Miracle-dz/UniFAR-FTUs huggingface dataset:
Lys-65 and Glu-168 are the residues for carbodiimide-catalyzed cross-linking between the two heads of rigor smooth muscle heavy meromyosin.

We have previously demonstrated that the two heads of chicken gizzard heavy meromyosin (HMM) in a rigor complex with rabbit skeletal F-actin could be cross-linked by the water-soluble carbodiimide 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide. Here, we report the location of the cross-linked sites in the amino acid sequence of the HMM heavy chain. One of the cross-linked residues was identified as Glu-168 by sequencing the CN1.CN6 cross-linked peptide containing residues 1-77 (CN1) and 164-203 (CN6). This site is located close to the ATP-binding site of HMM. Since the other site was further into the amino acid sequence of CN1, another cross-linked peptide corresponding to residues 53-66 and 145-182 was isolated from the 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide-treated acto-tryptic gizzard HMM digested further by other proteolytic enzymes. The amino acid sequence of this peptide and its cyanogen bromide fragment indicated that the cross-linking occurred between Glu-168 and Lys-65. Our results suggests that these two amino acid side chains are in contact with each other in the acto-gizzard HMM rigor complex and participate in the electrostatic interaction between the two HMM heads bound to F-actin. Based on the head-to-head contact, we propose a three-dimensional model for the attachment of gizzard HMM heads to F-actin.
Growth curves from birth to weaning for Thoroughbred foals raised on pasture

Abstract AIM: To mathematically describe the growth of a population of Thoroughbred foals reared on pasture in New Zealand from birth to weaning. METHODS: Twice-monthly liveweight data (including birthweight; BW) from 218 foals (98 colts and 120 fillies) born over a 6-year period, and reared on four different pasture types, were available for analysis. Data truncated to the time of weaning (107–217 days old) provided 3,200 data points. After testing for non-linearity of the relationship of age and liveweight (LW), five non-linear regression equations were tested for goodness of fit. RESULTS: Colts and fillies had similar BW, weaning ages, weaning weights (WW) and average daily gain (ADG) between birth and weaning (ADGb−w). Weaning age explained 48% (p<0.001) of the variation in WW and 11% (p<0.001) of the variation in ADGb−w. After correction for weaning age, BW explained 16% (p<0.001) of the variation in WW and 6% (p<0.001) of the variation in ADGb−w. The best fit of age and LW was the polynomial equations based on Akaike's information criteria (AIC), residual variance (RV), residual standard deviation (RSD), and coefficient of determination (R2). The most accurate, biologically sound representation of growth was provided by Brody's type equation: , and an equation including , that was developed in this study (b0 is an intercept, b1 and b2 are regression coefficients, and e is the base of natural logarithms). The advantage of the Brody's equation is that ADG at a given LW can simply be calculated as: . CONCLUSIONS AND CLINICAL RELEVANCE: The similarity of the present data with growth data from the Northern Hemisphere provides further recognition that foals reared on pasture can grow as well as foals reared in grain-based systems in the Northern Hemisphere. BW provides a logical set point for the explanation of growth of the foal up to weaning, rather than the use of polynomial equations, which do not fully describe the biology of growth, even though they provide an accurate mathematical description.
Crystal structures of bacterial lipoprotein localization factors, LolA and LolB

Lipoproteins having a lipid‐modified cysteine at the N‐terminus are localized on either the inner or the outer membrane of Escherichia coli depending on the residue at position 2. Five Lol proteins involved in the sorting and membrane localization of lipoprotein are highly conserved in Gram‐negative bacteria. We determined the crystal structures of a periplasmic chaperone, LolA, and an outer membrane lipoprotein receptor, LolB. Despite their dissimilar amino acid sequences, the structures of LolA and LolB are strikingly similar to each other. Both have a hydrophobic cavity consisting of an unclosed β barrel and an α‐helical lid. The cavity represents a possible binding site for the lipid moiety of lipoproteins. Detailed structural differences between the two proteins provide significant insights into the molecular mechanisms underlying the energy‐independent transfer of lipoproteins from LolA to LolB and from LolB to the outer membrane. Furthermore, the structures of both LolA and LolB determined from different crystal forms revealed the distinct structural dynamics regarding the association and dissociation of lipoproteins. The results are discussed in the context of the current model for the lipoprotein transfer from the inner to the outer membrane through a hydrophilic environment.
Comprehension improvement using local confidence measure: towards automatic transcription for classroom

