to determine whether it is safe to merge a given pair of transitions. Key proofs include the conditions necessary for subsumption to occur and that subsumption and direct subsumption are preorder relations. We also provide a number of different heuristics which can be used to abstract away concrete values into registers so that more states and transitions can be merged and provide proofs of the various conditions which must hold for these abstractions to subsume their ungeneralised counterparts. A Code Generator setup to create executable Scala code is also defined.
Respiration and Water Loss at the Higher Temperatures in the Desert Iguana, Dipsosaurus dorsalis

DE SERT lizards have been shown by many workers (Cowles, 1939; Cowles, 1940; Cowles, 1958; Bogert, 1949; BIogert, 1959; Norris, 1953; and Cole, 1943) to regulate their body temperature by behavioral and structural means. These animals lose or gain heat by conduction to or from the substrate, by convection to or from the air, by radiation to or from other objects, and, lastly, they can gain heat by radiation from the sun. Physiologically they gain heat from metabolism and lose heat by the evaporation of water in respiration. This latter process is enhanced at the higher temperatures by panting. However, the role of panting in the heat economy of lizards has not been examined quantitatively; consequently, the present study of the desert iguana, Dipsosaurus dorsalis was undertaken. This lizard, a resident of the desert regions of southwestern United States and northwestern Mexico, was selected for study because it is one of the most
A Multi-Annotator Survey of Sub-km Craters on Mars

We present here a dataset of nearly 5000 small craters across roughly 1700 km2 of the Martian surface, in the MC-11 East quadrangle. The dataset covers twelve 2000-by-2000 pixel Context Camera images, each of which is comprehensively labelled by six annotators, whose results are combined using agglomerative clustering. Crater size-frequency distributions are centrally important to the estimation of planetary surface ages, in lieu of in-situ sampling. Older surfaces are exposed to meteoritic impactors for longer and, thus, are more densely cratered. However, whilst populations of larger craters are well understood, the processes governing the production and erosion of small (sub-km) craters are more poorly constrained. We argue that, by surveying larger numbers of small craters, the planetary science community can reduce some of the current uncertainties regarding their production and erosion rates. To this end, many have sought to use state-of-the-art object detection techniques utilising Deep Learning, which—although powerful—require very large amounts of labelled training data to perform optimally. This survey gives researchers a large dataset to analyse small crater statistics over MC-11 East, and allows them to better train and validate their crater detection algorithms. The collection of these data also demonstrates a multi-annotator method for the labelling of many small objects, which produces an estimated confidence score for each annotation and annotator.
Development and Validation of the Neuropsychology Behavior and Affect Profile

This series of 4 studies describes the psychometric properties of the Neuropsychology Behavior and Affect Profile, which consists of 5 peer-rated scales (106 items) designed to measure personality change in brain-impaired individuals. Study 1 pertains to item derivation. Study 2 used relatives of 61 Ss identified as demented to determine the test's internal consistency. Results showed moderate levels of internal consistency across the 5 scales, with slightly higher coefficients (.6S-.82) obtained for present (vs. premorbid) emotional status. High test-retest reliability was demonstrated in Study 3 (intraclass correlation coefficients ranged from .92 to .99). Study 4 established discriminant validity; the instrument differentiated 61 demented Ss from 88 normal elderly controls on the basis of present behavioral affective style.
Pre-European Settlement Forest Composition in East New Jersey and Southeastern New York

A total of 5059 witness trees were counted from survey reports of "unappropriated lands" in 23 tallies from 14 towns and 13 counties of southeastern New York and East New Jersey. Southeastern New York and northern East New Jersey were dominated by oak, particularly white, red and black oaks, with hickory and chestnut common. Pre-European settlement forests in southern East New Jersey were dominated by oak and pine with cedar and maple, probably the species white cedar and red maple, common in some areas. Cedar was unrepresented in two of five S East Jersey tallies which encompass the modern white cedar-red maple swamp forest areas, while maple was common only in one of the tallies. Distribution of modern forest types and fossil pollen records were consistent with witness tree counts for oak and pine. As compared to pollen records, four tallies overrepresented walnut and underrepresented hickory.
Drug Designing for Biologically Important Organic Compound against COX-2 Enzyme: A Computational Approach

