Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic diversity of the wx flanking region in rice landraces in northern Laos

A glutinous texture of endosperm is one of the important traits of rice (Oyza sativa L.). Northern Laos is known as a center of glutinous rice diversity. We genotyped INDEL, SSR and SNP markers in a sample of 297 rice landraces collected in northern Laos. These glutinous varieties were confirmed to share a loss-of-function mutation in Granule bound starch synthase I (Wx). INDEL markers revealed a high frequency of recombinant genotypes between indica and japonica. Principal component analysis using SSR genotypes of Wx flanking region revealed that glutinous indica landraces were scattered between non-glutinous indica and glutinous-japonica types. High ratios of heterozygosity were found especially in glutinous indica. Haplotype analysis using SNP markers around Wx locus revealed that glutinous indica landraces would have a few chromosome segments of glutinous japonica. Frequent recombinations were confirmed outside of this region in glutinous indica. This intricate genetic structure of landraces suggested that glutinous indica landraces in Laos were generated through repeated natural crossing with glutinous-japonica landraces and severe selection by local farmers.
Genetic study of transthyretin amyloid neuropathies: carrier risks among French and Portuguese families

Among the hereditary systemic amyloidosis, transthyretin (TTR) neuropathies (OMIM #176300) are devastating disorders with an autosomal dominant transmission, expressed mainly as a progressive fibre length dependent sensorimotor polyneuropathy and life threatening autonomic dysfunction.1 Initially, the condition was recognised in northern Portugal, in the area of Povoa de Varzim, where the prevalence has been estimated at 1/1000.2,3 Other important clusters of families were subsequently reported in Japan, initially in two limited geographic areas (the districts of Arao and Ogawa),4 and in the north of Sweden.5 The condition is now known throughout the world, including various European countries.6 Among the 75 pathogenic TTR variants identified so far, Val30Met is the most frequent, and is virtually the only one described in Portugal and Sweden.7,8 By contrast, in Japan, the TTR point mutations are highly heterogeneous, with more than 20 different substitutions, including Val30Met, described.9 In France, a previous study found a similar heterogeneity.10 Depending on the geographic origin, the mean age of onset ranges from 30 to 70 years. A variable clinical expression is also observed, with restrictive cardiomyopathy, carpal tunnel syndrome, and vitreous opacities often encountered, whereas renal involvement is less common. These manifestations, along with the discrepancy in age of onset, account for phenotypic variations. However, virtually no genotype–phenotype correlation seems to exist. To supply the main source of mutant TTR, liver transplantation has been proposed as a treatment for the disease for the last 10 years, with promising results. In the Val30Met patients, it virtually suppresses the production of the mutant TTR in the serum and slows the progression of the neurological symptoms that otherwise have a fatal outcome in less than 10 years.11 Another important aspect of the management of affected families is the recent availability of predictive …
Taxonomy of Manufacturing Strategies: A Worldwide Perspective

The development of configurations and taxonomies is fundamental to strategy research. This taxonomy of manufacturing strategies is developed with cluster analysis, and is based on the relative importance attached to 11 competitive priorities. From the 2005 International Manufacturing Strategies Survey, 216 plants of 21 countries have been selected as samples and three distinct clusters of manufacturing strategy groups are observed. After comparison, these clusters have been named as Innovator, Caretaker and Allrounder. The two main underlying dimensions along which the manufacturing strategy groups differ are the order fulfillment and order creation and are founded with discriminant analysis. The empirical results offer us a clear panoramic picture of manufacturing strategies around the world.
Studying Possible Cross-Protection of Canada Geese Preexposed to North American Low Pathogenicity Avian Influenza Virus Strains (H3N8, H4N6, and H5N2) Against an H5N1 Highly Pathogenic Avian Influenza Challenge

