Miracle-dz/UniFAR-FTUs huggingface dataset:
Mood, anxiety, and incomplete seizure control affect quality of life after epilepsy surgery

Objective: We examined the complex relationship between depression, anxiety, and seizure control and quality of life (QOL) outcomes after epilepsy surgery. Methods: Seven epilepsy centers enrolled 373 patients and completed a comprehensive diagnostic workup and psychiatric and follow-up QOL evaluation. Subjects were evaluated before surgery and then at 3, 6, 12, 24, 48, and 60 months after surgery. Standardized assessments included the Quality of Life in Epilepsy Inventory–89, Beck Depression Inventory (BDI), and Beck Anxiety Inventory (BAI). A mixed-model repeated-measures analysis was used to analyze associations of depression, anxiety, seizure outcome, and seizure history with overall QOL score and QOL subscores (cognitive distress, physical health, mental health, epilepsy-targeted) prospectively. Results: The groups with excellent and good seizure control showed a significant positive effect on the overall QOL compared to the groups with fair and poor seizure control. The BDI and BAI scores were both highly and negatively associated with overall QOL; increases in BDI and BAI scores were associated with decreased overall QOL score. Conclusions: Depression and anxiety are strongly and independently associated with worse QOL after epilepsy surgery. Interestingly, even partial seizure control, controlling for depression and anxiety levels, improved QOL. Management of mood and anxiety is a critical component to postsurgical care.
Amylopectin Synthase of Eimeria tenella: Identification and Kinetic Characterization

ABSTRACT. A soluble enzyme amylopectin synthase (UDP‐glucose‐α 1,4‐glucan α‐4‐glucosyltransferase) which transfers glucose from uridine 5′‐diphosphate glucose (UDP‐glucose) to a primer to form α‐I,4‐glucosyl linkages has been identified in the extracts of unsporulated oocysts of Eimeria tenella. UDP‐glucose and not ADP‐glucose was the most active glucosyl donor. Corn amylopectin, rabbit liver glycogen, oyster glycogen and corn starch served as primers; the latter two were less efficient. The enzyme has an apparent pH optimum of 7.5 and exhibited typical Michaelis‐Menten kinetics with dependence on both the primer and substrate concentrations. The Michaelis constants (Km). with respect to UDP‐glucose, was 0.5 mM; and 0.25 mg/ml and 1.25 mg/ml with respect to amylopectin and rabbit liver glycogen. The product formed by the reaction was predominantly a glucan containing α‐1,4 linkages. The specificity of the enzyme suggests that this enzyme is similar to glycogen synthase in eukaryotes and has been designated as amylopectin synthase (UDP‐glucose‐α‐1,4‐glucosetransferase EC 2.4.1.11).
Co-infections and transmission dynamics in a tick-borne bacterium community exposed to songbirds.

We investigated the transmission dynamics of a community of tick-borne pathogenic bacteria in a common European songbird (Parus major). Tick-naïve birds were infested with three successive batches (spaced 5 days apart) of field-collected Ixodes ricinus nymphs, carrying the following tick-borne bacteria: Rickettsia helvetica (16.9%), Borrelia garinii (1.9%), Borrelia miyamotoi (1.6%), Anaplasma phagocytophilum (1.2%) and Candidatus Neoehrlichia mikurensis (0.4%). Fed ticks were screened for the pathogens after moulting to the next developmental phase. We found evidence for early transmission (within 2.75 days after exposure) of R. helvetica and B. garinii, and to a lesser extent of A. phagocytophilum based on the increased infection rates of ticks during the first infestation. The proportion of ticks infected with R. helvetica remained constant over the three infestations. In contrast, the infection rate of B. garinii in the ticks increased over the three infestations, indicating a more gradual development of host tissue infection. No interactions were found among the different bacterium species during transmission. Birds did not transmit or amplify the other bacterial species. We show that individual birds can transmit several pathogenic bacterium species at the same time using different mechanisms, and that the transmission facilitation by birds increases the frequency of co-infections in ticks.
The use of cellular and molecular biomarkers to manage COPD exacerbations