AbstractPyrazole, β-lactam, salicidine, pyren and oxazole derivatives exhibit a broad spectrum of biological activities such asantimicrobial, anti-inflammatory and antitumor activities. With growing application on their synthesis and bioactivity,chemists and biologists in recent years have considerable attention on the research of these derivatives. In the view ofpotential importance of these derivatives, we have crystallized few of the derivatives and its report has been published.The present study focuses on docking studies of these derivatives against COX-2 enzyme. Docking studies usingSchrodinger’s GLIDE reveals that these derivatives shows better binding energy and score in the defined active site. Theseresults may provide a guiding role to design a lead molecule which may reduce inflamation. Key words: Pyrazole, Oxazole, β-Lactam, Anti-inflammation, COX-2, Molecular Docking 1. Introduction Cyclooxygenase (COX-2) is one of the isoforms ofProstaglandin synthase H2 (PGH2) which synthesisprostaglandin necessary for organ and tissue homeosta-sis. COX-2 is expressed only in certain mammalian tis-sues in response to inflammatory stimuli. Hence COX-2 is responsible for the elevated prostaglandin levelswhich cause inflammation
Estimation of Carcass Composition by Computer Image Analysis in the Cross Sections of Japanese Black Steers

枝肉横断面から抽出した画像解析情報を用いて枝肉構成推定式の設定を行なった. 材料として黒毛和種去勢肥育牛25頭の枝肉を用いた. これらの屠殺前体重は567～701kgであり,ほぼ枝肉市場に出荷される肥育牛の体重に匹敵するものであった. 赤肉,脂肪および骨重量ならびにそれらの割合は枝肉左半丸の解体により測定し,画像解析情報は第6-7肋骨間で切断した枝肉横断面の写真から抽出した. 抽出した画像解析情報は総筋肉面積,総脂肪面積,総骨面積,個々の筋肉の面積,周囲長,長径,短径,離心率および主軸方向,ならびに異なる筋肉の重心間の距離である. 総赤肉重量,総脂肪重量,総骨重量とそれらの割合に関する枝肉構成推定式の設定のために変数増減型の重回帰分析を行なった. 枝肉横断面から抽出した画像解析情報とこれらの枝肉構成との間には低めから中程度の相関係数が推定された. 画像解析情報を用いて得られた枝肉構成推定式の自由度調整済み寄与率は総赤肉重量,総脂肪重量および総骨重量についてそれぞれ,0.847,0. 863および0. 529であったのに対して,赤肉割合,脂肪割合および骨割合についてはそれぞれ0. 813,0. 865および0. 597であった.
Interhemispheric interaction when both hemispheres have access to the same stimulus information

Right-handed Ss identified consonant-vowel-consonant (CVC) nonsense syllables presented tachistoscopically. The CVC on each trial was presented to the left visual field-right hemisphere (LVF-RH), to the right visual field-left hemisphere (RVF-LH), or the same CVC was presented to both visual fields (bilateral presentation). When recognition was incorrect, the pattern of errors was qualitatively different on LVF-RH and RVF-LH trials, suggesting that each cerebral hemisphere has its own preferred mode of processing the CVC stimuli. The qualitative pattern of errors on bilateral trials was identical to that obtained on LVF-RH trials. The bilateral results are described well by a model that assumes the mode of processing characteristic of the RH dominates on bilateral trials but is applied to both the LVF-RH and RVF-LH stimuli. Language: en
Drying characteristics and value addition of horticulture crops using thermally efficient indirect solar drier with temperature controller system