Abstract Highly pathogenic avian influenza (HPAI) H5N1 virus infections have caused unprecedented morbidity and mortality in different species of domestic and wild birds in Asia, Europe, and Africa. In our previous study, we demonstrated the susceptibility and potential epidemiologic importance of H5N1 HPAI virus infections in Canada geese. In this study, we investigated the potential of preexposure with North American lineage H3N8, H4N6, and H5N2 low pathogenicity avian influenza (LPAI) viruses to cross-protect Canada geese against a lethal H5N1 HPAI virus challenge. Based on our results, birds that were primed and boosted with an H5N2 LPAI virus survived a lethal H5N1 challenge. In contrast, only two of five birds from the H3N8 group and none of the birds preexposed to H4N6 survived a lethal H5N1 challenge. In vitro cell proliferation assays demonstrated that peripheral blood mononuclear cells collected from each group were no better stimulated by homologous vs. heterologous antigens.
Behavioral / Systems / Cognitive Processing Asymmetry of Transitions between Order and Disorder in Human Auditory Cortex

Maria Chait,1 David Poeppel,1,2,3 Alain de Cheveigné,5 and Jonathan Z. Simon1,3,4 1Neuroscience and Cognitive Science Program, 2Department of Linguistics, 3Department of Biology, 4Department of Electrical and Computer Engineering, University of Maryland, College Park, Maryland 20742, 5Laboratoire de Psychologie de la Perception (Formation de Recherche en Évolution 2929), Centre National de la Recherche Scientifique, Université Paris Descartes, and Département d’Etudes Cognitives, École Normale Supérieure, Paris 75230, France
A study of placental weight and birth weight ratio (PW/BW) and it's effects on perinatal outcome

Objective: The placenta weight/birth weight (PW/BW) ratio has been shown to be associated with certain long-term fetal outcomes; however, its association with short-term outcomes has not been evaluated. Our aim was to assess the correlation between the PW/BW ratio and short-term adverse obstetrics outcomes in full-term, appropriate-for-gestational-age (AGA) newborns. Design: Prospective, randomized. Setting: Dr. D.Y. Patil Medical College & Hospital, Pimpri, Pune Methods: In our study, three groups of full-term neonates have been taken, according to their PW/BW ratio (high, normal and low) and are compared. Our primary outcome includes the admission rate to the neonatal intensive care unit (NICU) and secondary outcomes included an Apgar score < 7 at 5 minutes. Results: Our study showed that the high PW/BW ratio group was associated with increased rates of admission to the NICU and Apgar scores < 7 at 5 minutes as compared to normal PW/BW ratio. The low PW/BW ratio group showed decreased rates of NICU admission. A high PW/BW ratio is significantly correlated with short-term adverse perinatal outcomes. Conclusion: The possibility of short term health risks for newborns can be predicted by the PW/BW ratio.
A comparative analysis of region pairs matching current and future climate conditions

Diese Arbeit beschaftigt sich mit einem neuen Ansatz, Klimaanderungen interaktiv kartographisch darzustellen. In der Regel werden Klimaanderungen mittels der Darstellung von Veranderungen der Durchschnittstemperaturen zwischen zwei Zeitpunkten kommuniziert, womit mogliche Erwarmungen und Abkuhlungen im langjahrigen Mittel offenbart werden. Methodisch ist dieser Ansatz zwar korrekt, jedoch erschwert er die Interpretation der tatsachlichen Bedeutung und der Effekte, welche Klimaanderungen mit sich bringen und zwar sowohl fur Laien als auch Experten. Klimamodelle simulieren die komplizierten physikalischen Zusammenhange innerhalb der Atmosphare und mit der Erdoberflache. Sie produzieren somit eine Fulle zeitlich hochaufgeloster Daten, mit welchen integrierte Indikatoren wie Temperaturmittelwerte und Niederschlagssummen fur eine bestimtme Zeitspanne (Jahr, Jahreszeit, Monat) fur eine bestimmte Flache berechnet werden. Effekte des Klimawandels werden dann mittels der Differenzen der Indikatoren die Zeitspannen des aktuellen und eines kunftigen Klimas beschreiben, quantifiziert. Doch diese integrierten Indikatoren liefern keinen gesamten Uberblick uber den zu erwartenden Klimawandel und die sich daraus ergebenden regoinalen Effekte. Aus diesem Grund hat das Austrian Institute of Technology (AIT) die „Climate Twins Applikation“ entwickelt, in welcher es dem Nutzer ermoglicht wird, Regionen zu identifizieren, welche jetzt bereits ein ahnliches Klima aufweisen, wie ein Ort in einem zukunftigen Zeitraum. Das vorrangige Ziel dieser Arbeit ist es also, eine geeignete Methode zu entwickeln, um aus vorhandenen Datensatzen Regionen mit ahnlichen klimatischen Eigenschaften auszumachen. Normalerweise werden Klimata anhand von Mittelwerten (Temperatur) oder Summenwerten (Niederschlag) uber grosere Zeitraume gebildet. Ein Mittelwert beinhaltet jedoch keine Informationen uber die Amplituden von Temperaturkurven oder uber Extremwerten von Niederschlagsereignissen. In ein geeignetes Ahnlichkeitsmas sollten also die wesentlichen Eigenschaften einer statistischen Verteilung wie deren Varianz, Schiefe, Krummung oder Bipolaritat einfliesen. Eine Evaluierung gegebener Ahnlichkeitsmase fur Verteilungen wurde von Jan Vegelius durchgefuhrt, bei der sich zwei Mase, die Proportional Similarity (PD) und der Hellinger Koeffizient (rH) herauskristallisierten, welche die besten Moglichkeiten fur derartige Anwendungen bieten. Die Verwendung derartiger Ahnlichkeitsmase fur Klimadaten erfordert deren Prufung anhand von Testdatensatzen. Dafur wurden die Stadte Wien, Munchen, Kopenhagen und Rom herangezogen. Wichtige weitere Schritte sind die Auswahl geeigneter Klimaindikatoren, deren Anwendbarkeit auf die Ahnlichkeitsmase, die (Unsicherheits-)Bandbreiten der Ahnlichkeit, sowie die Kombination und Gewichtung der einzelnen Ahnlichkeitswerte um aussagekraftige Ergebnisse, nicht nur anhand weniger integrierter Indikatoren sondern anhand des Vergleichs der gesamten Verteilung der Temperatur- und Niederschlagsdaten uber eine aktuelle und einer kunftige Zeitspanne, zu produzieren.
Responsiveness to Change of 10 Physical Tests Used for Patients With Back Pain

