Miracle-dz/UniFAR-FTUs huggingface dataset:
Fusion of intra- and extracellular forms of vaccinia virus with the cell membrane

The membrane fusion activities of the isolated single-envelope intracellular form of vaccinia virus (INV) and the double-envelope extracellular (EEV) form were studied by using a lipid-mixing assay based on the dilution of a fluorescent probe. Fluorescently labeled INV and EEV from both the IHD-J and WR strains of vaccinia virus fused with HeLa cells at neutral pH, suggesting that fusion occurs with the plasma membrane during virus entry. EEV fused more efficiently and with faster kinetics than INV: approximately 50% of bound EEV particles fused over the course of 1 h, compared with only 25% of the INV particles. Fusion of INV and EEV was strongly temperature dependent, being decreased by 50% at 34 degrees C and by 90% at 28 degrees C. A monoclonal antibody to a 14-kilodalton envelope protein of INV that has been implicated in the fusion reaction (J. F. Rodriguez, E. Paez, and M. Esteban, J. Virol. 61:395-404, 1987) completely suppressed the initial rate of fusion of INV but had no effect on the fusion activity of EEV, suggesting that vaccinia virus encodes two or more membrane fusion proteins. Finally, cells infected with the WR strain of vaccinia virus formed syncytia when briefly incubated at pH 6.4 or below, indicating that an acid-activated viral fusion protein is expressed on the cell surface. However, WR INV and EEV did not display increased fusion activity at acid pH, suggesting that the acid-dependent fusion factor is not incorporated into virions or that its activity there is masked.
Patterns of Coping Among Family Caregivers of Frail Older Adults

Past studies have extensively examined factors associated with coping strategies that caregivers use to ameliorate distress or solve problems. While these studies have found that stressors and individual resources influence choices of coping strategies, they have tended to overlook caregivers’ social resources and have rarely considered the possibility that distinct groups of caregivers may use different sets of coping strategies. We conducted latent-class analyses to identify distinct groups of caregivers: those using no particular patterns of coping (unpatterned-coping), those centering on ameliorating distress (emotional-coping), and those focusing on both ameliorating distress and solving problems (hybrid-coping). Stressors distinguished all three coping groups, individual resources differentiated the hybrid-coping group from the emotional-coping group and the unpatterned-coping group, and social resources separated the emotional-coping group and the hybrid-coping group from the unpatterned-coping group. These findings indicate different factors contributing to caregivers’ use of different coping styles and suggest ways to better help caregivers.
Recognizing Human Activity in Free-Living Using Multiple Body-Worn Accelerometers

Recognizing human activity is very useful for an investigator about a patient’s behavior and can aid in prescribing activity in future recommendations. The use of body worn accelerometers has been demonstrated to be an accurate measure of human activity; however, research looking at the use of multiple body worn accelerometers in a free living environment to recognize a wide range of activities is not evident. This paper aimed to successfully recognize activity and sub-category activity types through the use of multiple body worn accelerometers in a free-living environment. Ten participants (Age = 23.1 ± 1.7 years, height =171.0 ± 4.7 cm, and mass = 78.2 ± 12.5 Kg) wore nine body-worn accelerometers for a day of free living. Activity type was identified through the use of a wearable camera, and subcategory activities were quantified through a combination of free-living and controlled testing. A variety of machine learning techniques consisting of preprocessing algorithms, feature, and classifier selections were tested, accuracy, and computing time were reported. A fine k-nearest neighbor classifier with mean and standard deviation features of unfiltered data reported a recognition accuracy of 97.6%. Controlled and free-living testing provided highly accurate recognition for sub-category activities (>95.0%). Decision tree classifiers and maximum features demonstrated to have the lowest computing time. Results show that recognition of activity and sub-category activity types is possible in a free-living environment through the use of multiple body worn accelerometers. This method can aid in prescribing recommendations for activity and sedentary periods for healthy living.
Genetic Modifiers of comatose Mutations in Drosophila: Insights Into Neuronal NSF (N-Ethylmaleimide–Sensitive Fusion Factor) Functions