ABSTRACT Introduction: Chronic obstructive pulmonary disease (COPD) exacerbations are a common cause of respiratory morbidity and mortality, and have various etiologies. Multiple cellular and molecular biomarkers have been associated with exacerbations. Quantitative sputum cell counts are able to identify the presence and type of bronchitis, which is an important contributor to exacerbations. Their utility to monitor bronchitis and to help treat exacerbations has been evaluated, yet they are not used in routine clinical practice. Areas covered: This review will provide a brief summary of biomarkers utilized in COPD, with a focus on the application of cellular markers for the management of exacerbations. A case study will demonstrate the application of these methods. With quantitative sputum cell counts, the presence of eosinophilic bronchitis predicts corticosteroid-responsiveness, while neutrophilic bronchitis identifies infection and suggests the need for antibiotics. Gastroesophageal reflux-related aspiration and heart failure can also be identified by examining sputum. Expert commentary: Quantitative sputum cytometry is an essential tool in the management of exacerbations of COPD, particularly those prone to frequent exacerbations. Treatment based on sputum cell counts is superior to current guideline-based recommendations to prevent future exacerbations and hospitalizations in observational and single-centre controlled trials. Large multicentre clinical trials are necessary to confirm this.
Tauroursodesoxycholate-induced choleresis involves p38(MAPK) activation and translocation of the bile salt export pump in rats.

BACKGROUND & AIMS Canalicular secretion of bile acids is stimulated by tauroursodesoxycholate (TUDC). This study investigates the underlying mechanisms. METHODS TUDC effects on mitogen-activated protein (MAP) kinases, taurocholate (TC) excretion, proteolysis, and the localization of the bile salt export pump (Bsep) were studied in rat hepatocytes and perfused liver. RESULTS TUDC induced a transient and concentration-dependent activation of p38(MAPK) and of extracellular signal-regulated kinase 2 (Erk-2), but not of c-Jun-N-terminal kinase (JNK). In perfused liver, TUDC concentrations of 20 micromol/L was sufficient to elicit the MAP kinase responses and TC choleresis. SB 202190, a specific inhibitor of p38(MAPK), had no effect on TUDC- induced Erk activation but abolished the stimulatory effect of TUDC on TC excretion in perfused liver, indicating the requirement of p38(MAPK) in addition to the reported Erk dependence for the choleretic response. TUDC-induced stimulation of TC excretion was accompanied by a p38(MAPK)-dependent insertion of subcanalicular immunoreactive Bsep into the canalicular membrane. In addition TUDC induced a p38(MAPK)-sensitive inhibition of proteolysis. CONCLUSIONS TUDC-induced stimulation of canalicular TC excretion involves a MAP kinase-dependent translocation of subcanalicular Bsep to the canalicular membrane. Dual activation of Erks and p38(MAPK) is required for the choleretic effect of both TUDC and hypo-osmotic cell swelling.
Can Preoccupation With Alcohol Override the Protective Properties of Mindful Awareness on Problematic Drinking?

Objectives:To assess the mediating role of drinking restraint—specifically preoccupation with drinking—on the associations between mindful awareness and alcohol consumption and alcohol-related problems. Methods:A total of 390 heavy-drinking, undergraduate, college students (52% male) were assessed on measures of mindfulness, drinking restraint, alcohol consumption (prior 90 d), and alcohol-related problems through self-report surveys. Results:Mindfulness was negatively associated with alcohol consumption, problems, and both factors of drinking restraint (emotional preoccupation and behavioral constraint). Emotional preoccupation, but not behavioral constraint, statistically mediated these relationships and demonstrated positive associations with both alcohol consumption and related problems. Conclusions:Results replicate previous findings documenting a negative association between mindfulness and alcohol consumption and problems. Statistical mediation models suggest that preoccupation with drinking may be a risk factor that over-rides the health-promoting effects of mindfulness.
Intravenous administration of human embryonic stem cell‐derived neural precursor cells attenuates cuprizone‐induced central nervous system (CNS) demyelination

S. J. Crocker, R. Bajpai, C. S. Moore, R. F. Frausto, G. D. Brown, R. R. Pagarigan, J. L. Whitton and A. V. Terskikh (2011) Neuropathology and Applied Neurobiology37, 643–653
Apoptotic Susceptibility to DNA Damage of Pluripotent Stem Cells Facilitates Pharmacologic Purging of Teratoma Risk