We conducted a preliminary study to evaluate the contribution of conﬁdence measure for improving the comprehension of an automatic transcription. The future framework is deaf children studying in a standard school classroom. We deﬁned local conﬁdence measures that can be estimated as soon as possible without waiting for the recognition process to be completed. We then deﬁned diﬀerent modalities to highlight words of low conﬁdence in an automatic transcription and we presented the diﬀerent modiﬁed transcriptions to several subjects who had to answer to some questions of comprehension and to restore the sentences originally uttered. We showed that highlighting words of low conﬁdence can improve the comprehension of the automatic transcription.
Factors associated with low birth weight in a historical series of deliveries in Campinas, Brazil.

OBJECTIVE To identify the risk factors associated with low birth weight (< 2500 grams). METHODS Unmatched case-control study performed in a tertiary maternity hospital in Campinas, Brazil, involving 43,499 liveborn infants delivered in the institution between 1986 and 2004. Analysis of the database containing information on deliveries of women who gave birth to infants with low (6,477 cases) and normal (37,467) birth weight were performed. Factors associated with low birth weight were identified according to the odds ratio (OR) and 95% confidence interval (95%CI) in the bivariate analysis and according to the adjusted OR in the multivariate analysis. Sociodemographic characteristics, reproductive history, previous morbidity and factors related to current prenatal care were studied. RESULTS Extremes of reproductive age, poor education, low maternal weight, smoking beyond the fourth month of pregnancy, previous cesarean section, interdelivery interval < or = 24 months and > or 37 months, maternal history of hypertension, cardiopathy and premature delivery, few (< or = 5) prenatal visits and beginning prenatal care late in pregnancy (after the 3rd month), premature rupture of membranes, increased blood pressure, infectious diseases and hemorrhages during current pregnancy were all associated with low birth weight. Maternal obesity and being a primipara were found to be protective factors. CONCLUSION These results confirm the findings of previous studies. The detection and prenatal management of modifiable factors, counseling, pre-conception intervention, adequate prenatal care and the implementation of primary and secondary prevention of maternal morbidity should be a target for all obstetrician as a potential source for reducing the incidence of low birth weight.
Power Allocation for Secrecy Efficiency in Full-Duplex Relay Assisted Cooperative Networks

This paper investigates secrecy efficiency (SE) optimization in a friendly full-duplex (FD) decode- and-forward (DF) relay network with a passive eavesdropper. Targeting on SE maximization, the power allocation is optimized subject to the total power and minimum secrecy rate constraints adapting to the assumption of unknown eavesdropper's channel state information (CSI). By exploiting the properties of fractional programming (FP) and Difference of Convex functions (DC) programming, the resulting nonconvex optimization problem can be relaxed into a more tractable equivalent problem. Simulation results demonstrate that our proposed scheme can reach a better trade-off between security performance and energy consumption.
The Pathway From Genes to Gene Therapy in Glaucoma: A Review of Possibilities for Using Genes as Glaucoma Drugs

Abstract: Treatment of diseases with gene therapy is advancing rapidly. The use of gene therapy has expanded from the original concept of replacing the mutated gene causing the disease to the use of genes to control nonphysiological levels of expression or to modify pathways known to affect the disease. Genes offer numerous advantages over conventional drugs. They have longer duration of action and are more specific. Genes can be delivered to the target site by naked DNA, cells, nonviral, and viral vectors. The enormous progress of the past decade in molecular biology and delivery systems has provided ways for targeting genes to the intended cell/tissue and safe, long‐term vectors. The eye is an ideal organ for gene therapy. It is easily accessible and it is an immune‐privileged site. Currently, there are clinical trials for diseases affecting practically every tissue of the eye, including those to restore vision in patients with Leber congenital amaurosis. However, the number of eye trials compared with those for systemic diseases is quite low (1.8%). Nevertheless, judging by the vast amount of ongoing preclinical studies, it is expected that such number will increase considerably in the near future. One area of great need for eye gene therapy is glaucoma, where a long‐term gene drug would eliminate daily applications and compliance issues. Here, we review the current state of gene therapy for glaucoma and the possibilities for treating the trabecular meshwork to lower intraocular pressure and the retinal ganglion cells to protect them from neurodegeneration.
Exposure to Bisphenol AF disrupts sex hormone levels and vitellogenin expression in zebrafish

