Miracle-dz/UniFAR-FTUs huggingface dataset:
CsrA of Bacillus subtilis regulates translation initiation of the gene encoding the flagellin protein (hag) by blocking ribosome binding

The global regulatory Csr (carbon storage regulator) and the homologous Rsm (repressor of secondary metabolites) systems of Gram‐negative bacteria typically consist of an RNA‐binding protein (CsrA/RsmA) and at least one sRNA that functions as a CsrA antagonist. CsrA modulates gene expression post‐transcriptionally by regulating translation initiation and/or mRNA stability of target transcripts. While Csr has been extensively studied in Gram‐negative bacteria, until now Csr has not been characterized in any Gram‐positive organism. csrA of Bacillus subtilis is the last gene of a flagellum biosynthetic operon. In addition to the previously identified σD‐dependent promoter that controls expression of the entire operon, a σA‐dependent promoter was identified that temporally controls expression of the last two genes of the operon (fliW‐csrA); expression peaks 1 h after cell growth deviates from exponential phase. hag, the gene encoding flagellin, was identified as a CsrA‐regulated gene. CsrA was found to repress hag′–′lacZ expression, while overexpression of csrA reduces cell motility. In vitro binding studies identified two CsrA binding sites in the hag leader transcript, one of which overlaps the hag Shine–Dalgarno sequence. Toeprint and cell‐free translation studies demonstrate that bound CsrA prevents ribosome binding to the hag transcript, thereby inhibiting translation initiation and Hag synthesis.
Immobilization of Red Fox (Vulpes vulpes) with Medetomidine-Ketamine or Medetomidine-Midazolam and Antagonism with Atipamezole

Abstract Thirty-two free-ranging red foxes (Vulpes vulpes) were immobilized with one of three combinations: medetomidine (0.076 ± 0.017 mg/kg) and ketamine (2.1 ± 0.5 mg/kg; MK, n = 16), medetomidine (0.057 ± 0.008 mg/kg) and low-dose midazolam (0.6 ± 0.1 mg/kg; MM-0.5, n = 10), or medetomidine (0.067 ± 0.012 mg/kg) and high-dose midazolam (1.3 ± 0.2 mg/kg; MM-1, n = 6) by i.m. injection. Induction and recovery times were recorded. Pulse, respiratory rate, body temperature, systolic and diastolic blood pressure, and oxygen saturation were measured. Anesthesia depth indicators were observed. There was a significant difference between the MM-0.5 and the MM-1 groups regarding induction time, 8.1 ± 2.1 min and 5.0 ± 1.7 min, respectively. The MK induction time was 6.9 ± 2.5 min, which was not significantly different from the other two groups. All combinations provided effective immobilization for at least 20–25 min. During immobilization, there were significant differences regarding rectal temperature, which was higher in the MK group; and blood pressure, which was higher in the MM-1 group. After administration of atipamezole at 5 mg per 1 mg medetomidine given, there was a significant difference between the groups in recovery time; MK foxes were standing within 3.9 ± 1.7 min, MM-0.5 foxes within 10.6 ± 4.5 min, and MM-1 foxes within 10.2 ± 3.4 min. None of the combinations caused rough or prolonged recoveries. Subjectively, the MM groups had smoother and less ataxic recoveries than the MK group. In conclusion, the authors recommend the use of medetomidine at 0.07 mg/kg in combination with midazolam at 0.8 mg/kg or ketamine at 2 mg/kg for the immobilization of free-ranging red foxes. During immobilization, monitoring of body temperature and oxygenation is recommended.
A mathematical model of tumour angiogenesis incorporating cellular traction and viscoelastic effects.

Angiogenesis is defined as the outgrowth and formation of new vessels from a pre-existing vascular network (Rakusan, In: Cardiac Growth and Regeneration. Annals of the New York Academy of Sciences, 1995), and is of fundamental importance in understanding the processes by which a tumour achieves vascularization. Diffusible substances, collectively called tumour angiogenesis factors are released from the tumour to elicit a variety of responses from the surrounding tissues, most importantly the migration of endothelial cells (lining neighbouring vessels) towards the tumour. To facilitate locomotion, the cells exert appreciable traction forces upon the interstitial extracellular matrix which, in turn, influences the resulting direction of their migration. In this paper, we examine the role played by cellular traction during cell migration and the corresponding viscoelastic effects of the extracellular matrix.
Optimal PID Controller Design for AVR System

