Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonlinear Resonance Artifacts in Molecular Dynamics Simulations

The intriguing phenomenon of resonance, a pronounced integrator-induced corruption of a system's dynamics, is examined for simple molecular systems subject to the classical equations of motion. This source of timestep limitation is not well appreciated in general, and certainly analyses of resonance patterns have been few in connection to biomolecular dynamics. Yet resonances are present in the commonly used Verlet integrator, in symplectic implicit schemes, and also limit the scope of current multiple-timestep methods that are formulated as symplectic and reversible. The only general remedy to date has been to reduce the timestep. For this purpose, we derive method-dependent timestep thresholds (e.g., Tables 1 and 2) that serve as useful guidelines in practice for biomolecular simulations. We also devise closely related symplectic implicit schemes for which the limitation on the discretization stepsize is much less severe. Specifically, we design methods to remove third-order, or both the third- and fourth-order, resonances. These severe low-order resonances can lead to instability or very large energies. Our tests on two simple molecular problems (Morse and Lennard? Jones potentials), as well as a 22-atom molecule, N-acetylalanyl-N? -methylamide, confirm this prediction; our methods can delay resonances so that they occur only at larger timesteps (EW method) or are essentially removed (LIM2 method). Although stable for large timesteps by this approach, trajectories show large energy fluctuations, perhaps due to the coupling with other factors that induce instability in complex nonlinear systems. Thus, the methods developed here may be more useful for conformational sampling of biomolecular structures. The analysis presented here for the blocked alanine model emphasizes that one-dimensional analysis of resonances can be applied to a more complex, multimode system to analyze resonance behavior, but that resonance due to frequency coupling is more complex to pinpoint. More generally, instability, apparently due to numerically induced resonances, has been observed in the application of the implicit midpoint scheme to vibrating structures and could be expected also in the simulation of nonlinear wave phenomena; in such applications it is adequate not to resolve the highest frequency modes, so the proposed methods could be very useful.
EGFR is involved in control of gastric cell proliferation through activation of MAPK and Src signalling pathways in early‐weaned rats

Objectives: Early weaning (EW) increases proliferation of the gastric epithelium in parallel with higher expression of transforming growth factor alpha and its receptor epidermal growth factor receptor (EGFR). The primary objective of the present study was to examine involvement of EGFR signalling in regulating mucosal cell proliferation during the early weaning period.
Multiple keratoacanthomas arising in the setting of sorafenib therapy: novel chemoprophylaxis with bexarotene.

Address correspondence to Basil S. Cherpelis, MD, Department of Dermatology, University of South Florida, 12901 Bruce B. Downs Boulevard, MDC 79, Tampa, FL 33612. E-mail: bcherpel@hsc.usf. edu as two cycles of paclitaxel and carboplatin chemotherapy and four cycles of docetaxel and carboplatin. Subsequently, her serum CA-125 level returned to normal, indicating remission of the cancer. However, 5 months after completing chemotherapy, her serum CA-125 level again elevated to 95 from a nadir of 5, indicating that cancer had returned. A PET/CT scan confirmed multiple hypermetabolic peritoneal masses as well as right inguinal nodal activity. An excisional biopsy was performed on the right inguinal node, and histology disclosed metastatic adenocarcinoma. The patient was referred to our institute for consideration of a clinical trial. In late 2007, she began a clinical trial using a combination of carboplatin, paclitaxel, and sorafenib. The patient continued her monthly follow-up meetings in the Gynecologic Oncology Program. Three months after beginning treatment with carboplatin, tamoxifen, and sorafenib, she reported a rapidly enlarging, non-healing erythematous papule on her left nares and presented to dermatology for evaluation. By this time, she had developed a similar lesion on the left leg (Fig 1). Histologic examination of these lesions revealed well-demarcated crateriform squamous proliferations with a central keratin plug consistent with kerIntroduction Sorafenib is a novel antineoplastic drug that targets multiple intracellular and cell-surface kinases, inhibiting tumor cell proliferation and angiogenesis. While it is currently approved to treat metastatic or unresectable renal cell or hepatocellular carcinoma, studies are underway to evaluate its utility in other solid organ tumors. We present a case of a 61-year-old woman with metastatic ovarian cancer and no history of skin cancer who developed multiple keratoacanthomas while on a clinical trial using sorafenib. Surgical excision was performed palliatively for large and symptomatic lesions. Because of the patient’s terminal condition and unwillingness to undergo multiple surgical procedures, we instituted chemoprophylaxis with oral bexarotene. After two months of therapy, the patient has reported partial regression of some of the tumors and has not developed any new lesions. This is the second known report of multiple keratoacanthomas arising in the setting of sorafenib therapy.1 In addition, this is the first known report of using bexarotene for chemoprophylaxis or treatment of keratoacanthomas.
Cobalt and Vitamin B12 in Diets for Commercial Laying Hens on the Second Cycle of Production