Background Few studies have examined the responsiveness of physical tests. Objective The purpose of this study was to explore the responsiveness of 10 physical tests used for patients with back pain in order to illuminate the significance of changes in scores. Design Cross-sectional and longitudinal designs within a prospective cohort study were applied. Methods Distribution-based and anchor-based methods were used. Ninety-eight patients (18–65 years of age) with long-lasting back pain were recruited consecutively at an outpatient spine clinic. Measurements The participants were assessed using 10 physical tests and 2 questionnaires (Hannover Functional Ability Questionnaire and Roland-Morris Disability Questionnaire) at inclusion and after rehabilitation. Six predefined hypotheses for each test were examined regarding the association between changes in scores on the physical tests and the self-report measures of functioning and regarding the relationship of changes in scores on the physical tests and external anchors of important change. Results Five physical tests demonstrated responsiveness by both distribution-based and anchor-based methods: spondylometry, lateral flexion test, fingertip-to-floor test, lift test, and Back Performance Scale (4 hypotheses confirmed). The minimal important change values were all within the range of the smallest detectable change for individual patients. Responsiveness by distribution-based methods only (3 hypotheses confirmed) was shown for the Biering-Sørensen test and the loaded reach test, whereas little evidence of responsiveness (1 hypothesis confirmed) was shown for the Global Physiotherapy Examination flexibility subscale, the Progressive Isoinertial Lifting Evaluation, and the 15-m (50-ft) walk test. Limitations The smallest detectable change values were examined in a small sample of patients and need further exploration. Conclusions Responsiveness varied among the 10 physical tests.
Tensor-based off-axis noise suppression in pre-beamformed data to enhance the visualization of hyper echoic structures

Visualizing hyper-echoic structures, such as bones, in ultrasound imaging is challenging due to strong off-axis energy and many other factors arising from complex interactions between the ultrasound beam and the structures. Most previous research has focused on suppressing off-axis artifacts but is generally limited by factors such as high computation requirements, limited improvements, or ultrasound hardware modifications. This paper describes a new tensor based directional noise suppression method to suppress the off-axis energy. The pre-beamformed channel data are first delay compensated so signals of interest are aligned horizontally while off-axis distractions are aligned in different angles. Then we perform tensor analysis on the aligned channel data to identify regions with strong gradients vertically. Directional high pass filtering is then applied based on tensor analysed results so both weak horizontal lines and strong off-axis non-horizontal structures are suppressed. In a point phantom study, the contrast ratio (CR) is improved from 0.71 to 0.85. In a bone phantom study, the CR is improved from 0.60 to 0.87.
Ca2+ Influx through Mechanosensitive Channels Inhibits Neurite Outgrowth in Opposition to Other Influx Pathways and Release from Intracellular Stores

