Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Urine-Based Deer Lures to Mitigate CWD Transmission in Pennsylvania

The Pennsylvania Game Commission contacted Millersville University to perform tests to help combat the transmission and spread of Chronic Wasting Disease (CWD) via better detection of urine-based deer lures. The objective of this study was to use multiple methods and kits designed for detection of urine and blood to determine the best method of detection for urine-based deer lures. Methods included use of kits such as Uritrace ® , Nite-Site TM luminol, Hemascein ® and Ultra-violet (UV) light. We found that no one technique yielded a positive for all urine-based deer lures. The UV light and Uritrace methods were the most effective and the UV light was the best technique in field-testing. The spread of CWD throughout the Commonwealth has been confirmed and these findings provide a foundation to further develop methods to detect urine-based deer lures to help mitigate the spread of CWD.
Variable length chromosome GA for evolvable hardware

This paper proposes the variable-length chromosome GA (VGA) for hardware evolution. VGA is introduced for the evolvable hardware (EHW) which can change its own hardware structure by genetic learning to adapt best to the environment. VGA makes it possible to evolve larger circuits more quickly than simple GAs. The improvements by VGAs are demonstrated by two experiments; one is the evolution of combinatorial circuits, the other is the evolution of pattern classifier functions used in the pattern recognition system for hand-written inputs.
Regelbasierte Modellierung fremdsprachlich akzentbehafteter Aussprachevarianten. Grundlagen, Entwurf und Implementierung eines Regelsystems für sprachtechnologische Anwendungen

In der maschinellen Verarbeitung menschlicher Sprache (z.B. automatische Spracherkennung oder Sprachsynthese) werfen ausgepragte Abweichungen von der Sprachnorm stets besondere Probleme auf. Formen, die ausergewohnlich stark vom durchschnittlichen Sprechverhalten abweichen, gelten vielfach als nicht systemadaquat und fuhren zu deutlichen Leistungseinbusen sprachtechnologischer Systeme. Im Bereich der automatischen Spracherkennung ist dies z.B. dann der Fall, wenn als potentielle Nutzer eines Systems, welches fur die kanonische Aussprachenorm einer Sprache optimiert wurde, auch Nicht-Muttersprachler vorgesehen sind, Sprecher also, die einen fremdsprachlich gefarbten Akzent aufweisen. Hier ist die phonetische Diskrepanz zur Normlautung z.T. so erheblich, das die Performanz des Erkenners oftmals stark degradiert. Die Arbeit untersucht Abweichungen von der lautsprachlichen Norm, wie sie in fremdsprachlich gefarbten Aussprachevarianten auftreten. Ziel ist es, lautliche Invarianzen in fremdsprachlichen Akzenten zu ermitteln, diese zu systematisieren und schlieslich mittels eines regelbasierten Ansatzes zu modellieren, welcher in sprachverarbeitenden Systemen zum praktischen Einsatz kommen kann. Die Studie liefert somit einen neuartigen Beitrag zur multilingualen Ausrichtung sprachverarbeitender Systeme. Zu diesem Zweck werden charakteristische phonetische Realisierungsvarianten von Nicht-Muttersprachlern verschiedener Herkunft auf der Basis empirischer Sprachdaten ermittelt, klassifiziert und schlieslich auf Symbolebene (d.h. auf der Ebene phonetischer Transkriptionen) mittels Regeln automatisch generiert. Die Studie behandelt dabei exemplarisch eine Reihe europaischer Sprachen, die in verschiedenen Kombinationen als Muttersprache des Sprechers wie auch als Zielsprache in die Untersuchung einbezogen werden, mit dem Ziel, fur jede Kombination aus Muttersprache (L1) und Zielsprache (L2) je einen spezifischen Regelsatz zur Modellierung charakteristischer Aussprachefehler bzw. -varianten zu erstellen. Ausgehend von einer Synopsis der aktuellen Forschungsstandes in Sprachwissenschaft und Sprachtechnologie wird ein Modell einer regelhaften Beschreibung von Aussprachefehlern entwickelt und programmtechnisch umgesetzt. Dieses Modell bzw. seine technische Implementierung wird abschliesend mittels eines computerlinguistischen Verfahrens, welches ebenfalls im Rahmen der Arbeit entwickelt wird, einer quantitativen Evaluierung unterzogen. Auf dieser Grundlage werden abschliesend Leistung und Grenzen des Verfahrens sowie das Potential seiner kunftigen Weiterentwicklung diskutiert.
The vesicular stomatitis virus matrix protein inhibits transcription from the human beta interferon promoter