The supplementation of cobalt and vitamin B12 in diets for commercial laying hens on the second production cycle was studied. Four hundred and eighty light commercial laying hens, Lohmann LSL, were used at initial phase of forced molting laying period. The trial was conducted in a randomized design. The plots were the treatments which were constituted by combination of five cobalt levels (0.00; 0.30; 0.60; 0.90 and 1.20ppm) and two vitamin B12 levels (without and with 10µ/kg), and the split-plots were four periods (21, 42, 63 and 84 days) during the second period of production, with 4 repetitions and 12 hens per experimental unit. Food and water were provided ad libitum and eggs were collected twice daily. Performance and egg quality parameters were evaluated. At the end of experimental period, two layers from each treatment were slaughtered, and liver and blood samples were taken for analysis. Performance and egg quality were not different (p>0.05) among cobalt supplementation levels, although egg damage data were different (p<0.05). Supplementation with vitamin B12 decreased egg weight. No influence of cobalt or vitamin B12 supplementation was seen on the concentration of cobalt in the liver and yolk as well as on blood analysis (hematrocrit, hemoglobin, erythrocytes, and leukocytes). The results revealed that vitamin B12 supplementation was important for commercial laying hens on the second cycle of production, but not cobalt supplementation.
Volitional and accidental nonadherence to pediatric inflammatory bowel disease treatment plans: initial investigation of associations with quality of life and disease activity.

OBJECTIVE To examine rates of volitional and accidental nonadherence, and explore potential differential associations of each with disease activity and quality of life (QOL), in pediatric patients with inflammatory bowel disease (IBD). METHODS One hundred families (100 parents, 78 adolescents) recruited from a large Midwestern children's hospital reported on the child's medication nonadherence and QOL. Healthcare providers supplied disease activity ratings. RESULTS Most adolescents (73.1%) and parents (70.1%) reported engaging in accidental nonadherence, whereas a smaller group (35 and 30%, respectively) reported engaging in volitional nonadherence to the child's prescribed medication regimen. Frequency of accidental nonadherence was unrelated to disease activity or any specific QOL area examined, whereas greater frequency of volitional nonadherence was associated with greater disease activity and poorer parent reported psychosocial QOL. CONCLUSIONS Nonadherence and the relationship with disease severity and QOL may be more complex for children with IBD than understood through previous work.
Characterization of the Transcriptome and Gene Expression of Tetraploid Black Locust Cuttings in Response to Etiolation

Etiolation (a process of growing plants in partial or complete absence of light) promotes adventitious root formation in tetraploid black locust (Robinia pseudoacacia L.) cuttings. We investigated the mechanism underlying how etiolation treatment promotes adventitious root formation in tetraploid black locust and assessed global transcriptional changes after etiolation treatment. Solexa paired-end sequencing of complementary DNAs (cDNAs) from control (non-etiolated, NE) and etiolated (E) samples resulted in 107,564 unigenes. In total, 52,590 transcripts were annotated and 474 transcripts (211 upregulated and 263 downregulated) potentially involved in etiolation were differentially regulated. These genes were associated with hormone metabolism and response, photosynthesis, signaling pathways, and starch and sucrose metabolism. In addition, we also found significant differences of phytohormone contents, activity of following enzymes i.e., peroxidase, polyphenol oxidase and indole acetic acid oxidase between NE and E tissues during some cottage periods. The genes responsive to etiolation stimulus identified in this study will provide the base for further understanding how etiolation triggers adventitious roots formation in tetraploid black locus.
Hypoxic Cell Death in Human NT2‐N Neurons: Involvement of NMDA and Non‐NMDA Glutamate Receptors

