Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping the receptor site for α-scorpion toxins on a Na+ channel voltage sensor

The α-scorpions toxins bind to the resting state of Na+ channels and inhibit fast inactivation by interaction with a receptor site formed by domains I and IV. Mutants T1560A, F1610A, and E1613A in domain IV had lower affinities for Leiurus quinquestriatus hebraeus toxin II (LqhII), and mutant E1613R had ∼73-fold lower affinity. Toxin dissociation was accelerated by depolarization and increased by these mutations, whereas association rates at negative membrane potentials were not changed. These results indicate that Thr1560 in the S1-S2 loop, Phe1610 in the S3 segment, and Glu1613 in the S3-S4 loop in domain IV participate in toxin binding. T393A in the SS2-S6 loop in domain I also had lower affinity for LqhII, indicating that this extracellular loop may form a secondary component of the receptor site. Analysis with the Rosetta-Membrane algorithm resulted in a model of LqhII binding to the voltage sensor in a resting state, in which amino acid residues in an extracellular cleft formed by the S1-S2 and S3-S4 loops in domain IV interact with two faces of the wedge-shaped LqhII molecule. The conserved gating charges in the S4 segment are in an inward position and form ion pairs with negatively charged amino acid residues in the S2 and S3 segments of the voltage sensor. This model defines the structure of the resting state of a voltage sensor of Na+ channels and reveals its mode of interaction with a gating modifier toxin.
Illuminating the landscape of host–pathogen interactions with the bacterium Listeria monocytogenes

Listeria monocytogenes has, in 25 y, become a model in infection biology. Through the analysis of both its saprophytic life and infectious process, new concepts in microbiology, cell biology, and pathogenesis have been discovered. This review will update our knowledge on this intracellular pathogen and highlight the most recent breakthroughs. Promising areas of investigation such as the increasingly recognized relevance for the infectious process, of RNA-mediated regulations in the bacterium, and the role of bacterially controlled posttranslational and epigenetic modifications in the host will also be discussed.
Study on the frequency of pregnant ewes slaughtered in Khorram Abad abattoir, Iran

Summary The aim of this survey was to evaluate the frequency of pregnant ewes slaughtered in Khorram Abad abattoir and estimation of their gestational age. Over a period of five months in fall and winter, a total number of 3046 uterine tracts were collected. Pregnancy was detected in 56.50% of ewes, 52.36% and 4.13% of which carried singleton and twins, respectively. The highest frequency of pregnancy was detected in January (65.63%) and the lowest frequency was detected in March (35.02%). Among a total number of 1721 pregnant ewes, the most frequency of gestational age (34.68%) was recorded to be between 2 and 3 months of gestation, while 5.05% was detected to be above 121 days. Overall, the number of pregnant ewes with a gestational age over two months was considerable (59.83%). It was concluded that reproductive waste resulting from slaughtering of pregnant animals is important in ewes in Khorram Abad and could be prevented by an improved antemortem examination.
Vibrio cholerae chromosome 2 copy number is controlled by the methylation-independent binding of its monomeric initiator to the chromosome 1 crtS site

Abstract Bacteria contain a primary chromosome and, frequently, either essential secondary chromosomes or dispensable megaplasmids of plasmid origin. Incoming plasmids are often poorly adapted to their hosts and their stabilization requires integration with the host's cellular mechanisms in a process termed domestication. All Vibrio, including pathogenic species, carry a domesticated secondary chromosome (Chr2) where replication is coordinated with that of the primary chromosome (Chr1). Chr2 replication is triggered by the replication of an intergenic sequence (crtS) located on Chr1. Yet, the molecular mechanisms by which crtS replication controls the initiation of Chr2 replication are still largely unknown. In this study, we show that crtS not only regulates the timing of Chr2 initiation but also controls Chr2 copy number. We observed and characterized the direct binding of the Chr2 initiator (RctB) on crtS. RctB binding to crtS is independent of its methylation state. RctB molecules, which naturally form dimers, preferentially bind to crtS as monomers, with DnaK/J protein chaperones shown to stimulate binding of additional RctB monomers on crtS. In this study, we addressed various hypothesis of how replication of crtS could trigger Chr2 replication and provide new insights into its mode of action.
Feasibility and results of a randomised pilot-study of a work rehabilitation programme