In cells infected by wild-type (wt) vesicular stomatitis virus (VSV) Indiana, host transcription is severely inhibited. DNA cotransfection studies have implicated the VSV matrix (M) protein in this process (B. L. Black and D. S. Lyles, J. Virol. 66:4058-4064, 1992). The M protein inhibited transcription not only from viral promoters in plasmids but also from the chromosomally integrated human immunodeficiency virus type 1 (HIV-1) provirus promoter (S.-Y. Paik, A. C. Banerjea, G. G. Harmison, C.-J. Chen, and M. Schubert, J. Virol. 69:3529-3537, 1995). In this study, we investigated the effect of wt VSV M protein on expression of a reporter gene under control of a cellular promoter (beta-interferon [IFN-beta] promoter), using double transient transfections in BHK and COS-1 cells. The cellular IFN-beta promoter was as susceptible to the inhibitory effect of the M protein as the viral promoters used previously. Viral proteins N, P, and G had no significant effect on reporter gene expression. The M protein gene from VSV mutant T1026R1, which is defective in host transcription inhibition, was cloned and sequenced, and its effect on reporter gene expression was tested. The mutant M protein had a methionine-to-arginine change at position 51 in the protein sequence and did not inhibit transcription from either the IFN-beta promoter or viral promoters. This VSV mutant is a good inducer of IFN, as opposed to the wt virus, which suppresses IFN induction. These results show that the M protein inhibits transcription from cellular as well as viral promoters and that the M protein does not regulate the IFN promoter any differently from viral promoters. While the M protein may play a role in IFN gene regulation, other viral or cellular factors that provide specificity to the induction process must also be involved.
Production of enniatins by Fusarium sambucinum: selection of high-yield conditions from liquid surface cultures.

SUMMARY Enniatins were determined in the mycelium of Fusarium sambucinum grown in liquid surface culture on semidefined or undefined media. Light was required for significant enniatin production, which was also favoured by moderate growth temperature. Production was supported by various carbon and nitrogen sources. Growth on a medium containing (w/v) 5% lactose and 0.8% tryptone, at 20 °C, with daily I2 h photoperiods, yielded I.7 g enniatins/I (IO% of mycelial dry wt). Glucose inhibited sporulation of F. sambucinum.
In vitro study of stability and amyloid‐fibril formation of two mutants of human stefin B (cystatin B) occurring in patients with EPM1

Myoclonus epilepsy of type 1 (EPM1) is a rare monogenic progressive and degenerative epilepsy, also known under the name Unverricht‐Lundborg disease. With the aim of comparing their behavior in vitro, wild‐type (wt) human stefin B (cystatin B) and the G4R and the R68X mutants observed in EPM1 were expressed and isolated from the Escherichia coli lysate. The R68X mutant (Arg68Stop) is a peptide of 67 amino acids from the N terminus of stefin B. CD spectra have shown that the R68X peptide is not folded, in contrast to the G4R mutant, which folds like wild type. The wild type and the G4R mutant were unfolded by urea and by trifluoroethanol (TFE). It has been shown that both proteins have closely similar stability and that at pH 4.8, where a native‐like intermediate was demonstrated, TFE induces unfolding intermediates prior to the major transition to the all‐α‐helical state. Kinetics of fibril formation were followed by Thioflavin T fluorescence while the accompanying changes of morphology were followed by the transmission electron microscopy (TEM). For the two folded proteins the optimal concentration of TFE producing extensive lag phases and high fibril yields was predenaturational, 9% (v/v). The unfolded R68X peptide, which is highly prone to aggregate, formed amyloid fibrils in aqueous solution and in predenaturing 3% TFE. The G4R mutant exhibited a much longer lag phase than the wild type, with the accumulation of prefibrillar aggregates. Implications for pathology in view of the higher toxicity of prefibrillar aggregates to cells are discussed.
Gait analysis of incomplete spinal cord injured subjects walking with an active orthosis and crutches

