Miracle-dz/UniFAR-FTUs huggingface dataset:
Large Lateral Movement of Transmembrane Helix S5 Is Not Required for Substrate Access to the Active Site of Rhomboid Intramembrane Protease*

Background: The active site of rhomboid protease is embedded in the membrane and closed. Results: Cross-linking transmembrane helices S5 and S2 does not significantly affect the protease activity in reconstituted membrane vesicles. Conclusion: Contrary to the lateral gating model, large movement of the S5 helix is not required for substrate access to the active site of the protease. Significance: Clarifying the movement of S5 helix during catalysis improves our mechanistic understanding of rhomboid intramembrane protease. Rhomboids represent an evolutionarily ancient protease family. Unlike most other proteases, they are polytopic membrane proteins and specialize in cleaving transmembrane protein substrates. The polar active site of rhomboid protease is embedded in the membrane and normally closed. For the bacterial rhomboid GlpG, it has been proposed that one of the transmembrane helices (S5) of the protease can rotate to open a lateral gate, enabling substrate to enter the protease from inside the membrane. Here, we studied the conformational change in GlpG by solving the cocrystal structure of the protease with a mechanism-based inhibitor. We also examined the lateral gating model by cross-linking S5 to a neighboring helix (S2). The crystal structure shows that inhibitor binding displaces a capping loop (L5) from the active site but causes only minor shifts in the transmembrane helices. Cross-linking S5 and S2, which not only restricts the lateral movement of S5 but also prevents substrate from passing between the two helices, does not hinder the ability of the protease to cleave a membrane protein substrate in detergent solution and in reconstituted membrane vesicles. Taken together, these data suggest that a large lateral movement of the S5 helix is not required for substrate access to the active site of rhomboid protease.
A review of the diet and at-sea distribution of penguins breeding within the CAMLR Convention Area

Managing fisheries in an ecologically sensitive manner demands that catches do not depress stocks within the foraging areas used by predators to levels that reduce their reproductive success or survival. Spatially–explicit bioenergetics models that estimate the amount of prey consumed by predators are required to inform such policy. These models require information on the number of predators in a population, their nutritional demands, their diet composition and their seasonal distribution in the marine environment. This paper reviews all published information on the diet and at-sea distribution of the six penguin species that breed in the CAMLR Convention Area, the methods used to collect these data and the uncertainties inherent in them. The review will be of utility to modellers as a source of parameters, and to penguin biologists by providing comparative information for their own findings and by highlighting significant gaps in existing knowledge and methods that could be used to fill these.
Promising activity of gemcitabine in refractory high‐grade non‐Hodgkin's lymphoma

Three patients (aged 68–75 years) with histologically confirmed relapsed or refractory high‐grade non‐Hodgkin's lymphoma were entered in this pilot study in which gemcitabine 800 mg/m2 was given as a 30 min i.v. infusion once a week for 3 weeks. One patient responded with complete remission and the other two with partial remission and stable disease for 2 and 3 months, respectively. Haematological toxicity was modest with grade 4 leucopenia (one cycle) and grade 4 thrombocytopenia (two cycles). The activity and mild toxicity seen with gemcitabine suggest that this agent should be further evaluated in the treatment of high‐grade non‐Hodgkin's lymphoma.
How Renoir coped with rheumatoid arthritis