Objective: To investigate the feasibility of a randomised controlled trial in a usual clinical setting and the effect of work rehabilitation on improvement to the ability to work in chronic pain patients. Design: 33 patients with chronic musculoskeletal pain, valid job contracts and absence from work, random allocation. The interdisciplinary work rehabilitation contained work-specific exercises and education and lasted 8 weeks, 3.5 hours each working day. The control treatment took place with the allocating physician, who received recommendations concerning physical therapy and the uptake of work. Assessments took place at 0, 8 and 32 weeks. Measurements: ability to work, actual work status in % of a full time job, functional capacity tasks measured in kilograms. Results: Feasibility: the recruitment was of a long duration due to the rather restrictive inclusion criteria. Actual work status: the improvement between the groups was not significantly different, but the ability to work improved significantly from an overall median of 0% to 50% at 8 weeks (p = 0.004 for the intervention group, p = 0.026 for the control group). Conclusions: The evaluation of a running work rehabilitation programme in a clinical outpatient setting in clinical science is feasible, but a more effective recruitment strategy for a main study is favoured by application of a multi-centric or company based setting.
Assessment of effectiveness of spinal exercises and body mechanics on low back pain among post menopausal women

Aim: To assessment of effectiveness of spinal exercises and body mechanics on low back pain among post menopausal women. Participants and setting: A quasi experimental non equivalent control group pretest post test design was adapted. The study was conducted in the urban area of suryapet. 40 post menopausal women who fulfilled the inclusion criteria were selected by non–probability purposive sampling technique. Intervention: The intervention such as spinal exercises and body mechanics were performed to overcome the level of low back pain among post menopausal women. The pre and post assessment was done by using a combined numerical and categorical pain scale. Measurement and findings: The women completed the demographic and obstetrical information and pain was measured by 0- 10 Modified combined numerical categorical pain intensity scale. This study revealed that there was high significant difference found in low back pain at p<0.001level between study group. Conclusion: The overall findings in the present study revealed that the spinal exercises and body mechanics was effectives and had brought about significant change in the reduction of low back pain among post menopausal women compared to pre test level of low back pain.
Promiscuous archaeal ATP synthase concurrently coupled to Na+ and H+ translocation

ATP synthases are the primary source of ATP in all living cells. To catalyze ATP synthesis, these membrane-associated complexes use a rotary mechanism powered by the transmembrane diffusion of ions down a concentration gradient. ATP synthases are assumed to be driven either by H+ or Na+, reflecting distinct structural motifs in their membrane domains, and distinct metabolisms of the host organisms. Here, we study the methanogenic archaeon Methanosarcina acetivorans using assays of ATP hydrolysis and ion transport in inverted membrane vesicles, and experimentally demonstrate that the rotary mechanism of its ATP synthase is coupled to the concurrent translocation of both H+ and Na+ across the membrane under physiological conditions. Using free-energy molecular simulations, we explain this unprecedented observation in terms of the ion selectivity of the binding sites in the membrane rotor, which appears to have been tuned via amino acid substitutions so that ATP synthesis in M. acetivorans can be driven by the H+ and Na+ gradients resulting from methanogenesis. We propose that this promiscuity is a molecular mechanism of adaptation to life at the thermodynamic limit.
Clomipramine concentration and withdrawal symptoms in 10 neonates.

