Miracle-dz/UniFAR-FTUs huggingface dataset:
Sleep homeostasis in Drosophila melanogaster.

STUDY OBJECTIVES The fruit fly Drosophila melanogaster is emerging as a promising model system for the genetic dissection of sleep. As in mammals, sleep in the fruit fly is a reversible state of reduced responsiveness to the external world and has been defined using an array of behavioral, pharmacologic, molecular, and electrophysiologic criteria. A central feature of mammalian sleep is its homeostatic regulation by the amount of previous wakefulness. Dissecting the mechanisms of homeostatic regulation is likely to provide key insights into the functions of sleep. Thus, it is important to establish to what extent sleep homeostasis is similar between mammals and flies. This study was designed to determine whether in flies, as in mammals, (1) sleep rebound is dependent on prior time awake; (2) sleep deprivation affects the intensity, in addition to the duration, of sleep rebound; (3) sleep loss impairs vigilance and performance; (4) the sleep homeostatic response is conserved among different wild-type lines, and between female and male flies of the same line. DESIGN Motor activity of individual flies was recorded at 1-minute intervals using the infrared Drosophila Activity Monitoring System during 2 baseline days; during 6, 12, and 24 hours of sleep deprivation; and during 2 days of recovery. Sleep was defined as any period of uninterrupted behavioral immobility lasting > 5 minutes. Sleep continuity was measured by calculating the number of brief awakenings, the number and duration of sleep episodes, and a sleep continuity score. Vigilance before and after sleep deprivation was assessed by measuring the escape response triggered by 2 different aversive stimuli. SETTING Fly sleep research laboratory at UW-Madison. PARTICIPANTS AND INTERVENTIONS Adult flies of the Canton-S (CS) strain and 116 other wild-type lines (> or = 16 female and > or = 16 male flies per line). MEASUREMENTS AND RESULTS In wild-type CS flies, as in mammals, the amount of sleep recovered after sleep deprivation was dependent on prior time awake. Relative to baseline sleep, recovery sleep in CS flies was less fragmented, with longer sleep episodes, and was associated with a higher arousal threshold. Sleep deprivation in CS flies also reduced performance. Sleep duration and continuity increased after 24 hour of sleep deprivation in all the other wild-type lines tested. CONCLUSION The sleep homeostatic response in fruit flies is a stable phenotype and shares most of, if not all, the major features of mammalian sleep homeostasis, thus supporting the use of Drosophila as a model system for the genetic dissection of sleep mechanisms and functions.
Analysis of subsecond protein dynamics by amide hydrogen exchange and mass spectrometry using a quenched‐flow setup

Amide hydrogen exchange (HX) in combination with mass spectrometry (MS) is a powerful tool to analyze the folding and dynamics of proteins. In the traditional methodology the exchange time is controlled by manual pipetting, thereby limiting the time resolution to several seconds. Some conformational changes in proteins, however, occur in the subsecond time scale, making it desirable to perform HX at shorter time intervals down to the limit set by the intrinsic chemical exchange rate. We now report the development of the first completely on‐line quenched‐flow setup that allows the performance of HX experiments in the 100‐sec to 30‐sec time scale, on‐line proteolytic digestion using immobilized proteases, rapid desalting, and MS analysis. We show that conformational fluctuations in the range of seconds can be detected and protection factors as small as 10 reproducibly determined. Using this setup we investigated the conformational properties of Escherichia coli heat‐shock transcription factor σ32 free in solution. Our results indicate that the C‐terminal σ4 domain of σ32, which is responsible for the recognition of the −35 region of heat shock promoters, contains more extensive secondary structure than expected when compared with the structure of the homologous σ‐factor σA in complex with the RNA‐polymerase. This setup should be very useful for a more accurate analysis of structural motions in proteins in the subsecond to second time scale relevant to allostery and enzyme function.
Analysis of longitudinal studies with death and drop‐out: a case study

The analysis of longitudinal data has recently been an active area of biostatistical research. Two main approaches to analysis have emerged, the first concentrating on modelling evolution of marginal distributions of the main response variable of interest and the other on subject‐specific trajectories. In epidemiology the analysis is usually complicated by missing data and by death of study participants. Motivated by a study of cognitive decline in the elderly, this paper argues that these two types of incomplete follow‐up may need to be treated differently in the analysis, and proposes an extension to the marginal modelling approach. The problem of informative drop‐out is also discussed. The methods are implemented in the ‘Stata’ statistical package. Copyright © 2004 John Wiley & Sons, Ltd.
Competitive recruitment of the periplasmic translocation portal TolB by a natively disordered domain of colicin E9