The analysis of powered assisted gait is an open field of research in the biomechanics community. In the last years, a number of active orthoses and exoskeletons aimed at assisting human gait have been developed [1]. The objective of this work is to present results of the kinematic and dynamic analysis of the gait of incomplete spinal cord injured (SCI) subjects using crutches and the active orthosis presented in [2]. The target SCI patients are able to control hip flexor muscles and are classified with levels C or D in the ASIA impairment scale. The mentioned orthosis (stance-control knee-ankle foot orthosis, SCKAFO) has a compliant joint that constrains ankle plantar flexion and a powered knee unit with two systems: a mechanical locking system that is active during the stance phase and a conventional motor-gearbox group that assists the knee rotation during swing [2]. The developed controller uses the information of on-off plantar sensors, ankle encoders and inertial gyroscopes placed at the thighs to control the two systems installed at the knee. The gait of an incomplete SCI subject using elbow crutches and the two orthoses is captured in the lab by twelve infrared cameras that detect passive markers attached to the subject’s body and crutches. Foot-ground contact wrenches are measured using two force plates and crutch-ground contact forces are estimated through extensometry using three Wheatstone bridges on the crutch. A 3D whole-body model has been developed using a multibody dynamics formulation to solve the inverse dynamics problem. The two orthoses and the two crutches are assumed to be rigidly attached to body segments. The model incorporates the subject’s body segment parameters (BSP), as well as the orthoses and crutches geometric and inertial parameters. The control algorithm is also modelled in order to determine the motor assistance torque at the knee at each time step. From the motion capture data, the BSP and the ground reaction forces, the net joint torques are calculated following an inverse dynamics procedure. In order to validate the results, two approaches are used. First, the global ground reactions, which can be determined from kinematic information only, will be compared to those obtained from the force plate and extensometry measurements. Secondly, the experimental measurement of the knee assistance torque during swing will be compared to that obtained through the model. The development of this tool is aimed at analysing the motion and efforts of a specific patient to design a customized orthosis controller for his gait pattern, to evaluate the effect of different control strategies of the orthosis, to study the adaptation of the patient to the assistive device with training and to advance in the understanding of the interaction between the musculoskeletal system and the orthosis. It is expected that this will contribute to improve the design of such devices.
Electrostatics in protein–protein docking

A novel geometric‐electrostatic docking algorithm is presented, which tests and quantifies the electrostatic complementarity of the molecular surfaces together with the shape complementarity. We represent each molecule to be docked as a grid of complex numbers, storing information regarding the shape of the molecule in the real part and information regarding the electrostatic character of the molecule in the imaginary part. The electrostatic descriptors are derived from the electrostatic potential of the molecule. Thus, the electrostatic character of the molecule is represented as patches of positive, neutral, or negative values. The potential for each molecule is calculated only once and stored as potential spheres adequate for exhaustive rotation/translation scans. The geometric‐electrostatic docking algorithm is applied to 17 systems, starting form the structures of the unbound molecules. The results—in terms of the complementarity scores of the nearly correct solutions, their ranking in the lists of sorted solutions, and their statistical uniqueness—are compared with those of geometric docking, showing that the inclusion of electrostatic complementarity in docking is very important, in particular in docking of unbound structures. Based on our results, we formulate several “good electrostatic docking rules”: The geometric‐electrostatic docking procedure is more successful than geometric docking when the potential patches are large and when the potential extends away from the molecular surface and protrudes into the solvent. In contrast, geometric docking is recommended when the electrostatic potential around the molecules to be docked appears homogenous, that is, with a similar sign all around the molecule.
KDM1A/LSD1 regulates the differentiation and maintenance of spermatogonia in mice

The proper regulation of spermatogenesis is crucial to ensure the continued production of sperm and fertility. Here, we investigated the function of the H3K4me2 demethylase KDM1A/LSD1 during spermatogenesis in developing and adult mice. Conditional deletion of Kdm1a in the testis just prior to birth leads to fewer spermatogonia and germ cell loss before 3 weeks of age. These results demonstrate that KDM1A is required for spermatogonial differentiation, as well as germ cell survival, in the developing testis. In addition, inducible deletion of Kdm1a in the adult testis results in the abnormal accumulation of meiotic spermatocytes, as well as apoptosis and progressive germ cell loss. These results demonstrate that KDM1A is also required during adult spermatogenesis. Furthermore, without KDM1A, the stem cell factor OCT4 is ectopically maintained in differentiating germ cells. This requirement for KDM1A is similar to what has been observed in other stem cell populations, suggesting a common function. Taken together, we propose that KDM1A is a key regulator of spermatogenesis and germ cell maintenance in the mouse.
Estimating gene penetrance from family data