Pluripotent stem cells have been the focus of bioengineering efforts designed to generate regenerative products, yet harnessing therapeutic capacity while minimizing risk of dysregulated growth remains a challenge. The risk of residual undifferentiated stem cells within a differentiated progenitor population requires a targeted approach to eliminate contaminating cells prior to delivery. In this study we aimed to validate a toxicity strategy that could selectively purge pluripotent stem cells in response to DNA damage and avoid risk of uncontrolled cell growth upon transplantation. Compared with somatic cell types, embryonic stem cells and induced pluripotent stem cells displayed hypersensitivity to apoptotic induction by genotoxic agents. Notably, hypersensitivity in pluripotent stem cells was stage‐specific and consistently lost upon in vitro differentiation, with the mean half‐maximal inhibitory concentration increasing nearly 2 orders of magnitude with tissue specification. Quantitative polymerase chain reaction and Western blotting demonstrated that the innate response was mediated through upregulation of the BH3‐only protein Puma in both natural and induced pluripotent stem cells. Pretreatment with genotoxic etoposide purged hypersensitive pluripotent stem cells to yield a progenitor population refractory to teratoma formation upon transplantation. Collectively, this study exploits a hypersensitive apoptotic response to DNA damage within pluripotent stem cells to decrease risk of dysregulated growth and augment the safety profile of transplant‐ready, bioengineered progenitor cells.
Yin Yang 1 Negatively Regulates the Differentiation-Specific E1 Promoter of Human Papillomavirus Type 6

ABSTRACT Human papillomavirus type 6 (HPV-6) is a low-risk HPV whose replication cycle, like that of all HPVs, is differentiation dependent. We have previously shown that CCAAT displacement protein (CDP) binds the differentiation-induced HPV-6 E1 promoter and negatively regulates its activity in undifferentiated cells (W. Ai, E. Toussaint, and A. Roman, J. Virol. 73:4220–4229, 1999). Using electrophoretic mobility shift assays (EMSAs), we now report that Yin Yang 1 (YY1), a multifunctional protein that can act as a transcriptional activator or repressor and that can also inhibit HPV replication in vitro, binds the HPV-6 E1 promoter. EMSAs, using subfragments of the promoter as competitors, showed that the YY1 binding site is located at the 5′ end of the E1 promoter. When a putative YY1 site was mutated, the ability of YY1 to bind was greatly decreased. The activity of the mutated E1 promoter, monitored with the reporter gene luciferase, was threefold greater than that of the wild-type promoter, suggesting that YY1 negatively regulates HPV-6 E1 promoter activity. Nuclear extracts from differentiated keratinocytes showed decreased binding of YY1 to the wild-type promoter. Consistent with this, in differentiated keratinocytes, the activity of the transfected luciferasegene transcribed from the mutated promoter was comparable to that of the wild-type promoter; both promoters were up-regulated in differentiated keratinocytes compared to undifferentiated cells. These data suggest that YY1 functions in undifferentiated keratinocytes but not in differentiated keratinocytes. Both the wild-type and mutated promoters could be negatively regulated by overexpression of a plasmid encoding CDP. Thus, both YY1 and CDP appear to be negative regulators of the differentiation-induced HPV-6 E1 promoter and thereby the HPV life cycle. In contrast, only binding of CDP was detected using the E1 promoter of the high-risk HPV-31.
Morphological Diagnoses of Higher-Level Phyllostomid Taxa (Chiroptera: Phyllostomidae)

Phyllostomidae (New World leaf-nosed bats), the second most speciose chiropteran family, is one of the best-known and wellstudied chiropteran groups. Due to the ecological and morphological diversity of this family, comparative studies of phyllostomids abound in the literature, and numerous systematic and phylogenetic analyses have been published. Unfortunately, many of these studies have reached different conclusions concerning phyllostomid relationships, and have proposed different classification schemes. This has led to confusion, and highlighted the need for a well-supported and stable classification of the family, particularly at the level of subfamilies and tribes, areas of the greatest controversy. The goal of this paper is to provide morphological diagnoses of higher-level taxa (subtribes, tribes, and subfamilies). Herein we provide morphological diagnoses for 11 subfamilies (Macrotinae, Micronycterinae, Desmodontinae, Lonchorhininae, Phyllostominae, Glyphonycterinae, Glossophaginae, Lonchophyllinae, Carollinae, Rhinophyllinae, and Stenodermatinae), 12 tribes (Desmodontini, Diphyllini, Macrophyllini, Phyllostomini, Vampyrini, Choeronycterini, Glossophagini, Brachyphyllini, Lonchophyllini, Hsunycterini, Sturnirini, and Stenodermatini), and nine subtribes (Anourina, Choeronycterina, Brachyphyllina, Phyllonycterina, Vampyressina, Enchisthenina, Ectophyllina, Artibeina, and Stenodermatina).
Development of microsatellite markers for the neotropical vine Dalechampia scandens (Euphorbiaceae)1