AIM After in utero exposure to tricyclic antidepressants, neonatal withdrawal symptoms have been reported with an estimated incidence between 20 and 50%; however, few data are available for clomipramine. This could also be the case for neonatal pharmacokinetic clomipramine parameters and so this study was set up. METHODS Babies exposed to clomipramine in utero were included in an observational study, approved by the local ethics committee, after written informed consent. Withdrawal symptoms were scored at 12, 24 and 48 h after birth using the Finnegan score. Plasma concentrations were determined using an in-house-developed, validated liquid chromatography with mass detection (LC-MSMS) method at 0, 12, 24 and 48 h after birth. RESULTS We found that three of 11 pregnancies were complicated with pre-eclampsia. Ten neonates were observed for clomipramine withdrawal symptoms. The observed withdrawal symptoms were too short a period of sleep after feeding (6), poor feeding (3), mild to severe tremors (6), hyperactive Moro reflex (3) and respiratory rate >60 breaths min(-1). Serious withdrawal reactions, such as tachycardia and cyanosis, were seen. We calculated a half-life value of 42 ± 16 h for clomipramine in neonates. Only a weak correlation was found between withdrawal reactions and clomipramine plasma concentration or desmethylclomipramine plasma concentration. CONCLUSIONS In neonates, clomipramine is eliminated with a half-life value of 42 h, compared with 20 h in adults. In two of 10 neonates, tachycardia and cyanosis were seen as serious withdrawal symptoms after maternal use of clomipramine.
Axon guidance in the developing ocular motor system and Duane retraction syndrome depends on Semaphorin signaling via alpha2-chimaerin

Eye movements depend on correct patterns of connectivity between cranial motor axons and the extraocular muscles. Despite the clinical importance of the ocular motor system, little is known of the molecular mechanisms underlying its development. We have recently shown that mutations in the Chimaerin-1 gene encoding the signaling protein α2-chimaerin (α2-chn) perturb axon guidance in the ocular motor system and lead to the human eye movement disorder, Duane retraction syndrome (DRS). The axon guidance cues that lie upstream of α2-chn are unknown; here we identify candidates to be the Semaphorins (Sema) 3A and 3C, acting via the PlexinA receptors. Sema3A/C are expressed in and around the developing extraocular muscles and cause growth cone collapse of oculomotor neurons in vitro. Furthermore, RNAi knockdown of α2-chn or PlexinAs in oculomotor neurons abrogates Sema3A/C-dependent growth cone collapse. In vivo knockdown of endogenous PlexinAs or α2-chn function results in stereotypical oculomotor axon guidance defects, which are reminiscent of DRS, whereas expression of α2-chn gain-of-function constructs can rescue PlexinA loss of function. These data suggest that α2-chn mediates Sema3–PlexinA repellent signaling. We further show that α2-chn is required for oculomotor neurons to respond to CXCL12 and hepatocyte growth factor (HGF), which are growth promoting and chemoattractant during oculomotor axon guidance. α2-chn is therefore a potential integrator of different types of guidance information to orchestrate ocular motor pathfinding. DRS phenotypes can result from incorrect regulation of this signaling pathway.
Evidence for a functional role of epigenetically regulated midcluster HOXB genes in the development of Barrett esophagus

Barrett esophagus (BE) is a human metaplastic condition that is the only known precursor to esophageal adenocarcinoma. BE is characterized by a posterior intestinal-like phenotype in an anterior organ and therefore it is reminiscent of homeotic transformations, which can occur in transgenic animal models during embryonic development as a consequence of mutations in HOX genes. In humans, acquired deregulation of HOX genes during adulthood has been linked to carcinogenesis; however, little is known about their role in the pathogenesis of premalignant conditions. We hypothesized that HOX genes may be implicated in the development of BE. We demonstrated that three midcluster HOXB genes (HOXB5, HOXB6, and HOXB7) are overexpressed in BE, compared with the anatomically adjacent normal esophagus and gastric cardia. The midcluster HOXB gene signature in BE is identical to that seen in normal colonic epithelium. Ectopic expression of these three genes in normal squamous esophageal cells in vitro induces markers of intestinal differentiation, such as KRT20, MUC2, and VILLIN. In BE-associated adenocarcinoma, the activation midcluster HOXB gene is associated with loss of H3K27me3 and gain of AcH3, compared with normal esophagus. These changes in histone posttranslational modifications correlate with specific chromatin decompaction at the HOXB locus. We suggest that epigenetically regulated alterations of HOX gene expression can trigger changes in the transcriptional program of adult esophageal cells, with implications for the early stages of carcinogenesis.
Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase

Understanding the nature of energy transduction in life processes requires a quantitative description of the energetics of the conversion of ATP to ADP by ATPases. Previous attempts to do so have provided an interesting insight but could not account for the rotary mechanism by a nonphenomenological structure/energy description. In particular it has been very challenging to account for the observations of the 80° and 40° rotational substates, without any prior information about such states in the simulation procedure. Here we use a coarse-grained model of F1-ATPase and generate, without the adjustment of phenomenological parameters, a structure-based free energy landscape that reproduces the energetics of the mechanochemical process. It is found that the landscape along the relevant rotary path is determined by the electrostatic free energy and not by steric effects. Furthermore, the generated surface and the corresponding Langevin dynamics simulations identify a hidden conformational barrier that provides a new fundamental interpretation of the catalytic dwell and illuminate the nature of the energy conversion process.
Lack of effect of tofacitinib (CP-690,550) on the pharmacokinetics of the CYP3A4 substrate midazolam in healthy volunteers: confirmation of in vitro data.

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Tofacitinib (CP-690,550) is a novel, oral Janus kinase inhibitor being investigated as a targeted immunomodulator and disease-modifying therapy in rheumatoid arthritis. • Non-renal elimination accounts for 70% of the total clearance of tofacitinib and the metabolism is primarily mediated by cytochrome P450 (CYP) 3A4. • This study was required to determine the effect of tofacitinib on the in vivo pharmacokinetics of a sensitive CYP3A4 substrate. WHAT THIS STUDY ADDS • The pharmacokinetics of midazolam, a sensitive CYP3A4 substrate, are not altered when co-administered with tofacitinib in healthy subjects. • Tofacitinib is unlikely to affect the clearance of drugs metabolized by CYP enzymes. • There is no need for dose adjustments of CYP substrates when co-administered with tofacitinib. AIMS To investigate inhibitive and inductive effects of tofacitinib (CP-690,550), a Janus kinase inhibitor, on CYP3A4 function via in vitro and in vivo studies. METHODS In vitro experiments were conducted to assess the inhibition and induction potential of tofacitinib for major drug metabolizing enzymes (CYP1A2, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6 and CYP3A4). A phase 1, randomized, open-label, two-way crossover study (NCT00902460) was conducted to confirm the lack of inhibitive/inductive effect on a sensitive CYP3A4 substrate, midazolam, in healthy subjects. Midazolam pharmacokinetics were assessed over 24 h following single dose 2 mg administration prior to administering tofacitinib and after twice daily dosing of tofacitinib 30 mg for 6 days. The primary endpoint was midazolam area under the concentration-time profile, from time 0 to infinity (AUC(0,∞)). RESULTS In vitro studies demonstrated low potential for CYP inhibition (IC(50) estimates tofacitinib > 30 µm), CYP3A4 mRNA induction (observed at tofacitinib concentrations ≥ 25 µm) and no effect on enzymatic activity of CYP substrates. In the human study, AUC(0,∞) adjusted geometric mean ratio for midazolam plus tofacitinib to midazolam alone was 103.97% [90% confidence interval (CI) 95.57, 113.12], wholly within the pre-specified acceptance region (80, 125). The 90% CI for the ratio of adjusted geometric means of maximum plasma concentration (C(max) ) (95.98, 108.87) was also wholly within this acceptance region. CONCLUSIONS These data confirm a lack of an inhibitive or inductive effect of tofacitinib on CYP3A activity in humans and, in conjunction with in vitro data, support the conclusion that tofacitinib is unlikely to influence the CYP enzyme system as a whole.
Clathrin-mediated endocytosis is inhibited during mitosis

A long-standing paradigm in cell biology is the shutdown of endocytosis during mitosis. There is consensus that transferrin uptake is inhibited after entry into prophase and that it resumes in telophase. A recent study proposed that endocytosis is continuous throughout the cell cycle and that the observed inhibition of transferrin uptake is due to a decrease in available transferrin receptor at the cell surface, and not to a shutdown of endocytosis. This challenge to the established view is gradually becoming accepted. Because of this controversy, we revisited the question of endocytic activity during mitosis. Using an antibody uptake assay and controlling for potential changes in surface receptor density, we demonstrate the strong inhibition of endocytosis in mitosis of CD8 chimeras containing any of the three major internalization motifs for clathrin-mediated endocytosis (YXXΦ, [DE]XXXL[LI], or FXNPXY) or a CD8 protein with the cytoplasmic tail of the cation-independent mannose 6-phosphate receptor. The shutdown is not gradual: We describe a binary switch from endocytosis being “on” in interphase to “off” in mitosis as cells traverse the G2/M checkpoint. In addition, we show that the inhibition of transferrin uptake in mitosis occurs despite abundant transferrin receptor at the surface of HeLa cells. Our study finds no support for the recent idea that endocytosis continues during mitosis, and we conclude that endocytosis is temporarily shutdown during early mitosis.
Food Stamps and Obesity: What Do We Know?