In this paper, a real-valued genetic algorithm (RGA) and a particle swarm optimization (PSO) algorithm with a new fitness function method are proposed to design a PID controller for the Automatic Voltage Regulator (AVR) system. The proposed fitness function can let the RGA and PSO algorithm search a high-quality solution effectively and improve the transient response of the controlled system. The proposed algorithms are applied in the PID controller design for the AVR system. Some simulation and comparison results are presented. We can see that the proposed RGA and PSO algorithm with this new fitness function can find a PID control parameter set effectively so that the controlled AVR system has a better control performance.
Estrus performance of boran and boran × holstein friesian crossbred cattle synchronized with a protocol based on estradiol benzoate or gonadotrophin-releasing hormone

The objectives of this study were to determine estrus behavior, interval to estrus, duration of estrus and time of ovulation of Boran, and Boran × Holstein Friesian (HF) breeds. A total of 113 cows and heifers from the two breeds were synchronized with two estrus synchronization protocols: 1) estradiol benzoate (EB) + controlled internal drug release (CIDR) + prostaglandin (PGF2α); and 2) gonadotrophin (GnRH) + CIDR + PGF2α. The results (mean ± SE) showed that the Boran breed had significantly longer interval to estrus (70.67 ± 5.9 versus 54.58 ± 4 h), shorter duration of estrus (8.65 ± 0.83 versus 12.1 ± 0.7 h) and lower behavioral score (mean ± SD; 883 ± 639 versus 3,399 ± 957) compared to Boran × HF crossbred cattle. Animals treated with EB + CIDR + PGF2α had a significantly shorter interval to estrus (46.75 ± 4 versus 78.5 ± 4 h), higher behavioral score (3,058 ± 1,223 versus 2,663 ± 991) and longer duration of estrus (11.31 ± 0.71 versus 9.4 ± 0.75 h) compared to animals treated with GnRH + CIDR + PGF2α. The interval from estrus to ovulation (26 ± 2.5 h) was not different between breeds and between synchronization methods. The Boran (Bos indicus) breed tended to have a longer interval to estrus, shorter duration of estrus and an estrus behavior score lower than Boran × HF crossbred cattle treated and managed under similar conditions. The protocol using EB + CIDR + PGF2α was more effective than GnRH + CIDR + PGF2α in terms of enhancing estrus behavior and creating tight synchrony.
Collection of oocytes from donors in the growth phase of follicular development can enhance the production of bovine embryos for cryopreservation

The present study was designed to compare the efficiency of bovine embryo production for cryo- preservation between oocytes collected from donors in the growth phase of follicular development (GPFD) and those recovered from donors in the undefined phase (UPFD). Cyclic cows, Czech Siemental or Holstein dairy breeds, 4-6 years of age, slaughtered at the local abbatoir were used. They were divided into two groups based on ovarian morphology: I. GPFD donors with ovaries corresponding to the growth phase of the first follicular wave (estrus cycle days 3-4; n = 52), and II. UPFD donors with ovaries in any other phase of follicular development (undefined estrus cycle days; n = 89). A total of 3 771 oocytes were collected and 1 134 embryos were prepared as two separate populations by standard protocol. In total 352 excellent or good quality embryos at the early, advanced or expanded blastocyst stage from both donor groups were pooled and used for cryotolerance assessment. They were frozen on day 7 (D7) or day 8 (D8) after fertilization by the standard procedure. After thawing, the embryos were cultured for 72 h to the hatching stage. The percentages of both D7 embryos and advanced blastocysts were significantly higher (P ≤ 0.01) for oocytes collected from GPFD donors than for oocytes collected from UPFD donors (33.7 vs 28.6% and 43.0 vs 29.5%, respectively). The percentages of excellent or good quality embryos obtained from both D7 embryos and fertilized oocytes were significantly higher (P ≤ 0.01) for oocytes collected from GPFD donors than for oocytes collected from UPFD donors (63.6 vs 49.4% and 21.4 vs 14.1%, respectively). The post-thaw survival rates were significantly higher (P ≤ 0.01) for D7 than D8 embryos (80.4 vs 66.3%). In rela- tion to the developmental stage, the development and hatching rates were significantly higher (P ≤ 0.01) for D7 than D8 early blastocysts (75.0 vs 41.2% and 50.0 vs 5.9%, respectively) and for D7 than D8 advanced blastocysts, (73.7 vs 57.1 and 52.6 vs 28.6%, respectively). No differences were found between D7 and D8 expanded blastocysts after freezing-thawing. In conclusion, the collection of oocytes from donors in the growth phase positively influ- enced the in vitro production of bovine embryos for cryopreservation. The development of embryos produced with oocytes from GPFD donor group was accelerated and more excellent and good advanced blastocysts with greater cryotolerance were produced on day 7 after fertilization, as compared to embryos produced with oocytes from the UPFD donor group.
A study comparing the plaque removal efficacy of an advanced rotation-oscillation power toothbrush to a new sonic toothbrush.