Premise of the study: Microsatellite markers were developed to assess polymorphism and level of genetic diversity in four Mexican populations of the neotropical vine Dalechampia scandens (Euphorbiaceae). Methods and Results: Thirty-seven microsatellite markers representing bi-, tri-, tetra-, and pentanucleotide microsatellite repeats were developed. In total, 166 alleles were identified across 54 individuals. The number of alleles varied from one to 11 with an average of 4.49 alleles per locus. All loci except one were highly polymorphic between populations, whereas considerably less variation was detected within populations for most loci. The average observed and expected heterozygosities across study populations ranged from 0 to 0.63 and 0 to 0.59, respectively, for individual loci, and a deviation from Hardy–Weinberg equilibrium was observed for most loci. Conclusions: The developed markers may be useful for studying genetic structure, parentage analysis, mapping, phylogeography, and cross-amplification in other closely related species of Dalechampia.
Device parameter extraction in the linear region of MOSFET's

A self-consistent technique is proposed to extract device parameters from the I-V characteristics of MOSFET's in the linear region. The three parameters V/sub T/, B/sub m/(=/spl beta//sub 0/) and R/sub m/ are extracted from the implicitly weighed least square curve fitting of r/sub D/ against 1/(V/sub G/-V/sub T/-/spl alpha/V/sub D/). The series resistance R, the factor /spl theta/ of the V/sub G/ dependent /spl beta/, and L/sub eff/ are then obtained by comparing the long and short channel devices, Reasonable values are obtained for five technologies, and general agreement with Taur's method is confirmed. Based on the finding, a quick parameter extraction method using only three {r/sub D/, V/sub G/} data sets is proposed.
Sequence-dependent variations of DNA structure modulate radiation-induced strand breakage.

Using a 80 base pair DNA fragment, the sequence-dependence was compared for: (i) the probability of fast neutrons induced strand breakage, (ii) the accessibility of the H4'- and H5'-atoms to OH. attack, (iii) the width of the minor groove, and (iv) the probability of OH. reactions with H4'- or H5'-atoms. The probability of strand breakage was measured using sequencing gel electrophoresis. The accessibility and the probability of reaction were calculated for the energy-minimized modelled DNA fragment. A Monte-Carlo simulation was used for calculating the probabilities of H-atom abstraction by OH. It was observed that reduced breakage occurs in sequences exhibiting low accessibility of H4' and H5'2 and low probability of H-atom abstraction by OH. , due to a narrow, minor groove. This shows that the breakage probability at a given nucleotide site is not determined by the chemical nature of the nucleotide (A, T, G or C), but mainly by the local sequence-modulated intrinsic structure. Fitting the experimental results with the calculated probabilities of reaction suggests that a C4'-centered radical evolves towards a strand break three times more efficiently than the C5' one, and that half of the breaks occur via the 4'-path and half via the 5'-path.
Numerical Python for scalable architectures

In this paper, we introduce DistNumPy, a library for doing numerical computation in Python that targets scalable distributed memory architectures. DistNumPy extends the NumPy module[15], which is popular for scientific programming. Replacing NumPy with Dist-NumPy enables the user to write sequential Python programs that seamlessly utilize distributed memory architectures. This feature is obtained by introducing a new backend for NumPy arrays, which distribute data amongst the nodes in a distributed memory multi-processor. All operations on this new array will seek to utilize all available processors. The array itself is distributed between multiple processors in order to support larger arrays than a single node can hold in memory. We perform three experiments of sequential Python programs running on an Ethernet based cluster of SMP-nodes with a total of 64 CPU-cores. The results show an 88% CPU utilization when running a Monte Carlo simulation, 63% CPU utilization on an N-body simulation and a more modest 50% on a Jacobi solver. The primary limitation in CPU utilization is identified as SMP limitations and not the distribution aspect. Based on the experiments we find that it is possible to obtain significant speedup from using our new array-backend without changing the original Python code.
Fludarabine‐based reduced intensity conditioning regimens for allogeneic hematopoietic stem cell transplantation in patients with aplastic anemia and fungal infections