Ca2+ signals are known to be important regulators of neurite outgrowth and steering. Here we show that inhibiting Ca2+ influx through stretch-activated channels using various compounds, including a highly specific peptide isolated from Grammostola spatulata spider venom (GsMTx4), strongly accelerates the rate of neurite extension on diverse substrata and within the intact spinal cord. Consistent with the presence of stretch-activated channels, we show that Ca2+ influx is triggered by hypotonic solutions, which can be partially blocked by GsMTx4. Finally, chelating local, but not global, Ca2+ signals prevents the acceleration that is normally produced by GsMTx4. Blocking Ca2+ influx through other channel types has little or opposite effects, but release from intracellular stores is required for maximal acceleration. Together, our data suggest that Ca2+ functions at distinct microdomains in growth cones, with influx through mechanosensitive channels acting to inhibit outgrowth in opposition to influx through other plasma membrane channels and release from stores.
Mechanisms Regulating Protein Localization

Cellular functions are dictated by protein content and activity. There are numerous strategies to regulate proteins varying from modulating gene expression to post‐translational modifications. One commonly used mode of regulation in eukaryotes is targeted localization. By specifically redirecting the localization of a pool of existing protein, cells can achieve rapid changes in local protein function. Eukaryotic cells have evolved elegant targeting pathways to direct proteins to the appropriate cellular location or locations. Here, we provide a general overview of these localization pathways, with a focus on nuclear and mitochondrial transport, and present a survey of the evolutionarily conserved regulatory strategies identified thus far. We end with a description of several specific examples of proteins that exploit localization as an important mode of regulation.
Modulation of the ERK pathway of signal transduction by cysteine proteinase inhibitors

Cell proliferation requires the coordinate synthesis and degradation of many proteins. In addition to the well‐characterized involvement of the proteasome in the degradation of several cell cycle‐regulated proteins, it has been established that cysteine proteinases are also involved in the control of cell proliferation, but their role is currently not understood. By using both synthetic cysteine proteinase inhibitors and overexpression of T‐kininogen (T‐KG), a physiologically relevant cysteine proteinase inhibitor, we show that inhibition of cysteine proteinases results in a severe inhibition of the ERK pathway of signal transduction. Mechanistically, this effect appears to be the result of stabilization of the ERK phosphatase MKP‐1, which leads to an enhanced dephosphorylation (and hence inactivation) of ERK molecules. These results are specific to cysteine proteinase inhibitors and are not observed when either serine proteinases or the proteasome are inhibited. We hypothesize that inhibition of cysteine proteinases in vivo leads to a dysregulation of the ERK pathway, which results in an inability of the cell to transmit to the nucleus the signals generated by the presence of growth factors, thus resulting in loss of cell proliferation. J. Cell. Biochem. 80:11–23, 2000. © 2000 Wiley‐Liss, Inc.
CE to monitor endotoxins by protein complexation

A new CE method for fast and efficient analysis of bacterial endotoxins (lipopolysaccharides) is described. It is based on the strong interaction between proteins and endotoxins. The UV absorption of the protein component in the complex is used for the detection. The electrophoretic mobility of the complex hemoglobin/endotoxin can be employed for qualitative analysis of the endotoxin. For instance, the structural differences between “smooth” and “rough” lipopolysaccharides from Salmonella minnesota (wild‐type), Salmonella minnesota R595 and Shigella sonnei R562H are reflected in the electrophoretic mobilities of their hemoglobin complex.
A Method of Above-water Iceberg 3D Modelling Using Surface Imaging

This paper reports on an algorithm to build a 3-D model of the abovewater portion of icebergs using surface imaging. The goal is to work towards the automation of iceberg surveys allowing Unmanned Surface Craft to acquire shape and size information to fulfill the iceberg database. The presented methodology is made up of 3 parts: volume intersection, occluding contour finding, data collection, and integration. This method is investigated in field trials conducted through the summer of 2014 by surveying 8 icebergs during 3 expeditions.
KIZUKI Processing for Visual Inspection: A Smart Pattern Pop-Out Algorithm Based on Human Visual Architecture