Out of doom and misery, the most beautiful song may rise 1 Few people know that Pierre-Auguste Renoir, who lived from 1841 to 1919, suffered from severe rheumatoid arthritis for the last 25 years of his life. At the 13th European congress of rheumatology in Amsterdam in 1995 Mr Paul Renoir, the artist's 70 year old grandson, revealed several previously unpublished aspects of his grandfather's disease. There is little doubt that Renoir suffered from rheumatoid arthritis, but there is still some discussion about the precise year the arthritis started.2 It must have been around 1892, when Renoir was about 50 and in the prime of life. He was married to Aline Charigot, and two of his three sons had already been born. He was recognised as an established painter, having had exhibitions not only in Paris and other places in France but also in Brussels, London, Boston, and New York. He was active and hardworking, painting and making study tours to Algiers, Italy, Germany, and Spain. His friends included the painters Manet, Sisley, and Cezanne and the writers Zola and de Montpassant. Although no medical records remain, it is possible, thanks to photographs, his personal letters, and biographical notes by people who knew him well to get a reasonable idea about the course of his disease. The arthritis started around the age of 50, took on an aggressive form from 1903 onwards, when he was about 60, and made him quite handicapped from the age of 70 for the last seven years of his life. In a photograph of 1896, when he was 55, the swelling of the metacarpophalangeal joints can be clearly seen (fig 1). Five years later, in 1901, when he was 60, he could still use his hands fully as witnessed in the way he holds …
Morphological and mitochondrial DNA characters for identification and phylogenetic analysis of the myiasis‐causing flesh fly Wohlfahrtia magnifica and its relatives, with a description of Wohlfahrtia monegrosensis sp. n. Wyatt & Hall

Abstract Wohlfahrtia magnifica (Schiner) (Diptera: Sarcophagidae) is a major cause of traumatic myiasis in livestock in Central and Eastern Europe and in countries bordering the Mediterranean. The present study explored the utility of external body characters, genitalia characters and mitochondrial DNA characters for identification of this and related species in the subfamily Paramacronychiinae. Sequence analyses of the 3′ terminal 273 bp of the mitochondrial cytochrome b gene revealed two lineages of W. magnifica, one from Spain and France and the other from the rest of Eurasia, differing by only two base pairs. Phylogenetic analysis of cytochrome b showed that W. magnifica and Wohlfahrtia vigil Walker were sister species; this conclusion was not contradicted by a phylogenetic analysis of the morphological characters. Based on cytochrome b, the genetic distance between specimens of W. vigil from Europe and North America was sufficiently large to justify the recognition of more than one species. A new species, Wohlfahrtia monegrosensis, from northern Spain, was described, based on morphology and cytochrome b. A unique combination of external body characters of males or females were diagnostic for W. magnifica, the W. vigil group and Wohlfahrtia bella, but only the genitalia characters were diagnostic for all nine species studied.
Shock-induced transformation of liquid deuterium into a metallic fluid

Simultaneous measurements of shock velocity and optical reflectance at 1064, 808, and 404 nm of a high pressure shock front propagating through liquid deuterium show a continuous increase in reflectance from below 10% and saturating at approximately (40-60)% in the range of shock velocities from 12 to 20 &mgr;m/ns (pressure range 17-50 GPa). The high optical reflectance is evidence that the shocked deuterium reaches a conducting state characteristic of a metallic fluid. Above 20 &mgr;m/ns shock velocity (50 GPa pressure) reflectance is constant indicating that the transformation is substantially complete.
Machines, statues, and people: strategies for promoting RSI awareness in computing curricula

The ACM and IEEE-CS have endorsed the idea that computing curricula should consider problems created by malfunctioning and misapplied computer systems [22]. Key ACM and IEEE-CS publications, however, have devoted scant attention to problems created by occupational hazards in computing. This paper’s authors believe that a responsible computing curriculum should discuss at least one computer-related occupational hazard: a potentially crippling and increasingly common disorder known as repetitive strain injury (RSI). RSI is a soft-tissue disorder that results from the repetitive use of some part of the body. Among computer users, RSI is typically caused by the excessive or improper use of keyboards and mice [17, p. 25ffJ. If allowed to progress, RSI can eventually produce chronic numbness, weakness, pain, and even paralysis in affhcted muscles [17, p. 611. One reason for focusing on RSI is that anyone who uses a computer for more than 2 to 4 hours daily is at risk for RSI [17, p. 403. A second is that a little information regarding the recognition, prevention, and treatment of RSI will reduce this risk. In an hour, an instructor can convey the basic information that a computer user needs to know about RSI. This knowledge is important for three reasons:
Chromatographic analysis of vegetable oils: a review.