Abstract: By the middle of the 20th century, development of powerful genetic approaches had ensured that the fruit fly would remain a model organism of choice for genetic and developmental studies. But in the 1970s, a few pioneering groups turned their attention to the prospect of using the fly for neurophysiological experiments. They proposed that in a poikilothermic organism such as Drosophila, temperature-sensitive or “ts” mutations in proteins that controlled nerve function would translate to a “ts” paralytic phenotype. This was by no means an obvious or even a likely assumption. However, following directed screens these groups soon reported dramatic demonstrations of reversible ts paralysis in fly mutants. Resultantly, these “simple” experiments led to the isolation of a number of conditional mutations including shibire, paralytic, and comatose. All have since been cloned and have enabled deep mechanistic insights into synaptic transmission and nerve conduction. comatose (comt) mutations, for example, were found to map to missense changes in dNSF1, a neuron-specific fly homolog of mammalian NSF (N-ethylmaleimide–sensitive fusion factor). Studies on comt were also some of the first to discriminate between nuanced models of NSF function during presynaptic transmitter release that have since been borne out by experiments in multiple preparations. Here, the authors present an overview of NSF function as it is understood today, with an emphasis on contributions from Drosophila beginning with experiments carried out by Obaid Siddiqi in the Benzer laboratory. The authors also outline initial results from a genetic screen for phenotypic modifiers of comt that hold the promise of further elucidating NSF function at the synapse. Over the years, the neuromuscular system of Drosophila has served as a uniquely accessible model to unravel mechanisms underlying synaptic transmission. To this day, ts paralysis remains one of the most emphatic demonstrations of nerve function in an intact organism.
Dissociation between phase‐locked and nonphase‐locked alpha oscillations in a working memory task

The functions of human alpha oscillations (∼10 Hz) were related to cognitive processes such as memory and top‐down control. Recent models suggest that alpha phase serves as a mechanism especially relevant for the timing of neural activity, whereas alpha amplitude is important for the inhibition of task‐irrelevant brain areas. This study investigates directly the influence of top‐down modulation on phase‐locked and nonphase‐locked alpha rhythms. We conducted an EEG experiment where subjects performed a working memory task. In the encoding phase of the task subjects had to learn presented pictures of nonliving objects that could later be asked to be retrieved. We varied the top‐down modulation by including cues indicating either to remember or to forget (not to remember) the next following item. Spectral analyses showed that nonremember cues elicited pronounced alpha amplitude increase compared to remember cues. Furthermore, phase‐locking in low frequencies, especially in the alpha range (7–12 Hz), was stronger for remember as opposed to not‐to‐remember items. In conclusion, we propose that alpha amplitude reflects top‐down modulated inhibition and that alpha phase is important for the exact timing of neural activity and can be related to binding processes. Hum Brain Mapp, 2009. © 2009 Wiley‐Liss, Inc.
A Binomial and Species-Independent Approach to Trap Capture Analysis of Flying Insects

Abstract Traps for monitoring of flying insect pests constitute a critical part of integrated pest management strategies. However, interpretation of trap captures is hampered by 1) factors associated with the performance of traps (i.e., lure, trap design, placement); 2) an often poorly defined relationship between trap captures and population density; and 3) interpretation approaches being highly specific to a certain insect species, trapping method, or trapping environment. The main purpose of this study was to identify a trap capture interpretation approach with little sensitivity to characteristics specific to a given data set, which would allow easier comparison of trapping data sets and make it easier to standardize sampling plans across insect pests and trapping environments. Based on fits of trapping data sets to standard distributions (normal, Poisson, and negative binomial), evaluations of the index of aggregation, k, and linear regression coefficients from Taylor’s power law, we concluded that these characteristics varied considerably among data sets, which means that enumerative sampling plans may not be appropriate. Across 13 trapping data sets of six insect species, we showed a consistent nonlinear relationship between average trap captures and number of traps with zero captures and that the k can be stabilized by converting trapping data into binomial data. A trap interpretation approach based on number of zero captures is both easy to use, was found to be species-independent, and means that it may be possible to establish meaningful and reliable action thresholds based on trap captures of flying insects. Although developed using trapping data from food facilities, this approach may have application to trapping data from other environments as well.
In vitro antioxidant activity and in vivo efficacy of topical formulations containing vitamin C and its derivatives studied by non‐invasive methods