In the present investigation, apple and tomato were dried in three modes of drying viz. indirect solar drier, electric drier and open sun. The shelf life and quality parameters of dried products were compared between these three modes of drying. It has been found that shelf life of dried products dried in solar drier is higher than other modes of drying. The quality parameters such as, TSS, reducing sugars, total sugars, total solids and titratable acidity of dried products were better in solar drier as compared to other modes of drying. The drying efficiency of the solar drier ranged between 33.84% to 40.45%. The carbon emission has been reduced in solar drier as compared to electric oven between 15.52 to 19.83 kg.
Movie Recommendation System: A Review Report

Recommendation system plays important role in Internet world and used in many applications. It has created the collection of many application, created global village and growth for numerous information. This paper represents the overview of Approaches and techniques generated in recommendation system. Recommendation system is categorized in three classes: Collaborative Filtering, Content based and hybrid based Approach. This paper classifies collaborative filtering in two types: Memory based and Model based Recommendation . The paper elaborates these approaches and their techniques with their limitations. The result of our system provides much better recommendations to users because it enables the users to understand the relation between their emotional states and the recommended movies
Mixing commonly used crystalloid solutions with red blood cells in five common additives does not negatively impact hemolysis, aggregometry, or deformability

Literature is beginning to challenge the belief that it is unsafe to coinfuse red blood cells (RBCs) with solutions other than isotonic saline. We recently showed that additive‐free RBCs tolerated coincubation with Plasma‐Lyte or catecholamines dissolved in normal saline (NS), though 5% dextrose in water (D5W) promoted hemolysis. Herein, we evaluate the effect of coincubating crystalloids on additive‐preserved RBC hemolysis, aggregation, and membrane deformability.
Reduced-intensity therapy of pediatric lymphoblastic leukemia: Impact of residual disease early in remission induction.

Legacy data show that approximately 40% of children with acute lymphoblastic leukemia (ALL) were cured with limited antimetabolite-based chemotherapy regimens. However, identifying patients with very-low-risk (VLR) ALL remains imprecise. Patients selected based on a combination of presenting features and a minimal residual disease (MRD) level of <0.01% on day 19 of induction therapy had excellent outcomes with low-intensity treatment. We investigated the impact of MRD levels between 0.001% and <0.01% early in remission induction on the outcome of VLR ALL treated with a low-intensity regimen. Between October 2011 and September 2015, 200 consecutive patients with B-precursor ALL with favorable clinicopathologic features and MRD levels of <0.01%, as assessed by flow cytometry in the bone marrow on day 19 and at the end of induction therapy, received reduced-intensity therapy. The 5-year event-free survival was 89.5% (± 2.2% SE), and the overall survival was 95.5% (± 1.5% SE). The 5-year cumulative incidence of relapse (CIR) was 7% (95% CI, 4% to 11%). MRD levels between 0.001% and <0.01% on day 19 were detectable in 29 patients. These patients had a 5-year CIR significantly higher than that of patients with undetectable residual leukemia (17.2% ± 7.2% vs 5.3% ± 1.7%, respectively; P = .02). Our study shows that children with VLR ALL can be treated successfully with decreased-intensity therapy, and it suggests that the classification criteria for VLR can be further refined by using a more sensitive MRD assay.
Evolving Use of fMRI in Medicare Beneficiaries

SUMMARY: Using the Medicare Physician-Supplier Procedure Summary Master File, we evaluated the evolving use of fMRI in Medicare fee-for-service beneficiaries from 2007 through 2017. Annual use rates (per 1,000,000 enrollees) increased from 17.7 to 32.8 through 2014 and have remained static since. Radiologists have remained the dominant specialty group from 2007 to 2017 (86.4% and 88.6% of all services, respectively), and the outpatient setting has remained the dominant place of service (65.4% and 65.4%, respectively).
Tumor DNA as a Cancer Biomarker through the Lens of Colorectal Neoplasia