OBJECTIVE Recently, a new sonic power toothbrush has been marketed. The purpose of this study was to compare the plaque removal efficacy of a control rotation-oscillation power toothbrush (Oral-B Triumph) to this new sonic-powered toothbrush (Sonicare FlexCare) following a single brushing. METHODS This study was a randomized, controlled, examiner-blind, two-treatment, four-period crossover design, which examined plaque removal with the two toothbrushes following replicate single uses in 48 subjects. Plaque was scored before and after brushing using the Turesky Modification of the Quigley-Hein Plaque Index (TMQHPI). RESULTS Baseline plaque scores were 2.87 for the sonic toothbrush and 2.85 for the rotation-oscillation toothbrush treatment groups. With respect to all surfaces examined, the sonic toothbrush delivered an adjusted (via Analysis of Covariance) mean difference between baseline and post-brushing plaque scores of 0.95, while the rotation-oscillation toothbrush delivered an adjusted mean difference of 1.06. The difference between treatment groups was statistically significant (p = 0.003). CONCLUSION The rotation-oscillation toothbrush delivered superior plaque removal by reducing plaque scores, on average, 12.1% more than the new sonic toothbrush.
Design, Validation, and Clinical Implementation of a Gap-Polymerase Chain Reaction Method for α-Thalassemia Genotyping Using Capillary Electrophoresis

Abstract α-Thalassemia (α-thal) is genetically heterogeneous with most cases caused by variably sized deletions of the HBA1 and/or HBA2 loci. In this report, we describe the development, validation, and implementation of a novel gap-polymerase chain reaction (gap-PCR)/capillary electrophoresis (CE). method. This assay utilizes two multiplex reactions and CE to detect the following deletions: –α3. 7 (rightward), –α4.2 (leftward), –(α)20.5, – –SEA (Southeast Asian), – –MED, – –FIL and – –THAI. Validation studies using 36 previously characterized patient samples and plasmid controls demonstrated 100.0% accuracy. Following clinical implementation, 423 patients were analyzed over 24 months. Two hundred and twenty-seven cases (46.0%) showed abnormal results including heterozygous –α3. 7 (n = 114, 27.0%), homozygous –α3. 7 (n = 96, 23.0%), heterozygous – –SEA (n = 9, 2.0%), heterozygous –α 4.2 (n = 5, 1.0%), heterozygous – –MED (n = 1, <1.0%), and compound heterozygous –α3. 7/–α4.2 (n = 2, <1.0%) deletions. Correlation with red blood cell (RBC) parameters showed that patients with a deletion of two or more genes were associated with significantly lower mean corpuscular volume (MCV) and mean corpuscular hemoglobin (Hb) (MCH) levels than patients with wild-type results. This novel multiplex gap-PCR protocol reliably detects the seven most common deletions giving rise to α-thal. Use of the fluorescently labeled CE method provides for a high throughput workflow suitable to a clinical diagnostic laboratory serving a multiethnic population.
Attention Problems in Epilepsy: Possible Significance of the Epileptogenic Focus

Summary: Investigation of the relation between epilepsy and cognition presents serious methodologic problems because several factors may contribute to impair neuropsychological performances in epileptic persons. Benign epilepsy of childhood with rolandic paroxysmal discharges (EPR) may be a very useful model of investigation in relation to opportunity to examine subjects without brain damage, therapy, and negative environmental influences. Thus, neuropsychological dysfunction in patients with EPR may support the hypothesis that epilepsy itself plays a specific role in the genesis of cognitive disturbances. We assessed the impact of the laterality of the epileptogenic focus on cognition of children with EPR. All subjects performed a figure cancellation task, a test used to evaluate mainly attention mechanisms and abilities in processing visuospatial information. Results showed that children with right‐sided (or bilateral) focus scored worse, whereas children with left‐sided focus performed as well as the control subjects. Our data agree with those of studies suggesting that focal discharges may be related to poor cognitive performance. Evidence of a concordance between neurophysiologic and neuropsy‐chologic findings may have great practical and theoretical implications in management of epileptic patients.
Production and properties of a raw‐starch‐degrading amylase from the thermophilic and alkaliphilic Bacillus sp. TS‐23