Vegetable oils has become more attractive recently because of its economical benefits as they are used as components in many manufactured products and the fact that it is made from renewable resources. The determination of the minor components is of great importance in establishing the oil quality and their genuineness. The qualitative and quantitative determination of the constituents is done by gas chromatography of compounds or their derivatives. High precision in the gas chromatographic analysis of fatty acid methyl esters is possible with careful attention to detail during sample preparation, injection, chromatographic and data collection. This paper shows the applications of solid-phase extraction for the isolation of certain lipid classes prior to chromatographic analysis and also the most commonly used chromatographic techniques that can be applied for accuracy.
Crawling Microblog by Common-Designed Software

A mount of data of microblogs is needed to be crawled for research, business analyzing, and so on. However, a lot of dynamic Web techniques are used in microblog Web pages. That makes it hard to crawl data by parsing the contents of Web pages for traditional Web page crawlers. Fortunately, microblogs provide APIs. Well-structured data can be returned to users simply by accessing those APIs in form of URLs. Basing on that mechanism, researchers have obtained some data from microblogs to research. Nevertheless, no common software for crawling microblog has been published up to now. Everyone has to start designing a microblog crawler from very beginning. A common software architecture based on microblog APIs for microblog crawler is proposed in this paper, which is named as MBCrawler. Its structure, architecture, and key classes are introduced. It can be seen that MBCrawler is modular and scalable. By implementing a real microblog crawler for Sina Weibo, it is shown that MBCrawler can fit specific features of different microblogs. DOI: http://dx.doi. org/10.11591/telkomnika.v11i7. 2805 Full Text: PDF
Design considerations of a CMOS envelope detector for low power wireless receiver applications

Previous studies have shown that a transistor's transconductance-to-drain-current ratio is useful for optimizing analog circuits. In this paper, we derive an expression that captures the second order distortion generated at the output of an envelope detector. We use the derived expression, along with the nonlinear Taylor series coefficients to design a 3 µA envelope detector in 0.13 µm CMOS process.
Exploring Immersive AR Instructions for Procedural Tasks: The Role of Depth, Motion, and Volumetric Representations

Wearable Augmented Reality (W-AR) is based on getting a computer as intimate as possible with the wearers' bodies and senses. We need to understand the cognitive and perceptual mechanisms leveraged by this technology and use them for designing AR applications. In this study we explored the potential benefit of W-AR to guide a procedural task of assembling a LEGO™ compared to traditional paper instructions. We measured the time used to complete each step and the subjective perception of helpfulness and effectiveness of the instructions along with the perceived time spent doing the task. The results show that adding motion cues to an AR stereo visualization of the instructions (Dynamic 3D) improved performance compared to both the paper instructions and an AR version with stereo only but no motion (Static 3D). Interestingly, performance for the Static 3D condition was the slowest of the three. Subjective reports did not show any difference across different instruction types, suggesting that advantage of Dynamic 3D instructions are not accessible by covert awareness of the participants. The results provide support to the idea that principles of neurosciences may have direct implications for the product development in Wearable Augmented Reality.
MF3D: Model-free 3D semantic scene parsing

We present a novel model-free method for online 3D semantic scene parsing from video sequences. MF3D (Model-Free 3D) is different from conventional methods for 3D scene parsing in that voxel labelling is approached via search-based label transfer instead of discriminative classification. This non-parametric approach makes MF3D easy to scale with an online growth in the database, as no model re-training is required with the addition of new examples or categories. Experimental results on the KITTI benchmark demonstrate that our model-free approach enables accurate online 3D scene parsing while retaining extensibility to new categories. In addition, we show that unsupervised binary encoding (hashing) techniques can be easily incorporated into our framework for scalability to larger databases.
Social network, support and influence: relationships with drug use and protective AIDS behavior.