There are many cases in which it is difficult to detect defects by visual inspection. These defects, such as very small cracks and thin stains, etc., are slight difference and hide in background texture. Even if a skilled inspector can detect these defects, they are undetectable by basic image processing algorithms. This special ability of the inspectors is called "KIZUKI" in Japanese. This paper describes how to develop irregular region extraction programs based on human visual architectures. Two theories have been used to model the "defects pop-out = KIZUKI" process of visual inspection: the peripheral vision and the involuntary eye micro-vibration theories in the field of psychology of vision. We have implemented this model experimentally. It consists of two steps: forming low resolution images by variable re-sampling, and then detecting relatively salience regions at each low resolution image and integrating these regions. Experiment results indicate that our approach have been reasonable. Since our programs have been very simple and effective, it might be incorporable into different visual examination systems widely.
Subgraph Matching: on Compression and Computation

Subgraph matching finds a set I of all occurrences of a pattern graph in a target graph. It has a wide range of applications while suffers an expensive computation. This efficiency issue has been studied extensively. All existing approaches, however, turn a blind eye to the output crisis, that is, when the system has to materialize I as a preprocessing/intermediate/final result or an index, the cost of the export of I dominates the overall cost, which could be prohibitive even for a small pattern graph. This paper studies subgraph matching via two problems. 1) Is there an ideal compression of I? 2) Will the compression of I reversely boost the computation of I? For the problem 1), we propose a technique called VCBC to compress I to code (I) which serves effectively the same as I. For problem 2), we propose a subgraph matching computation framework CBF which computes code(I)instead of I to bring down the output cost. CBF further reduces the overall cost by reducing the intermediate results. Extensive experiments show that the compression ratio of VCBC can be up to 105 which also significantly lowers the output cost of CBF. Extensive experiments show the superior performance of CBF over existing approaches.
Combined Tomography and Epithelial Thickness Mapping for Diagnosis of Keratoconus

Purpose Scanning Scheimpflug provides information regarding corneal thickness and 2-surface topography while arc-scanned high-frequency ultrasound allows depiction of the epithelial and stromal thickness distributions. Both techniques are useful in detection of keratoconus. Our aim was to develop and test a keratoconus classifier combining information from both methods. Methods We scanned 111 normal and 30 clinical keratoconus subjects with Artemis-1 and Pentacam data. After selecting one random eye per subject, we performed stepwise linear discriminant analysis on a dataset combining parameters generated by each method to obtain classification models based on each technique alone and in combination. Results Discriminant analysis resulted in a 4-variable model (R2 = 0.740) based on Artemis data alone and a 4-variable model (R2 = 0.734) using Pentacam data alone. The combined model (R2 = 0.828) consisted of 3 Artemis- and 4 Pentacam-derived variables. The combined model R value was significantly higher than either model alone (p = 0.031, one-tailed). In cross-validation, Artemis had 100% sensitivity and 99.2% specificity, Pentacam had 97.3% sensitivity and 98.0% specificity, and the combined model had 97.3% sensitivity and 100% specificity. Conclusions Pentacam, Artemis, and combined models were all effective in distinguishing normal from clinical keratoconus subjects. From the standpoint of variance explained by the model (R2 values), the combined model was most effective. Application of the model to early and subclinical keratoconus will ultimately be required to assess the effectiveness of the combined approach.
An Empirical Process for the Design of High-Throughput Screening Deck Filters

A process for objective identification and filtering of undesirable compounds that contribute to high-throughput screening (HTS) deck promiscuity is described. Two methods of mapping hit promiscuity have been developed linking SMARTS-based structural queries with historical primary HTS data. The first compares an expected assay hit rate to actual hit rates. The second examines the propensity of an individual compound to hit multiple assays. Statistical evaluation of the data indicates a correlation between the resultant functional group filters and compound promiscuity. These data corroborate a number of commonly applied filters as well as producing some unexpected results. Application of these models to HTS collection triage reduced the number of in-house compounds considered for screening by 12%. The implications of these findings are further discussed in the context of the HTS screening set and combinatorial library design as well as compound acquisition.