Background/purpose: Vitamins C and its derivatives, mainly due to their antioxidant properties, are being used in cosmetic products to protect and to reduce the signs of ageing. However, there are no studies comparing the effects of vitamin C [ascorbic acid (AA)] and its derivatives, magnesium ascorbyl phosphate (MAP) and ascorbyl tetra‐isopalmitate (ATIP), when vehiculated in topical formulations, mainly using objective measurements, which are an important tool in clinical efficacy studies. Thus, the objective of this study was to determine the in vitro antioxidant activity of AA and its derivatives, MAP and ATIP, as well as their in vivo efficacy on human skin, when vehiculated in topical formulations.
Transcriptional Repressor Functions of Drosophila E2F1 and E2F2 Cooperate To Inhibit Genomic DNA Synthesis in Ovarian Follicle Cells

ABSTRACT Individual members of the E2F/DP protein family control cell cycle progression by acting predominantly as an activator or repressor of transcription. In Drosophila melanogaster the E2f1, E2f2, Dp, and Rbf1 genes all contribute to replication control in ovarian follicle cells, which become 16C polyploid and subsequently undergo chorion gene amplification late in oogenesis. Mutation of E2f2, Dp, or Rbf1 causes ectopic DNA replication throughout the follicle cell genome during gene amplification cycles. Here we show by both reverse transcription-PCR and DNA microarray analysis that the transcripts of prereplication complex (pre-RC) genes are elevated compared to the wild type in E2f2, Dp, and Rbf1 mutant follicle cells. For some genes the magnitude of this transcriptional derepression is greater in Rbf1 than in E2f2 mutants. These differences correlate with differences in the magnitude of the replication defects in follicle cells, which attain an inappropriate 32C DNA content in both Rbf1 and Dp mutants but not in E2f2 mutants. The ectopic genomic replication of E2f2 mutant follicle cells can be suppressed by reducing the Orc2, Orc5, or Mcm2 gene dose by half, indicating that small changes in pre-RC gene expression can affect DNA synthesis in these cells. We conclude that RBF1 forms complexes with both E2F1/DP and E2F2/DP that cooperate to repress the expression of pre-RC genes, which helps confine DNA synthesis to sites of gene amplification. In contrast, E2F1 and E2F2 repressors function redundantly for some genes in the embryo. Thus, the relative functional contributions of E2F1 and E2F2 to gene expression and cell cycle control depends on the developmental context.
Repeated contractions alter the geometry of human skeletal muscle.

The aim of this study was to investigate the effect of repeated contractions on the geometry of human skeletal muscle. Six men performed two sets (sets A and B) of 10 repeated isometric plantarflexion contractions at 80% of the moment generated during plantarflexion maximal voluntary contraction (MVC), with a rest interval of 15 min between sets. By use of ultrasound, the geometry of the medial gastrocnemius (MG) muscle was measured in the contractions of set A and the displacement of the MG tendon origin in the myotendinous junction was measured in the contractions of set B. In the transition from the 1st to the 10th contractions, the fascicular length at 80% of MVC decreased from 34 +/- 4 (means +/- SD) to 30 +/- 3 mm (P < 0.001), the pennation angle increased from 35 +/- 3 to 42 +/- 3 degrees (P < 0.001), the myotendinous junction displacement increased from 5 +/- 3 to 10 +/- 3 mm (P < 0.001), and the average fascicular curvature remained constant (P > 0.05) at approximately 4.3 m(-1). No changes (P > 0.05) were found in fascicular length, pennation angle, and myotendinous junction displacement after the fifth contraction. Electrogoniometry showed that the ankle rotated by approximately 6.5 degrees during contraction, but no differences (P > 0.05) were obtained between contractions. The present results show that repeated contractions induce tendon creep, which substantially affects the geometry of the in-series contracting muscles, thus altering their potential for force and joint moment generation.
A probability model for the meiosis I non‐disjunction fraction in numerical chromosomal anomalies