Family data are useful for estimating disease risk in carriers of specific genotypes of a given gene (penetrance). Penetrance is frequently estimated assuming that relatives' phenotypes are independent, given their genotypes for the gene of interest. This assumption is unrealistic when multiple shared risk factors contribute to disease risk. In this setting, the phenotypes of relatives are correlated even after adjustment for the genotypes of any one gene (residual correlation). Many methods have been proposed to address this problem, but their performance has not been evaluated systematically. In simulations we generated genotypes for a rare (frequency 0.35%) allele of moderate penetrance, and a common (frequency 15%) allele of low penetrance, and then generated correlated disease survival times using the Clayton‐Oakes copula model. We ascertained families using both population and clinic designs. We then compared the estimates of several methods to the optimal ones obtained from the model used to generate the data. We found that penetrance estimates for common low‐risk genotypes were more robust to model misspecification than those for rare, moderate‐risk genotypes. For the latter, penetrance estimates obtained ignoring residual disease correlation had large biases. Also biased were estimates based only on families that segregate the risk allele. In contrast, a method for accommodating phenotype correlation by assuming the presence of genetic heterogeneity performed nearly optimally, even when the survival data were coded as binary outcomes. We conclude that penetrance estimates that accommodate residual phenotype correlation (even only approximately) outperform those that ignore it, and that coding censored survival outcomes as binary does not substantially increase the mean‐square errror of the estimates, provided the censoring is not extensive. Genet. Epidemiol. 34: 373–381, 2010. © 2010 Wiley‐Liss, Inc.
Does the bleomycin sensitivity assay express cancer phenotype?

The bleomycin (BLM) sensitivity assay has been associated with the measuring of increased risk of individual susceptibility to cancer, when chromatid breaks per cell (b/c) induced by an in vitro treatment of lymphocytes with BLM are elevated. The high heritability of BLM sensitivity indicates a genetic background. We wished to clarify whether the test characterizes the head and neck cancer phenotype as compared not only with healthy individuals, but also with alcoholic patients (ALCs) whose exposure to tobacco and alcohol consumption were similar to that of head and neck cancer patients (HNCPs), but whose liver diseases were not cancerous. If the BLM test quantifies merely cancer susceptibility on an inherited basis, the mutagen sensitivity of HNCPs should differ from that of ALCs. Conventional chromosome analysis and the BLM assay were carried out on 156 HNCPs, 51 ALCs, 146 healthy non-smokers and non-drinkers and 149 non-drinking smokers. The spontaneous rates of chromosomal aberrations (CAs) in HNCPs, ALCs and healthy smokers were identical (2.8%), but differed significantly from the non-smoking controls (2.25%). Sporadic CAs were clearly associated with tobacco smoking, but not with health status. Mutagen sensitivity measured by the BLM test showed significantly (P < 0.04) elevated values not only in HNCPs (1.13 b/c), but also in ALCs (1.29 b/c) as compared with the controls (1.01 b/c). The main finding of the study was that a considerable proportion (46%) of Hungarian controls were mutagen sensitive, twice as many as in those populations reported by others so far. Our data suggest that the BLM test does not characterize susceptibility to cancer due to insignificant differences between HNCPs and ALCs (P = 0.12) under our conditions. However, the assay might be used as a biomarker to predict cancer susceptibility under circumstances when aberrant cell frequency is >or=2% and b/c is >or=1.
Lisfranc injuries in children and adolescents

In this descriptive analysis of pediatric Lisfranc injuries, records of 56 children treated for bony or ligamentous Lisfranc injuries over a 12-year period were reviewed. Overall, 51% of fractures and 82% of sprains were sports-related (P=0.03). A total of 34% of the cohort underwent open reduction internal fixation, which was more common among patients with closed physes (67%). Full weight bearing was allowed in open reduction internal fixation patients at a mean of 14.5 weeks, compared to 6.5 weeks in the nonoperative group. Complications were rare (4%) and included physeal arrest in one patient and a broken, retained implant in one patient.
Most Frequent and Severe Symptoms and Learning Needs among CABG Patients