Abstract: Human NTera2 teratocarcinoma cells were differentiated into postmitotic NT2‐N neurons and exposed to hypoxia for 6 h. The cultures were evaluated microscopically, and percent lactate dehydrogenase (LDH) release after 24 and 48 h was used as an assay for cell death. After 48 h LDH release was 24.3 ± 5.6% versus 13.8 ± 3.7% in controls (p < 0.001). Cell death was greatly diminished by MK‐801 pretreatment (15.4 ± 5.1%, p < 0.001). If glutamate was omitted from the medium, glutamate levels after 6 h of hypoxia were reduced from 101 ± 63 to 2.3 ± 0.3 µM, and cell death at 48 h was also markedly reduced (15.4 ± 4.5%, p < 0.001). The α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionate antagonist 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione (18.7 ± 5.1%, p < 0.001) and mild hypothermia (33.5–34°C) during hypoxia (19.5 ± 2.75, p < 0.05) were moderately protective. Basic fibroblast growth factor (24.1 ± 3.2%), the nitric oxide synthase inhibitor NG‐nitro‐l‐arginine methyl ester (22.8 ± 8.1%), the antioxidant N‐tert‐butyl‐o‐phenylnitrone (18.9 ± 5.9%), and the 21‐aminosteroid U74389G (24.0 ± 3.4%) did not protect the cells. N‐Acetyl‐l‐cysteine even tended to increase cell death (30.1 ± 2.5%, p = 0.06). Treatment with MK‐801 at the end of hypoxia did not reduce cell death (23.3 ± 2.3%). In separate experiments, a 15‐min exposure to 1 mM glutamate without hypoxia did not result in significant cell death (14.7 ± 2.4 vs. 12.2 ± 2.1%,p = 0.07). We conclude that, although somewhat resistant to glutamate toxicity when normoxic, NT2‐N neurons die via an ionotropic glutamate receptor‐mediated mechanism when exposed to hypoxia in the presence of glutamate. As far as we know, this is the first reported analysis of the mechanism of hypoxic cell death in cultured human neuronlike cells.
Type III Secretion System

Sylvie Mazurier, Annabelle Merieau, Dorian Bergeau, Victorien Decoin, Daniel Sperandio, Alexandre Crépin, Corinne Barbey, Katy Jeannot, Maïté Vicré-Gibouin, Patrick Plésiat, Philippe Lemanceau, Xavier Latour INRA, UMR 1347 Agroécologie, Dijon, France; Normandie Université, Laboratoire de Microbiologie, Signaux et Microenvironnement—EA 4312 & IRIB Université de Rouen—IUT Evreux, Evreux, France; Université de Franche-Comté, Laboratoire de Bacteriologie, Faculté de médecine, Besançon, France; Normandie Université, Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale—EA 4358 —VASI-PRIMACEN (IRIB), Université de Rouen, Mont-Saint-Aignan, France
ScatterBlogs: Geo-spatial document analysis

We presented Scatterblogs, a system for microblog analysis that seamlessly integrates search backend and visual frontend. It provides powerful, automatic algorithms for detecting spatio-temporal ‘anomalies’ within blog entries as well as corresponding visual representations and interaction facilities for inspecting anomalies or exploiting them in further analytic steps. Apart from that, we consider the system's combinatoric facilities for building complex hypotheses from temporal, spatial, and content-related aspects an important feature. This was the key for creating a cross-checked analysis for MC1.
Automated assay for the determination of methylmalonic acid, total homocysteine, and related amino acids in human serum or plasma by means of methylchloroformate derivatization and gas chromatography-mass spectrometry.