Numerical chromosome abnormalities (aneuploidies) are among the most common known causes of mental retardation and the leading cause of pregnancy loss in humans. They primarily arise by the process of meiotic non‐disjunction. We still know very little about the contribution of genetic and environmental causes for non‐disjunction in humans. In order to increase our understanding of the epi‐ demiology of human trisomies, it is necessary to establish the proportion of cases occurring in the first or second division of meiosis. Trisomic patients will display, in study of microsatellite typed by the polymerase chain reaction (PCR), three fragment peaks of equal intensity, two fragments at an average 2: 1 dosage or one individual fragment. In this work we describe a statistical approach for estimation of the fraction of meiosis I non‐disjunctions (F) in the absence of the parental information. First we determine a probability model for the number of peaks in a polymorphic microsatellite locus, which is a function of F. Based on this model, we obtain a maximum likelihood estimator for F, using the observed proportion of one, two and three allele patterns in trisomic individuals. Relying on the properties of maximum likelihood theory, we also calculate the asymptotic variance and confidence intervals for F. Owing to the fact that the samples of trisomic patients are limited in number, the use of asymptotic theory may be compromised. Thus, we employ the bootstrap technique to build confidence intervals for F and compare the results with those obtained from the normal theory. This estimator that dispenses the need to study parents opens the possibility of using archival material for comparative epidemiological studies of Down's syndrome and other aneuploidies. In this paper we propose a probability model to estimate the fraction of meiosis I non‐disjunction, F, by only using the proportion of allele patterns of trisomy individuals, while traditional methods require typing pericentromeric markers from those affected and their parents. Copyright © 2003 John Wiley & Sons, Ltd.
Oscillating behavior of carbohydrate granule formation and dinitrogen fixation in the cyanobacterium Cyanothece sp. strain ATCC 51142

It has been shown that some aerobic, unicellular, diazotrophic cyanobacteria temporally separate photosynthetic O2 evolution and oxygen-sensitive N2 fixation. Cyanothece sp. ATCC strain 51142 is an aerobic, unicellular, diazotrophic cyanobacterium that fixes N2 during discrete periods of its cell cycle. When the bacteria are maintained under diurnal light-dark cycles, N2 fixation occurs in the dark. Similar cycling is observed in continuous light, implicating a circadian rhythm. Under N2-fixing conditions, large inclusion granules form between the thylakoid membranes. Maximum granulation, as observed by electron microscopy, occurs before the onset of N2 fixation, and the granules decrease in number during the period of N2 fixation. The granules can be purified from cell homogenates by differential centrifugation. Biochemical analyses of the granules indicate that these structures are primarily carbohydrate, with some protein. Further analyses of the carbohydrate have shown that it is a glucose polymer with some characteristics of glycogen. It is proposed that N2 fixation is driven by energy and reducing power stored in these inclusion granules. Cyanothece sp. strain ATCC 51142 represents an excellent experimental organism for the study of the protective mechanisms of nitrogenase, metabolic events in cyanobacteria under normal and stress conditions, the partitioning of resources between growth and storage, and biological rhythms.
Gas Spectroscopy System for Breath Analysis at mm-wave/THz Using SiGe BiCMOS Circuits

The unique fingerprint spectra of volatile organic compounds for breath analysis and toxic industrial chemicals make an mm-wave (mmW)/THz gas sensor very specific and sensitive. This paper reviews and updates results of our recent work on sensor systems for gas spectroscopy based on integrated transmitter (TX) and receiver (RX), which are developed and fabricated in IHP’s <inline-formula> <tex-math notation="LaTeX">$0.13~\mu \text{m}$ </tex-math></inline-formula> SiGe BiCMOS technology. In this paper, we present an mmW/THz spectroscopic system including a folded gas absorption cell of 1.9 m length between the TX and RX modules. We discuss the results and specifications of our sensor system based on integrated TX and RX. We demonstrate TXs and RXs with integrated antennas for spectroscopy at 238–252 GHz and 494–500 GHz using integer-<inline-formula> <tex-math notation="LaTeX">$N$ </tex-math></inline-formula> phase-locked loops (PLLs). We present a compact system by using fractional-<inline-formula> <tex-math notation="LaTeX">${N}$ </tex-math></inline-formula> PLLs allowing frequency ramps for the TX and RX, and for TX with superimposed frequency shift keying or reference frequency modulation. In another configuration, the voltage controlled oscillators of the TX and RX local oscillator are tuned directly without PLLs by applying external voltages. Further developments of our system are aimed at realizing an even wider frequency span by switching between frequency bands, and to use a more compact gas absorption cell.
Enhancing student interactions with the instructor and content using pen‐based technology, youtube videos, and virtual conferencing