Results from reviewed studies indicate that for most participants in the Food Stamp Program—children, nonelderly men, and the elderly—use of food stamp benefits does not result in an increase in either Body Mass Index (BMI) or the likelihood of being overweight or obese. However, for nonelderly women, who account for 28 percent of the food stamp caseload, some evidence suggests that participation in the Food Stamp Program may increase BMI and the probability of obesity. Different results for age and sex subgroups remain unexplained. Further, because food stamp benefits are issued to households, not individuals, mixed results across age and sex subgroups make it difficult to target policy alternatives to address potential weight gain among some participants while not affecting others in the household.
Large-scale, spatially-explicit test of the refuge strategy for delaying insecticide resistance

The refuge strategy is used worldwide to delay the evolution of pest resistance to insecticides that are either sprayed or produced by transgenic Bacillus thuringiensis (Bt) crops. This strategy is based on the idea that refuges of host plants where pests are not exposed to an insecticide promote survival of susceptible pests. Despite widespread adoption of this approach, large-scale tests of the refuge strategy have been problematic. Here we tested the refuge strategy with 8 y of data on refuges and resistance to the insecticide pyriproxyfen in 84 populations of the sweetpotato whitefly (Bemisia tabaci) from cotton fields in central Arizona. We found that spatial variation in resistance to pyriproxyfen within each year was not affected by refuges of melons or alfalfa near cotton fields. However, resistance was negatively associated with the area of cotton refuges and positively associated with the area of cotton treated with pyriproxyfen. A statistical model based on the first 4 y of data, incorporating the spatial distribution of cotton treated and not treated with pyriproxyfen, adequately predicted the spatial variation in resistance observed in the last 4 y of the study, confirming that cotton refuges delayed resistance and treated cotton fields accelerated resistance. By providing a systematic assessment of the effectiveness of refuges and the scale of their effects, the spatially explicit approach applied here could be useful for testing and improving the refuge strategy in other crop–pest systems.
Computer Assisted Orthopedic Surgery in TKA

Since Campbell and Boyd first developed a mold hemiarthroplasty in 1940, the procedure for a total knee arthroplasty has advanced greatly with the development of new materials and the increasing understanding of the knee joint biomechanics. And accurate alignment of the component and soft tissue balancing has been cited as the essential for the success of total knee arthroplasty. Although mechanical alignment guides have been designed to improve alignment accuracy, there are several fundamental limitations of this technology that will inhibit additional improvements. The long-term survival rate of a total knee arthroplasty after a 10-year follow up was reported to be 80% to 95% (Knutson et al., 1986; Ranawat et al., 1993; Scuderi et al., 1989). Various factors affect this long-term survival, the most closely related factor being the physiologic recovery of the leg alignment (Laskin, 1984; Ritter et al., 1994). Upon a follow-up study of more than 8 years, the loosening rate was only 3% in those patients with a correctly recovered leg alignment, but was 24% in those with an incomplete recovery of the leg alignment(Stulberg et al., 2002). There are limits on improving the alignment accuracy using a conventional total knee arthroplasty. Teter et al. (Teter et al., 1995) found that when a tibial extramedullary alignment guide was used, approximately 8% of the cuts were deviated 4 degrees of the ideal 90 degrees cut (perpendicular to the mechanical axis). However, this finding was based on coronal imaging, and the rate of malalignment may be considerably greater when the sagittal imaging is considered. Computer-assisted surgery(CAS) was introduced to overcome these difficulties and errors. Computer-assisted total knee arthroplasty has gained increasing acceptance among orthopedic surgeons as a technique to improve surgical precision and patient outcomes.