BACKGROUND The combined measurement of methylmalonic acid (MMA) and total homocysteine (tHcy) in serum or plasma is useful in diagnosing and distinguishing between cobalamin and folate deficiencies. We developed and validated an isotope-dilution gas chromatography-mass spectrometry (GC-MS) method with automated sample workup for the determination of MMA, tHcy, and the related amino acids Met, total cysteine (tCys), Ser, and Gly in serum or plasma. METHODS Serum or plasma samples (100 microL) were treated with a reductant (dithioerythritol), deproteinized with ethanol, and derivatized and extracted in a single step by the addition of methylchloroformate and toluene. All liquid handling was performed in 96-well (1 mL) microtiter plates by a robotic workstation. The N(S)-methoxycarbonyl ethyl ester derivatives were analyzed by GC-MS in the selected-ion monitoring mode. RESULTS Detection limits (signal-to-noise ratio, 5:1) were between 0.03 micromol/L (MMA) and 10 micromol/L (Ser, tCys). The assay was linear to 100 micromol/L for MMA and tHcy and to 1000 micromol/L for Met, tCys, Ser, and Gly. The within-day CVs ranged from 0.7% to 3.6% (n = 20), and the between-day CVs from 2.1% to 8.1% (n = 20). The recovery was between 79% and 99% for the different analytes. CONCLUSION This assay combines a simple and automated sample preparation with selective and sensitive GC-MS analysis and is well suited for the combined measurement of MMA, tHcy, and the related amino acids.
A simple fault detection of the open-switch damage in BLDC motor drive systems

This paper proposes a novel fault detection algorithm for a brushless DC (BLDC) motor drive system. This proposed method is configured without the additional sensor for fault detection and identification. The fault detection and identification are achieved by a simple algorithm using the operating characteristic of the BLDC motor. The drive system after the fault identification is reconfigured by four-switch topology connecting a faulty leg to the middle point of DC-link using bidirectional switches. This proposed method can also be embedded into existing BLDC motor drive systems as a subroutine without excessive computational effort. The feasibility of a novel fault detection algorithm is validated in simulation.
Modeling of Human Body for Animation by Micro-sensor Motion Capture

We present a human motion model and animation for micro-sensor motion capture system. It consists of a sensor data-driven layered human motion model and an animation method using polygon group to achieve skin deformation. This method is based on biomechanics. The joints of human body were categorized according to the motion characteristics. Motion parameters estimated from sensor data are used to control the movement of human skeleton model and the deformation of skin model, and consequently reconstruct the human body motion in real-time animation. The experiments have shown that the proposed model is suitable for sensor data-driven virtual human in real time animation.
High-Affinity Transporters for NAD+ Precursors in Candida glabrata Are Regulated by Hst1 and Induced in Response to Niacin Limitation

ABSTRACT The yeast Candida glabrata is an opportunistic pathogen of humans. C. glabrata is a NAD+ auxotroph, and its growth depends on the availability of niacin (environmental vitamin precursors of NAD+). We have previously shown that a virulence-associated adhesin, encoded by EPA6, is transcriptionally induced in response to niacin limitation. Here we used transcript profiling to characterize the transcriptional response to niacin limitation and the roles of the sirtuins Hst1, Hst2, and Sir2 in mediating this response. The majority of genes transcriptionally induced by niacin limitation are regulated by Hst1, suggesting that it is the primary sensor of niacin limitation in C. glabrata. We show that three highly induced genes, TNA1, TNR1, and TNR2, encode transporters which are necessary and sufficient for high-affinity uptake of NAD+ precursors. Strikingly, if a tna1tnr1tnr2 mutant is starved for niacin, it exhibits an extended lag phase, suggesting a central role for the transporters in restoring NAD+ homeostasis after niacin limitation. Lastly, we had previously shown that the adhesin encoded by EPA6 is induced during experimental urinary tract infection (UTI); we show here that EPA6 transcriptional induction during UTI is strongly enhanced in the tna1tnr1tnr2 mutant strain, implicating the transporters in the growth of C. glabrata during infection.
Interactionof Chlorpromazinewith Bile