Abstract: Eighteen patients (12 men and 6 women) with aplastic anemia and active fungal infections (10 proven/probable; 8 possible) underwent stem cell transplantation using fludarabine combined with cyclophosphamide or total body irradiation. Peripheral blood stem cells (PBSC) were the main graft source and a combination of cyclosporine with either methotrexate or methylprednisolone was used for graft versus host disease prophylaxis. Fourteen patients (77.8%) achieved neutrophil engraftment after a median time of 11 d, while four died of fungal sepsis. Resolution of fungal infection occurred in 60% of patients with proven/probable infections and in 100% with possible fungal infections. At a median follow up of 30 months, 11 patients (61.1%) were alive and well. Fludarabine‐based conditioning regimens with PBSC transplantation can be used successfully in patients with aplastic anemia and fungal infections.
Structural modeling of TAL effector–DNA interactions

TAL (transcriptional activator‐like) effectors are DNA‐binding repeat proteins recently shown to recognize their target sites by an unprecedented, 1:1 mapping between repeat residues and DNA bases. The structural basis for this recognition is not known; in particular, it is not clear whether such 1:1 recognition can be accommodated by standard major‐groove readout of B‐form DNA. Here we describe a structure prediction protocol tailored to the TAL–DNA system, and report simulation results that shed light on observed repeat‐base associations and overall TAL structure. Our models demonstrate that TAL–DNA interactions can be explained by a model in which the TAL repeat domain forms a superhelical repeat structure that wraps around undistorted B‐form DNA, paralleling the geometry of the major groove, with contacts between position 13 of each repeat and its associated base pair on the sense strand determining the specificity of DNA recognition.
The psychological impact of forced displacement and related risk factors on Eastern Congolese adolescents affected by war.

BACKGROUND While the current knowledge base on the mental health effects of displacement is mainly limited to refugees residing in industrialised countries, this paper examines the impact of war-induced displacement and related risk factors on the mental health of Eastern Congolese adolescents, and compares currently internally displaced adolescents to returnees and non-displaced peers. METHODS Data were collected from a community sample of 819 adolescents aged 13 to 21 years, attending one of 10 selected schools across the Ituri district in the Democratic Republic of Congo. Respondents completed culturally adapted self-report measures of posttraumatic stress symptoms (using the Impact of Event Scale - Revised) and internalising and externalising behaviour problems (by means of the Hopkins Symptoms Checklist - 37 for Adolescents). Associated factors studied were age, sex, parental death, exposure to war-related violence and daily stressors. RESULTS Internally displaced persons (IDPs) reported highest mean scores for the IES-R and the HSCL-37A internalising scale, followed by returnees, while non-displaced adolescents scored significantly lower. However, ANCOVA tests showed that posttraumatic stress and internalising symptoms were mainly associated with traumatic exposure and daily stressors and not with displacement status. Externalising problem scores were associated with traumatic exposure, daily stressors and displacement. Remarkably, death of father was associated with fewer externalising problems. Sex was differently associated with internalising and externalising problems through traumatic and daily stressors. CONCLUSIONS As IDPs are highly exposed to violence and daily stressors, they report most psychological distress, when compared to returnees and non-displaced peers. The distinct mental health outcomes for returned youngsters illustrate how enhancing current socio-economic living conditions of war-affected adolescents could stimulate resilient outcomes, despite former trauma or displacement.
Self-tuning PSM controller based on state machine

A self-tuning pulse skip modulation (PSM) controller based on state machine is proposed in this paper. Four kinds of duty ratios are designed in the self-tuning PSM controller to balance the input energy and output energy. With which, the self-tuning PSM controller can make the power switch converter response quickly and the energy transfer better, as well as, avoid the real switching frequency entering into audible range with small output voltage ripple besides good stability and high efficiency. Analyses, simulations and experiments show the self-tuning PSM control technique based on the state machine is a good regulating mode for power converter.