One reason for difficulty in long-term maintenance of behavior changes by injection drug users (IDUs) is the concomitant support or distraction from the IDUs social environment. This study explored the relationship of social factors--e.g., encouragement from friends, beliefs about social norms--with drug injection behaviors. Subjects were clients in a short-term residential detoxification program. Self-reports of drug and AIDS-protective behaviors were gathered at baseline and at least 6 months following a trial of enhanced vs. informational educational interventions. Results provide support both for the general hypothesis about the influence of peers and drug-use partners prior and subsequent to detoxification and for the greater effectiveness of the enhanced intervention on social factors. Particularly important to improved drug use behavior were decreased number of friends who inject drugs (social network), increased number of people to talk with when upset (social support), and increased argument skills about safe drug use (social influence).
Possible bias from rating behavior when subjects rate both exposure and outcome.

OBJECTIVES In many epidemiologic studies the subjects rate both the exposure and the outcome, assigning numerical values to the variables according to their perceptions and judgments. Hypothetically, subjects who tend to overestimate, exaggerate, or use high numerical values in rating tasks would rate both exposure and outcome higher than subjects who tend to underestimate, dissimulate, or use low numerical values. A range of such rating behaviors among the subjects would introduce uncontrollable bias to relative risk estimates, in most cases an overestimation. The aim of this study was to assess the possible presence of and effects on relative risk estimates of such high and low rating behavior among subjects in an epidemiologic study of musculoskeletal disorders. METHODS Rating behavior was analyzed by intercorrelating the ratings of 19 different stimuli. High positive correlations would indicate the presence of high and low rating behavior. RESULTS The correlations were, however, both positive and negative and close to zero. Adjusting for rating behavior did not affect relative risk estimates, based on subjective ratings of both exposure and outcome. CONCLUSION There is no support in this study for the existence of a range of high and low rating behavior among subjects who rate neutral and nonaffective stimuli, such as time, weight, number and physical exposure, as well as pain and other symptoms. There is therefore no support for the idea of a bias to relative risk estimates from such rating behavior in studies where subjects rate both exposure and outcome variables of this kind.
Recent advances in the study of the sulfate-reducing bacteria.

The sulfate-reducing bacteria form a specialized group of microbes that use sulfate as terminal electron acceptor for their respiration. Though many microbes generate H2S metabolically, sulfate often being the primary source of that H2S, the process is normally a small-scale one involving the incorporation of sulfur into cell protein and its subsequent degradation by catabolic and autolytic processes. Dissimilatory (or respiratory) sulfate reduction is a direct process that involves 10to 100-fold greater turnovers of sulfur. It is of great physiological interest because of the analogies sulfate respiration provides with oxygen and nitrate respiration; for example, the metabolism of these bacteria is essentially oxidative, involving a cytochrome system and respiratory chain phosphorylation, yet to the bacteriologist they are among the most awkward and exacting of anaerobes. Their carbon metabolism is generally incomplete, yielding fatty acids as well as C02, yet with certain substrates (pyruvate, choline), some strains can conduct "sulfate-free" growth analogous to the facultatively anaerobic growth of an aerobe. Recently a most exciting vista of anaerobic assimilatory processes, such as that performed with iso-butanol, has been uncovered. Despite their anaerobic habit, representatives of the group tolerate some of the most extreme terrestial conditions of heat, cold, salinity, and pressure, so that, in an era when science may be poised on the discovery of a true exobiology, knowledge of bacteria so firmly independent of the common terrestial environment assumes renewed interest. In more mundane terms, the ubiquity of these bacteria and their proneness to generate large quantities of H2S lead to a variety of impressive industrial, economic, and ecological effects, and for this reason papers relevant to them tend to be scattered over journals ranging from purely academic to those devoted to detailed technology. During the past 20 years, considerable advances have been made in our understanding of these bacteria; yet, no doubt because of its scattered character, information about these bacteria is not always readily accessible, and, as a glance at any text book of microbiology will show, this information has not penetrated far beyond the circle of those directly concerned with sulfate-reducing bacteria. In two previous reviews (137, 139) I covered several aspects of academic knowledge of sulfatereducing bacteria and attempted to deal exhaustively with their economic activities. Because of space limitations, certain aspects of the
Caudate Gray Matter Volume in Obsessive-Compulsive Disorder Is Influenced by Adverse Childhood Experiences and Ongoing Drug Treatment