Bisphenol AF (BPAF) is widely used in food‐contact products, electronic devices, and as a cross‐linking reagent in fluoroelastomers. There are growing concerns about its toxicity and endocrine‐disrupting effects based on its structural similarity with bisphenol A (BPA). The endocrine‐disrupting effects of BPAF were studied by exposing 2‐month‐old zebrafish to 0, 0.05, 0.25, or 1 mg/L BPAF for 28 days and evaluating the effect on growth, histopathology, hormone levels, enzyme activity, and gene expression. The overall fitness was not significantly affected. There were no apparent alterations in the gills and intestine tissues of both sexes after BPAF exposure. However, exposure to 1 mg/L BPAF caused damage to the liver in the male fish, characterized by hepatocellular swelling and vacuolation. There was no obvious effect in the liver of female fish, suggesting that the hepatic toxicity of BPAF is gender dependent. Gonadal examination indicated that exposure to 1 mg/L BPAF caused induction of acellular areas in the testis and retardation of oocyte development in the ovary. BPAF exposure increased free triiodothyronine levels of females in a dose‐dependent manner. In males, the testosterone levels decreased in a concentration‐dependent manner. In contrast, estradiol levels increased in a concentration‐dependent manner and were significantly higher in males exposed to 1 mg/L BPAF compared with the controls. In females, 0.05 and 0.25 mg/L BPAF caused an increase in testosterone levels. Furthermore, the estradiol levels increased in females exposed to 0.05 and 1 mg/L. We observed an upregulation of hepatic vitellogenin in both sexes and significantly higher levels in males exposed to 1 mg/L BPAF and females exposed to 0.25 mg/L BPAF, suggesting that BPAF has an estrogenic activity. Our results indicate that BPAF is an endocrine‐disrupting chemical that exerts reproductive toxicity and estrogenic effects on zebrafish. © 2014 Wiley Periodicals, Inc. Environ Toxicol 31: 285–294, 2016.
Performance of Authenticated Encryption for Payment Cards with Crypto Co-processors

—Many security protocols rely on authentication of communicating entities and encryption of exchanged data. Traditionally, authentication and encryption have been separate processes, however there are combined solutions, referred to as authenticated-encryption (AE). The payment card industry is revising its protocol speciﬁcations and considering AE, however there has been uncertainty around performance and feasibility on traditional issued smart cards and when loaded as applications on security chips pre-installed within devices. It is difﬁcult to predict performance using results from generic CPUs as typical smart card chips used in payment, have slow CPUs yet fast crypto-coprocessors. This report is based on a practical investigation, commissioned by a standards body, that compared secure platform level (MULTOS) and low-level native implementations of AE on crypto-coprocessor smart cards. The work also suggests a technology independent benchmark for a CPU with crypto-coprocessor.
Rate of penicillin killing of Staphylococcus aureus and Autobac 1 susceptibility test results

A clinical isolate of Staphylococcus aureus interpreted as resistant to penicillin by the Autobac 1 susceptibility testing method (i.e., light-scattering index of 0.77) was found to be susceptible to penicillin by both the disk diffusion and broth dilution techniques. The growth rate of the clinical isolate during a 4-h incubation interval was similar to that of a known sensitive reference strain (S. aureus ATCC 25923) used as a control organism for the Autobac test. The bactericidal effect of penicillin was evaluated by measuring the rate of killing over a 4-h interval. The percentages of organisms surviving exposure to 5.0 or 2.5 U of penicillin G per ml (number of organisms recovered at 3 h/number of organisms introduced as inoculum) were 68 and 76%, respectively, for the clinical isolate and 15 and 21%, respectively, for the reference strain. After 24 h of incubation, penicillin was bactericidal for both strains. The need to increase the time of incubation for those S. aureus isolates resistant to penicillin after 3 h of standard incubation time in the Autobac system is discussed.
A Review on Emerging Fungal Infections and Their Significance