The natively disordered N-terminal 83-aa translocation (T) domain of E group nuclease colicins recruits OmpF to a colicin-receptor complex in the outer membrane (OM) as well as TolB in the periplasm of Escherichia coli, the latter triggering translocation of the toxin across the OM. We have identified the 16-residue TolB binding epitope in the natively disordered T-domain of the nuclease colicin E9 (ColE9) and solved the crystal structure of the complex. ColE9 folds into a distorted hairpin within a canyon of the six-bladed β-propeller of TolB, using two tryptophans to bolt the toxin to the canyon floor and numerous intramolecular hydrogen bonds to stabilize the bound conformation. This mode of binding enables colicin side chains to hydrogen-bond TolB residues in and around the channel that runs through the β-propeller and that constitutes the binding site of peptidoglycan-associated lipoprotein (Pal). Pal is a globular binding partner of TolB, and their association is known to be important for OM integrity. The structure is therefore consistent with translocation models wherein the colicin disrupts the TolB–Pal complex causing local instability of the OM as a prelude to toxin import. Intriguingly, Ca2+ ions, which bind within the β-propeller channel and switch the surface electrostatics from negative to positive, are needed for the negatively charged T-domain to bind TolB with an affinity equivalent to that of Pal and competitively displace it. Our study demonstrates that natively disordered proteins can compete with globular proteins for binding to folded scaffolds but that this can require cofactors such as metal ions to offset unfavorable interactions.
Permanent magnet synchronous traction motor torque close-loop control based on stator flux observation for urban rail train

The output torque is the control objective of PMSM (Permanent Magnet Synchronous Motor) in urban rail train traction system. The commonly used torque control methods are affected by the variation of motor inductance parameters, which reduces the torque control precision. Based on mathematical model of PMSM extended flux, a minimum order state observer is established in this paper. Stator flux is got by extended flux observation. Then feedback troque is caculated by stator flux and currents, which is not affected by the inductance parameters variation. Limited by pole assignment of the flux observer, the torque calculation method based on inductance identification is adopted in motor start-up stage and switch to flux observation method in follow-up stage. Double current regulators control is used when the motor speed is not special high, and voltage phase method is used as flux-weakening control when stator voltage is limited on six-step operation. Thus, a torque close-loop vector control scheme based on flux observation in whole speed range is given out, which is verifid by simulation and experiment on a 300kW PMSM platform.
Molecular diagnostics for human leptospirosis

Purpose of review The definitive diagnosis of leptospirosis, which results from infection with spirochetes of the genus Leptospira, currently relies on the use of culture, serological testing (microscopic agglutination testing), and molecular detection. The purpose of this review is to describe new molecular diagnostics for Leptospira and discuss advancements in the use of available methods. Recent findings Efforts have been focused on improving the clinical sensitivity of Leptospira detection using molecular methods. In this review, we describe a reoptimized pathogenic species-specific real-time PCR (targeting lipL32) that has demonstrated improved sensitivity, findings by two groups that real-time reverse-transcription PCR assays targeting the 16S rrs gene can improve detection, and two new loop-mediated amplification techniques. Quantitation of leptospiremia, detection in different specimen types, and the complementary roles played by molecular detection and microscopic agglutination testing will be discussed. Finally, a protocol for Leptospira strain subtyping using variable number tandem repeat targets and high-resolution melting will be described. Summary Molecular diagnostics have an established role for the diagnosis of leptospirosis and provide an actionable diagnosis in the acute setting. The use of real-time reverse-transcription PCR for testing serum/plasma and cerebrospinal fluid, when available, may improve the detection of Leptospira without decreasing clinical specificity.
A Mobile Phone Food Record App to Digitally Capture Dietary Intake for Adolescents in a Free-Living Environment: Usability Study