This report describes the incorporation of digital learning elements in organic chemistry and biochemistry courses. The first example is the use of pen‐based technology and a large‐format PowerPoint slide to construct a map that integrates various metabolic pathways and control points. Students can use this map to visualize the integrated nature of metabolism and how various hormones impact metabolic regulation. The second example is the embedding of health‐related YouTube videos directly into PowerPoint presentations. These videos become a part of the course notes and can be viewed within PowerPoint as long as students are online. The third example is the use of a webcam to show physical models during online sessions using web‐conferencing software. Various molecular conformations can be shown through the webcam, and snapshots of important conformations can be incorporated into the notes for further discussion and annotation. Each of the digital learning elements discussed in this report is an attempt to use technology to improve the quality of educational resources available outside of the classroom to foster student engagement with ideas and concepts. Biochemistry and Molecular Biology Education Vol. 39, No. 1, pp. 4–9, 2011
OATP1B1, OATP1B3, AND MRP2 ARE INVOLVED IN HEPATOBILIARY TRANSPORT OF OLMESARTAN, A NOVEL ANGIOTENSIN II BLOCKER

Hepatic uptake and biliary excretion of olmesartan, a new angiotensin II blocker, were investigated in vitro using human hepatocytes, cells expressing uptake transporters and canalicular membrane vesicles, and in vivo using Eisai hyperbilirubinemic rats (EHBR), inherited multidrug resistance-associated protein (mrp2)-deficient rats. The uptake by human hepatocytes reached saturation with a Michaelis constant (Km) of 29.3 ± 9.9 μM. Both Na+-dependent and Na+-independent uptake of olmesartan by human hepatocytes were observed. The uptake by Na+-independent human liver-specific organic anion transporters OATP1B1 and OATP1B3 expressed in Xenopus laevis oocytes was also saturable, with Km values of 42.6 ± 28.6 and 71.8 ± 21.6 μM, respectively. The Na+-dependent taurocholate-cotransporting polypeptide expressed in HEK 293 cells did not transport olmesartan. The cumulative biliary excretion in EHBR was one-sixth compared with that in Sprague-Dawley rats. ATP-dependent uptake of olmesartan was observed in both human canalicular membrane vesicles (hCMVs) and MRP2-expressing vesicles. An MRP inhibitor, MK-571 ([[[3-[2-(7-chloro-2-quinolinyl)ethenyl]phenyl][3-(dimethylamino)-3-oxopropyl]thio]methyl]thio]-propanoic acid) completely inhibited the uptake of olmesartan by hCMVs. In conclusion, the hepatic uptake and biliary excretion of olmesartan are mediated by transporters in humans. OATP1B1 and OATP1B3 are involved in hepatic uptake, at least in part, and MRP2 plays a dominant role in the biliary excretion.
Syphilis testing, typing, and treatment follow-up: a new era for an old disease

Purpose of review The past 15 years have seen a dramatic increase in syphilis diagnoses in several regions including China, North America, Western Europe and Australia. Worldwide, the disease remains prevalent, contributing to substantial adult morbidity and neonatal mortality. Testing and treatment strategies are largely informed by data from the early antibiotic era, but increasing use of molecular diagnostics and new screening strategies could improve the management of syphilis substantially. Recent findings The review explores new testing strategies for syphilis, including the importance of screening test selection and advances in point-of-care diagnostics. It then examines molecular studies of Treponema pallidum, covering typing; macrolide resistance; association between genotype and phenotype and the use of PCR in testing and monitoring strategies. Summary Clinicians should be aware of testing strategies employed by their laboratories to ensure optimal sensitivity and specificity. Locally available T. pallidum PCR assays may improve the diagnosis of early disease and inform antibiotic choice. Robust serologic follow-up is still required, but predictors of potential treatment failure, including PCR-measured bacterial load, have been identified. Re-treatment should be considered for patients in the serofast state. The publication of T. pallidum genomes would allow further and more detailed study of strains and disease pathogenesis.