The incidence of fungal infections is increasing at an alarming rate, presenting an enormous pressure and challenge to healthcare professionals for their diagnosis and treatment. Emerging fungal infections is also cause of significant morbidity and mortality. This emergence is directly related to the growing population of immune-compromised individuals. Patient with condition such as Granulocytopenia, advanced HIV infection, bone marrow and solid organ transplantation, cancer, diabetes mellitus, severe burn and trauma and severe malnutrition are among many others predisposing factor for low immunity. Demographics changes, Microbial adaptation and Technological advances are few factors which promote these emergences. Infection may be caused by various types of fungi such as yeast and mould including hyaline as well as dematiaceous mould. Populations which are not exposed to endemic fungi and are healthy may also are at risk by dimorphic fungi. Increase in surveillance, availability of rapid noninvasive diagnostic test, monitoring of development of resistance to antifungal agents, research on pathogenesis, prevention, and control of fungal infection are few steps we may put together to cope up with these emerging health problems.
Some methods and models for analyzing time-series gene expression data

Experiments in a variety of fields generate data in the form of a time-series. Such time-series profiles, collected sometimes for tens of thousands of experiments, are a challenge to analyze and explore. In this work, motivated by gene expression data, we provide several methods and models for such analysis. The methods developed include new clustering techniques based on nonparametric Bayesian procedures, and a confirmatory methodology to validate that the clusters produced by any of these methods have statistically different mean paths. Thesis Supervisor: David K. Gifford Title: Professor
An efficient Scalable structure-Free Inter cluster multicast Routing (SAFIR) protocol for large tactical Mobile Ad hoc Networks

Scalability is a fundamental requirement in the field of Mobile Ad hoc Networks with the current significant growth in military network capabilities, such as greater node counts, increased bandwidth, better routing times and decreased latencies. Indeed, the advent of the digitized battlefield defines the needs for tactical Mobile Ad hoc Networks, which are formed by hundreds to thousands of nodes. Consequently, the well-known challenging issues of multicasting in MANET become even more significant with these networks, since the legacy routing protocols do not scale with such tactical environments. We propose in this paper an efficient solution that meets the needs for a scalable multicast routing protocol for a large-scale tactical MANET. Relying on a clustered network, which is an appropriate solution to handle scalability, the protocol proposed in this paper defines how to achieve multicast communications between nodes that belong to different clusters.
Effect of everolimus therapy on skeletal muscle wasting in patients with metastatic renal cell carcinoma (mRCC): Results from a placebo-controlled study.

319 Background: We have previously reported that sorafenib induces muscle wasting in mRCC (Antoun, JCO 2010). As everolimus exerts its antineoplastic through inhibition of the mammalian target of rapamycin (mTOR), a key element of intracellular signalling of protein synthesis in skeletal muscle, we hypothesized that muscle wasting would be also an important side effect of everolimus therapy. METHODS All patients with mRCC enrolled in RECORD 1 (everolimus (E) or placebo (P) post TKI failure) in IGR (n=40) were analyzed for this study. Patients were eligible if at least 2 CT scans were available. CT image analysis, which has high precision and specificity for evaluation of specific muscles, was used to define change in total skeletal muscle. The third lumbar vertebra (L3) was chosen as a landmark. Images were analyzed using Slice-O-Matic software V4.3 (Tomovision). Tissue Hounsfield unit thresholds were employed: -29 to +150 for skeletal muscle. Subsequently, tissue cross-sectional areas (cm2) were computed. RESULTS 35 patients (83% male, median age 60y) were evaluable, 10 on P and 25 on E. In addition, 9 patients initially on P could cross to E (as per protocol) and were analyzed both on P and on E. Median durations of treatment were 79 and 263 days respectively on P and E. Placebo patients had stable body weight, with no significant mean gain or loss of muscle. By contrast, patients on E lost body weight over time: -2.5±3.6 kg by 83 d (p=0.02), -4.9±5.7 (p=0.005) by 167 d and -5.0±7.6 kg (p=0.02) by 286 d. E patients progressively lost skeletal muscle compared . with baseline from -2.5±5.9% at 83d (p=0.06), to -4.0±7.5% at 167d (p=0.03) and -4.8±6.8% at 263d (p=0.01). Interstingly, the 9 patients who had maintained body weight (+2.0 kg) and muscle (+2.7%) whilst on placebo, and crossed to E, promptly lost weight (-4.8 kg, p<0.03) and skeletal muscle (-5.3%) (about 1.5 kg of muscle) when crossed to E. CONCLUSIONS Body weight and muscle wasting are induced by everolimus in mRCC, and are not related to progressive disease. These changes increase over time. Relation between these changes and outcome will be presented at the meeting. [Table: see text].
Hydrodeoxygenation of Bio-Oil on Bimetallic Catalysts: From Model Compound to Real Feed