Coronary artery disease accounts for over 7.9% of total healthcare expenditure in all industrialized countries and is a global concern (WHO, 2007). The common surgical treatment method for CAD, and a life saving intervention since the 1960s is Coronary Artery Bypass Graft surgery (CABG) (Gao, et al., 2009; Wijns, et al., 2010). Globally, on average one in every 500 individuals annually undergoes a CABG procedure (WHO, 2007). Surgery for CAD may be indicated for symptomatic or prognostic reasons. The decision to advise CABG is based on the balance between the expected benefit and the risks that the patient faces.
The Critical Imagination: Emancipatory Interests in Consumer Research

Critical theory is presented as an interdisciplinary approach to seeking knowledge about consumers. Critical theory holds that social problems often result from groups in society being constrained by social structures and processes that they themselves construct and maintain. Critical research involves grasping both the intersubjective understandings of the groups involved and the historical-empirical understanding of the potentially constraining objective social conditions. Contradictions that are discovered provide the stimuli for change. Through the process of critique and dialogue the critical researcher tries to help people imagine alternative social organizations that facilitate the development of human potential free from constraints. Copyright 1991 by the University of Chicago.
The glyoxalase system: new developments towards functional characterization of a metabolic pathway fundamental to biological life.

The glyoxalase system is present in the cytosol of cells and cellular organelles, particularly mitochondria. It is found throughout biological life and is thought to be ubiquitous. The widespread distribution and presence of the glyoxalase system in living organisms suggests it fulfils a function of fundamental importance to biological life. Recent investigations have brought new developments in the involvement of the glyoxalase in cell growth and vesicle mobilization, with increasing evidence of changes in the glyoxalase system during tumor growth and diabete mellitus, particularly relating to the development of associated clinical complications.
Measuring unemployment persistence of different labor force groups in the Greater São Paulo Metropolitan Area

This article makes use of ARFIMA models and unit root tests with structural breaks to examine the unemployment persistence of different labor forces in the Greater Metropolitan Area of Sao Paulo. To this purpose, not only is the region's open unemployment rate analyzed but it is also disaggregated by gender, age, color and position within the household. The period ranges from January 1985 to November 2008 and, despite using a range of estimation methods, the presence of a unit root cannot be rejected in general. The exceptions are the series related to Age 15-17 and over 40. But even in these cases the parameter "d" lies above 0.5. This is an indication that the unemployment rates in Sao Paulo can be defined as non stationary and the majority of the series are not mean-reverting. Therefore, the disinflation policies implemented by the Brazilian policymakers in the last two decades, as well as changes in real variables, have had long-lasting effects on the unemployment rates in Sao Paulo.
Promoter hypermethylation of p15INK4B, HIC1, CDH1, and ER is frequent in myelodysplastic syndrome and predicts poor prognosis in early‐stage patients

Abstract: The propensity of myelodysplastic syndrome (MDS) to transform into acute myeloid leukemia (AML) suggests the existence of common pathogenic components for these malignancies. Here, four genes implicated in the development of AML were examined for promoter CpG island hypermethylation in cells from 37 patients with different stages of MDS. Aberrant methylation was detected by polymerase chain reaction amplification of bisulfite‐treated DNA followed by denaturing gradient gel electrophoresis. The highest rate of methylation was found for p15INK4B (51%), followed by HIC1 (32%), CDH1 (27%), and ER (19%). Concurrent hypermethylation of ≥3 genes was more frequent in advanced compared with early‐stage MDS (P ≤ 0.05), and hypermethylation of p15INK4B was associated with leukemic transformation in early MDS (P ≤ 0.05). The median overall survival was 17 months for cases showing hypermethylation of ≥1 genes vs. 67 months for cases without hypermethylation (P = 0.002). Specifically, promoter hypermethylation identified a subgroup of early MDS with a particularly poor prognosis (median overall survival 20 months vs. 102 months; P = 0.004). In multivariate analysis including stage and thrombocyte count, hypermethylation of ≥1 genes was an independent negative prognostic factor (P < 0.05). These data suggest that hypermethylation of p15INK4B, HIC1, CDH1, and ER contribute to the development and outcome of MDS.