Background Exposure to adverse childhood experiences (ACE) increases the risk of adult physical and mental health disorders, including obsessive-compulsive disorder (OCD), and influences adult cortical neural responses and gray matter (GM) volumes. Robust neuroimaging findings associated OCD with corticostriatal dysfunction and with abnormal morphology and metabolism of cortical areas and basal ganglia. Methods We explored the GM correlates of ACE in 40 patients with OCD (15 drug-naive and 25 drug-treated patients) with magnetic resonance imaging voxel-based morphometry at 3.0 T. Regional GM volumes were the dependent variable, and drug treatment (naive vs treated) and breadth of exposure to ACE (high vs low) were the factors of interest. Sex, duration of illness, and handedness were considered as nuisance covariates. Whole brain statistical threshold was P < 0.05 familywise error corrected for multiple comparisons. Results Patients with higher levels of exposure to ACE showed increased GM volume in the head of the left caudate nucleus. Ongoing drug treatment was associated with reduced GM volume in the same area. Earlier age at onset of OCD, need for medication treatment, and mixed handedness were correlated with higher levels of ACE. Conclusions Exposure to ACE increased, and ongoing drug treatment decreased, caudate GM in OCD. Increased volume and metabolism of the caudate nucleus have been consistently associated with OCD. Our findings suggest a detrimental effect of ACE on the brain underpinnings of OCD, with an opposite effect of medications.
Exact Linearization Nonlinear Neutral-Point Voltage Control for Single-Phase Three-Level NPC Converters

This letter proposes a new control scheme for the neutral-point (NP) balance in single-phase three-level NP-clamped converters. The control is addressed considering the plant under study, a nonlinear time-variant system. A quasi-exact linearization is applied allowing the application of classic control techniques. The described method is simple, general, and suitable for buck and boost topologies, as well as for inverter or rectifier operating modes under either linear or nonlinear loading. Correct operation is verified under simulated and experimental operation.
Oocyte retrieval for in vitro fertilization.

Present methods to monitor follicular development, and to determine the time for oocyte retrieval are described: LH and estradiol determinations, ultrasonography. The two techniques, available for oocyte pick-up, namely laparoscopic and ultrasound guided follicle aspiration, are reviewed. The methods and results of the University of Bonn IVF team are discussed, e.g. ovarian stimulation schemes, including the use of pure FSH for patients with a high LH/FSH ratio, and the use of GnRH analogues, for patients with premature LH discharges; the reasons for failed oocyte retrieval; pregnancy rates.
NPY genes and AGC kinases define two key steps in auxin-mediated organogenesis in Arabidopsis

Auxin is an essential regulator of plant organogenesis. Most key genes in auxin biosynthesis, transport, and signaling belong to gene families, making it difficult to conduct genetic analysis of auxin action in plant development. Herein we report the functional analysis of several members of 2 gene families (NPY/ENP/MAB4 genes and AGC kinases) in auxin-mediated organogenesis and their relationships with the YUC family of flavin monooxygenases that are essential for auxin biosynthesis. We show that 5 NPY genes (NPY1 to NPY5) and 4 AGC kinases (PID, PID2, WAG1, and WAG2) have distinct, yet overlapping, expression patterns. Disruption of NPY1 does not cause obvious defects in organogenesis, but npy1 npy3 npy5 triple mutants failed to make flower primordia, a phenotype that is also observed when AGC kinase PID is compromised. Inactivation of YUC1 and YUC4 in npy1 background also phenocopies npy1 npy3 npy5 and pid. Simultaneous disruption of PID and its 3 closest homologs (PID2, WAG1, and WAG2) completely abolishes the formation of cotyledons, which phenocopies npy1 pid double mutants and yuc1 yuc4 pid triple mutants. Our results demonstrate that NPY genes and AGC kinases define 2 key steps in a pathway that controls YUC-mediated organogenesis in Arabidopsis.