Two series of bimetallic Ni-Co catalysts and corresponding monometallic catalysts with ca. 20 wt% metal loading were evaluated in hydrodeoxygenation (HDO) of phenol as a model compound for bio-oil. The bimetallic catalysts outperformed the corresponding monometallic catalyst in terms of conversion and cyclohexane selectivity. This could be attributed to the formation of Ni-Co alloy, which caused a decrease in metal particle size and stabilized Ni active sites in the near surface region. The balanced combination of formed Ni-Co alloy with acidity from supports allowed performing all individual steps in the reaction network toward desired products at high rate. Consequently, the two best-performing catalysts were tested in HDO of wood based bio-oil, showing that the bimetallic catalyst 10Ni10Co/HZSM-5 was more effective than 20Ni/HZSM-5 in terms of degree of deoxygenation and upgraded bio-oil yield. These findings might open an opportunity for development of a novel cheap but effective catalyst for a key step in the process chain from biomass to renewable liquid fuels.
Small RNA on the Move

Molecular biology experienced a significant shift in thinking in recent years with growing evidence that microRNAs (miRNAs) play a major role in the control of eukaryotic gene expression during development. miRNAs and related small interfering RNAs (siRNAs) are 21- to 25-nucleotide long noncoding
Technological, pedagogical and content knowledge in one-to-one classroom: teachers developing “digital wisdom”

One-to-one (1X1) laptop initiatives become prevalent in schools aiming to enhance active learning and assist students in developing twenty-first-century skills. This paper reports a qualitative investigation of all 7th graders and their 15 teachers in a junior high-school in Northern Israel gradually implementing 1X1 model. The research was conducted during a second year of 1X1 implementation at the school level, which was a first year of teaching and learning with laptops for all study participants. The study triangulates non-participant lessons’ observations and semi-structured interviews with 15 teachers. The data were collected twice: at the beginning and toward the end of the 2011–2012 academic year – in total, 30 observations and 30 interviews were conducted. The results were examined through phenomenological research techniques and discussed in terms of the technological, pedagogical and content knowledge (TPACK) and “digital wisdom” approaches. The teachers showed significant increase of technological knowledge. However, only moderate connections between technology and pedagogy as well as between technology and content were found. Some of the teachers functioned as moderators, scaffolding students and supporting their individual or collaborative learning. However, many teachers struggled with effective management of 1X1 classroom. Neither conjunction of teacher TPACK nor facilitation of student digital skills was observed. The paper suggests an overlap of the TPACK framework and the digital wisdom approach and provides implications for curriculum developers and educational policy-makers.
Intravascular Platelet Aggregation in the Heart Induced by Norepinephrine: Microscopic Studies

Aggregated platelets and occlusive platelet thrombi were found in small myocardial vessels of dogs on electron-microscope examination after prolonged infusion of norepinephrine. The etiology of the myocardial necrosis and fibrosis induced by catecholamines in experimental animals and seen in patients with pheochromocytoma and patients after norepinephrine treatment for shock may be related to this intravascular platelet-aggregating effect of catecholamines. The link between stress and acute myocardial infarction may be via catecholamine-induced intravascular platelet thrombosis. If the thrombogenic theory of atherosclerosis is valid, platelet aggregation induced by catecholamines may be the mechanism whereby arteriosclerotic heart disease is related to stress.