Background Mobile technologies are emerging as valuable tools to collect and assess dietary intake. Adolescents readily accept and adopt new technologies; thus, a food record app (FRapp) may be a useful tool to better understand adolescents’ dietary intake and eating patterns. Objective We sought to determine the amenability of adolescents, in a free-living environment with minimal parental input, to use the FRapp to record their dietary intake. Methods Eighteen community-dwelling adolescents (11-14 years) received detailed instructions to record their dietary intake for 3-7 days using the FRapp. Participants were instructed to capture before and after images of all foods and beverages consumed and to include a fiducial marker in the image. Participants were also asked to provide text descriptors including amount and type of all foods and beverages consumed. Results Eight of 18 participants were able to follow all instructions: included pre- and post-meal images, a fiducial marker, and a text descriptor and collected diet records on 2 weekdays and 1 weekend day. Dietary intake was recorded on average for 3.2 (SD 1.3 days; 68% weekdays and 32% weekend days) with an average of 2.2 (SD 1.1) eating events per day per participant. A total of 143 eating events were recorded, of which 109 had at least one associated image and 34 were recorded with text only. Of the 109 eating events with images, 66 included all foods, beverages and a fiducial marker and 44 included both a pre- and post-meal image. Text was included with 78 of the captured images. Of the meals recorded, 36, 33, 35, and 39 were breakfasts, lunches, dinners, and snacks, respectively. Conclusions These data suggest that mobile devices equipped with an app to record dietary intake will be used by adolescents in a free-living environment; however, a minority of participants followed all directions. User-friendly mobile food record apps may increase participant amenability, increasing our understanding of adolescent dietary intake and eating patterns. To improve data collection, the FRapp should deliver prompts for tasks, such as capturing images before and after each eating event, including the fiducial marker in the image, providing complete and accurate text information, and ensuring all eating events are recorded and should be customizable to individuals and to different situations. Trial Registration Clinicaltrials.gov NCT01803997. http://clinicaltrials.gov/ct2/show/NCT01803997 (Archived at: http://www.webcitation.org/6WiV1vxoR).
Increased temperature disrupts chemical communication in some species but not others: The importance of local adaptation and distribution

Abstract Environmental conditions experienced by a species during its evolutionary history may shape the signals it uses for communication. Consequently, rapid environmental changes may lead to less effective signals, which interfere with communication between individuals, altering life history traits such as predator detection and mate searching. Increased temperature can reduce the efficacy of scent marks released by male lizards, but the extent to which this negative effect is related to specific biological traits and evolutionary histories across species and populations have not been explored. We experimentally tested how increased temperature affects the efficacy of chemical signals of high‐ and low‐altitude populations of three lizard species that differ in their ecological requirements and altitudinal distributions. We tested the behavioral chemosensory responses of males from each species and population to male scent marks that had been incubated at one of two temperatures (cold 16°C or hot 20°C). In high‐altitude populations of a mountain species (Iberolacerta monticola), the efficacy of chemical signals (i.e., latency time and number of tongue flicks) was lower after scent marks had been exposed to a hot temperature. The temperature that scent marks were incubated at did not affect the efficacy of chemical signals in a ubiquitous species (Podarcis muralis) or another mountain species (I. bonalli). Our results suggest that specific ecological traits arising through local adaptation to restricted distributions may be important in determining species vulnerability to climatic change.
Functional theories of thermoelectric phenomena

We review the progress that has been recently made in the application of time-dependent density functional theory to thermoelectric phenomena. As the field is very young, we emphasize open problems and fundamental issues. We begin by introducing the formal structure of thermal density functional theory, a density functional theory with two basic variables—the density and the energy density—and two conjugate fields—the ordinary scalar potential and Luttinger’s thermomechanical potential. The static version of this theory is contrasted with the familiar finite-temperature density functional theory, in which only the density is a variable. We then proceed to constructing the full time-dependent non equilibrium theory, including the practically important Kohn–Sham equations that go with it. The theory is shown to recover standard results of the Landauer theory for thermal transport in the steady state, while showing greater flexibility by allowing a description of fast thermal response, temperature oscillations and related phenomena. Several results are presented here for the first time, i.e. the proof of invertibility of the thermal response function in the linear regime, the full expression of the thermal currents in the presence of Luttinger’s thermomechanical potential, an explicit prescription for the evaluation of the Kohn–Sham potentials in the adiabatic local density approximation, a detailed discussion of the leading dissipative corrections to the adiabatic local density approximation and the thermal corrections to the resistivity that follow from it.
A New Software Tool for Design, Optimization, and Complete Analysis of Rotating Electrical Machines Windings

In this paper, a new software tool developed by the authors for ac winding design, optimization, and complete analysis is presented. In particular, this software can be used as a valid aid in design and analysis for a wide variety of motor and generator windings with generic number of phases (including the case of those machines in which some slots are left empty), pole pairs, slot number, and so on. The calculation of winding factors and the evaluation of their harmonic distribution is also accomplished. The software is implemented in the MATLAB programming environment. By means of some examples, covering the most relevant winding types, the capabilities of this software will be shown. In particular, integer and fractional slot, single- and double-layer winding, concentrated windings, imbrication, belt widening, and belt shifting techniques can be treated to reduce particular harmonics in the electromotive force (EMF) or in the magnetomotive force (MMF). Finally, the connections, the winding factor harmonic distribution, the total harmonic distortion (THD) of EMF and spatial distribution of both the MMF, the Görges polygon, and the flux density are shown together with an estimate of the differential leakage and the air-gap flux density spatial distribution. The software presented in this paper is very modular, highly structured, and flexible due to the conspicuous number of operations that it can fulfill. Clearly, for the sake of brevity and clarity, the authors limit to represent the main features of the software, without going into specific details of programming and coding. All the main mathematical relationships that are useful to solve the problem of design and optimization of the windings of rotating machines are hereafter presented.
Influence of Branched-Chain Amino Acid Supplementation on Urinary Protein Metabolite Concentrations after Swimming