Chlorpromazine causes precipitation both of the glycoprotein and protein components of bile in vitro. The reaction depends on an electrostatic interaction between the negatively charged carboxyl groups on the bile components and the positively charged amine groups on the drug molecules in solution. The optimum conditions for the interaction between chiorprom. azine and bile components have been established, and the suggestion is made that this precipitation may be responsible in part, for cholestatic jaundice associated with the administration of chlorpromazine.
Conceptualising Resourcefulness as a Dispersed Practice

In research on health and wellbeing, resourcefulness is seen as an important skill that can improve quality of life. In design and HCI literature, it has long been acknowledged that resourcefulness is about more than human skills and involves the adaptation, modification and reinvention of technologies in everyday life. In this paper we argue how certain aspects of resourcefulness have so far remained under-theorized, and present a new design perspective on resourcefulness that is grounded in practice theory. In this view, resourcefulness is conceptualised as the dispersed practice of dealing with everyday crises of routine. By elaborating on the complex interplay between means and purpose, we tease out resourcefulness as a practice of reconfiguration. The paper closes by discussing implications of this conceptualisation by zooming in on ways of capturing and designing for resourcefulness.
Characteristics of the collective dielectric relaxation mode of the incommensurate SmCα* phase

Employing the dielectric relaxation spectroscopy technique, we have observed two different characteristics of the collective relaxation mode of an incommensurate SmCα* phase. Recent theoretical advances predict two different natures for the dielectric relaxation mode in the SmCα* phase. Our experimental results confirm two different behaviours of the relaxation mode in different temperature ranges for this phase for one unique compound having an exceptionally wide temperature range (∼9 °C) for the SmCα* phase.
Grado de competencia, presión de la deuda y productividad empresarial: un análisis empírico desde la perspectiva del gobierno corporativo

Este trabajo ofrece evidencia empirica acerca del impacto sobre la productividad empresarial derivado del grado de competencia, el poder de mercado, la presion financiera del endeudamiento y la estructura de la propiedad de la empresa. En el analisis, se estiman varios modelos dinamicos de regresion mediante el metodo generalizado de momentos propuesto por Arellano y Bond (1991), a partir de una muestra de datos de panel constituida por 4.947 empresas manufactureras espanolas pertenecientes a 19 sectores industriales diferentes, durante un periodo que abarca del ano 1994 al ano 2003. Vistos en su conjunto, los resultados alcanzados sugieren que la competencia, junto con la presion financiera y el tipo de accionista de control en cada empresa, influyen sobre la productividad empresarial, detectandose alguna evidencia de que pueden actuar a veces como mecanismos complementarios de los codigos de buen gobierno corporativo y de los habituales sistemas de disciplina aplicados por los mercados financieros.
Gait transition for a quadrupedal robot by replacing the gait matrix of a central pattern generator model

The pattern-generator-based approach for legged robot control is inspired by biological neural mechanisms of locomotion, in which a special challenge is gait transition. In this paper we build a holosymmetric central pattern generator model and propose parameter-setting principles for a gait matrix capable of producing typical quadrupedal gaits, and based on them present an approach of directly replacing the gait matrix for gait transition, with a focus on three problems emerging during transition: breakpoint, phase-lock and oscillation-stop. Breakpoints are smoothed by remaining the current outputs during transition, similar to a zero-order holder. Breaking the phase-lock is accomplished by adding a perturbation to the state matrix at the transiting point. An oscillation-stop of less than one period can be ignored. With such treatments, it is proved that gait transitions between any two gaits on a quadrupedal robot can be achieved at arbitrary phase locations in a walk cycle, theoretically and experimentally in part.
Treatment of Persistent Rhinovirus Infection With Pegylated Interferon α2a and Ribavirin in Patients With Hypogammaglobulinemia

quent laboratory values, serum creatinine levels normalized after an average of 15.9 days postoperatively (range, 10–26 days). The data provide evidence of systemic tobramycin absorption from ACSs placed during revision joint arthroplasty. This finding suggests that patients receiving an ACS may have prolonged exposure to elevated serum aminoglycoside levels, which could increase the risk of toxicity, including nephrotoxicity. Prospective studies are warranted to determine the true incidence of systemic aminoglycoside absorption from ACSs and the operative and patient risk factors that lead to nephrotoxicity.