Biomarkers have a wide range of applications in the clinical management of cancer, including screening and therapeutic management. Tumor DNA released from neoplastic cells has become a particularly active area of cancer biomarker development due to the critical role somatic alterations play in the pathophysiology of cancer and the ability to assess released tumor DNA in accessible clinical samples, in particular blood (i.e., liquid biopsy). Many of the early applications of tumor DNA as a biomarker were pioneered in colorectal cancer due to its well-defined genetics and common occurrence, the effectiveness of early detection, and the availability of effective therapeutic options. Herein, in the context of colorectal cancer, we describe how the intended clinical application dictates desired biomarker test performance, how features of tumor DNA provide unique challenges and opportunities for biomarker development, and conclude with specific examples of clinical application of tumor DNA as a biomarker with particular emphasis on early detection. See all articles in this CEBP Focus section, “NCI Early Detection Research Network: Making Cancer Detection Possible. ”
Rising Prostate Cancer Incidence in Sub-Saharan Africa: A Trend Analysis of Data from the African Cancer Registry Network

Background: Prostate cancer is the leading cancer in men in sub-Saharan Africa (SSA) regarding incidence and mortality. Published data from a few registries in SSA suggest that the rates are still rising, but there is little comprehensive information on the time trends of prostate cancer incidence. Methods: We analyzed registry data on 13,170 incident prostate cancer cases in men aged 40 years or above, from 12 population-based cancer registries in 11 SSA countries, with at least a 10-year time span of comparable data. Results: We observed an increase in cumulative risks (CR) and age-standardized incidence rates (ASR) over time in all registries (statistically significant in all but one). The highest values of CR were found in Seychelles and Harare (Zimbabwe). The highest annual increase in the ASRs was seen in Seychelles and Eastern Cape (South Africa), whereas the lowest was seen in Mauritius. We mainly found a steady increase in incidence with age and during successive periods. Conclusions: This analysis reveals that prostate cancer incidence rates are rising in many populations in SSA—often very rapidly—which is in contrast to recent observations worldwide. We acknowledge that the reasons are multifactorial and largely remain unclear, but believe that they are primarily associated with improvements in health care systems, for example, a broader use of prostate-specific antigen testing. Impact: This study is the first to compare population-level data on time trends of prostate cancer incidence between multiple countries of SSA, presenting the different rates of increase in 11 of them.
Circadian Gene Expression Rhythms During Critical Illness.

OBJECTIVES Core clock genes regulate tissue-specific transcriptome oscillations that synchronize physiologic processes throughout the body, held in phase by the central circadian rhythm. The central circadian rhythm rapidly dampens with onset of critical illness, but the effect of critical illness on gene expression oscillations is unknown. The objective of this study was to characterize the rhythmicity and phase coherence of core clock genes and the broader transcriptome after onset of critical illness. DESIGN Cross-sectional study. SETTING ICUs and hospital clinical research unit. PATIENTS Critically ill patients within the first day of presenting from the community and healthy volunteers. INTERVENTIONS Usual care (critically ill patients) and modified constant routine (healthy volunteers). MEASUREMENTS AND MAIN RESULTS We studied 15 critically ill patients, including 10 with sepsis and five with intracerebral hemorrhage, and 11 healthy controls. The central circadian rhythm and rest-activity rhythms were profiled by continuous wrist actigraphy, and serum melatonin sampled every 2 hours along with whole blood for RNA isolation over 24 hours. The gene expression transcriptome was obtained by RNA sequencing. Core clock genes were analyzed for rhythmicity by cosinor fit. Significant circadian rhythmicity was identified in five of six core clock genes in healthy controls, but none in critically ill patients. TimeSignature, a validated algorithm based on 41 genes, was applied to assess overall transcriptome phase coherence. Median absolute error of TimeSignature was higher in individual critically ill patients than healthy patients (4.90 vs 1.48 hr) and was correlated with encephalopathy severity by Glasgow Coma Scale in critically ill patients (rho, -0.54; p = 0.036). CONCLUSIONS Gene expression rhythms rapidly become abnormal during critical illness. The association between disrupted transcriptome rhythms and encephalopathy suggests a path for future work to elucidate the underlying pathophysiology.