Objective: The influence of branched-chain amino acid (BCAA) supplementation on urinary urea nitrogen, hydroxyproline (HP), and 3-methylhistidine (3MH) concentrations after 25 min of breast stroke exercise (65–70% maximum heart rate reserved, 65–70% HRRmax) followed by a 600 m crawl stroke competition was investigated in a double-blind, counter-balanced study. Methods: Male university students (19–22 years old) majoring in physical education participated in the study. Based on the previous swimming time of a 600 m crawl stroke, the participants were divided into two groups: placebo (n = 9, BMI = 24.2 ± 2.1 kg/m2; 12 g of glucose/day; in capsules) and BCAA (n = 10, BMI = 22.7 ± 1.5 kg/m2; 12 g of BCAAs/day; in capsules: leucine 54%, isoleucine 19%, valine 27%) groups. The participants maintained a regular dietary intake (except the prescribed breakfast on day 15) and exercise activity at a moderate/low intensity (60–70% HRRmax, swimming and rowing, ∼1.5 hour/day) during the 15-day study. A prescribed exercise program was performed on day 15. Urinary and blood samples were collected before, during, and after the prescribed exercise for the measurements of the urinary urea nitrogen, HP, and 3MH concentrations in urine, as well as the glucose, lactate, glutamine, alanine, and BCAA concentrations in plasma. Results: Two weeks of dietary supplementation did not induce any changes in the plasma glucose and total BCAA concentrations of either group, nor in the urinary urea nitrogen, HP, and 3MH concentrations in urine. On day 15, after 25 min of breast stroke exercise and a 600 m crawl stroke competition, plasma glucose concentration decreased significantly (p < 0.05) whereas plasma lactate concentration increased significantly (p < 0.05) in both groups. The exercise program prescribed in the study did not affect urinary urea nitrogen, HP, and 3MH concentrations. Twenty hours after the competition, however, a significant increase in the concentrations of urinary urea nitrogen, HP, and 3MH was found in the placebo group (p < 0.05), but not in the BCAA group. Conclusions: The results obtained in this study suggest that swimming induced muscle proteolysis was prevented by BCAA supplementation. The mechanism could be attributed to the availability of ammonia provided by the oxidation of supplemented BCAAs during exercise.
Public funding of political parties when campaigns are informative

The paper considers public funding of political parties when some voters are poorly informed about parties candidates and campaigns are informative. For symmetric equilibria, it is shown that more public funding leads parties to chose more moderate candidates, and that an increase in the fundings dependence on vote shares induces further moderation and improves welfare. If parties are asymmetric, vote share dependent public funding bene ts the large party and makes it moderate its candidate, while the smaller party reacts by choosing a more extremist candidate. On balance, however, if the parties are not too asymmetric, an increase in vote share dependent funding improves welfare and increases the likelihood that a moderate candidate wins the election.
Developmental expression of H‐2K major histocompatibility complex class I transgenes requires the presence of proximal introns

The pattern of expression of the H‐2K major histocompatibility complex (MHC) class I gene is complex. During embryonic development H‐2K mRNA, detectable from midgestation, is poorly expressed. In the adult, H‐2K expression is nearly ubiquitous but transcriptional regulation occurs leading to different mRNA levels in the different organs of the mouse. In vitro studies have shown that most of the regulatory elements controlling H‐2K gene transcription are located in the 5′ region of the gene. However, using fusion transgenes in which reporter genes were under the control of 2 kb of H‐2K 5′ regulatory region, we have previously shown that this region, was not sufficient to ensure correct developmental transgene expression. By contrast, a native 9.25 kb H‐2K transgene was expressed appropriately both in the adult and in the embryo. In order to localise more precisely the cis‐acting regulatory sequences involved in H‐2K developmental expression, we have now constructed new transgenic lines containing H‐2Kb transgenes that were deleted from specific parts of the H‐2Kb gene. We show that deletion of either the H‐2K 3′ flanking region or the 5 (out of 7) distal introns results in an expression of the transgenes which is similar to that of the endogenous H‐2K gene, both in the adult and during embryonic development. By contrast, deletion of all the introns or of the two proximal ones abrogates H‐2K transgene expression. Our data reveal the complexity of H‐2K regulation and highlight the crucial role of proximal introns in H‐2K expression in the living organism. © 1995 wiley‐Liss, Inc.