The optimum temperature and initial medium pH for amylase production by Bacillus sp. TS‐23 were 55 °C and 8.5 respectively. Maximum amylase activity was obtained in a medium containing peptone and soluble starch as nitrogen and carbon sources. Activity staining revealed that two amylases with molecular masses of 150 and 42 kDa were produced when maltose, soluble starch or amylose was used as carbon source for growth, whereas only the 150 kDa protein was detected in the medium containing water‐ insoluble carbon sources. A raw‐starch‐degrading amylase was purified from culture supernatant of Bacillus sp. TS‐23. The molecular mass of the purified amylase was estimated at 42 kDa by electrophoresis. The enzyme had a pI of 4.2. The optimal pH and temperature for activity were 9.0 and 70 °C respectively. The thermoactivity of the purified enzyme was enhanced in the presence of 5 mM Ca2+; under this condition, enzyme activity could be measured at a temperature of 90 °C. The enzyme was strongly inhibited by Hg2+, Pb2+, Zn2+, Cu2+ and EDTA, but less affected by Ni2+ and Cd2+. The enzyme preferentially hydrolysed high‐molecular‐mass substrates with an α‐1,4‐glucosidic bond except glycogen. The raw starches were partly degraded by the purified amylase to yield predominantly oligosaccharides with degrees of polymerization 3, 4 and 5.
Global analysis of reptile elevational diversitygeb

Aim Latitudinaland regional-scale studies of reptile diversity suggest a predominant temperature effect, unlike many other vertebrate richness patterns which tend to be highly correlated with both temperature and water variables. Here I examine montane gradients in reptile species richness with separate analyses of snakes and lizards from mountains around the world to assess a predominant temperature effect and three additional theories of diversity, including a temperature–water effect, the species–area effect and the mid-domain effect (MDE).
Relationship between Body Mass Index, Self-esteem and Quality of Life among Adolescent Saudi Female

Objective: to examine the relationship between BMI, self-esteem and quality of life among Saudi Adolescent females. Method: A descriptive correlational design was used. A convenience sample of 416 participants was included. An explanation about the purpose and the nature of the study was offered for each participant. Qualified subjects were asked to complete the survey questionnaire and get their weight and height measured. Voluntary participation was assured. The inclusion criteria were Saudi nationality, age range between 14 to 21, and no history of chronic diseases, Three tools were used to collect data: the sociodemographic part, Rosenberg’s (1965) Self-Esteem Scale (RSE), and Quality of Life Scale (QOLS). The validity and reliability of the measurements were ensured. Data was collected from public places. Results: The mean age was 19.19+ 1.92. The mean BMI was 25.04+ 5.45. The mean total self esteem score was 29.23+4.29 and the mean total score of the quality of life was 82.83+ 17.08. Persons correlation showed that there was a significant negative correlation between Body Mass Index (BMI) and total self esteem score (r = -0.421, p = 0.000). Also there was a significant negative correlation between BMI and total Quality of life score (r = -0.325, p = 0.000). There were no statistical relationship between age, self esteem and quality of life, However there was a significant positive correlation between self esteem and quality of life (r = 0.276, P = 0. 000). Conclusion: The self esteem as well as the quality of life decrease with the increase in body mass index among adolescence female.
Smoking cessation treatment and outcomes in medium to heavy cigarette smokers being treated for cancer in Jordan.

BACKGROUND Studies evaluating smoking cessation treatment outcomes in cancer patients are scarce, despite smoking cessation importance in cancer care. We sought to add to the literature by evaluating smoking cessation in a challenging group of cancer patients (medium-to-heavy smokers) visiting an out-patient smoking cessation clinic (SCC) in a cancer center in Amman, Jordan. MATERIALS AND METHODS Patients smoking >9 cigarettes per day (CPD) and referred to the SCC between June 2009 and May 2012 were studied. Clinic records were reviewed to measure demographic and baseline clinical characteristics, and longitudinal (3-, 6- and 12- month) follow- up by phone/clinic visit was conducted. At each follow-up, patients were asked if they experienced medication side-effects, if they had returned to smoking, and reasons for failing to abstain. Descriptive and multivariable logistic regression analyses were performed. RESULTS A total of 201 smokers were included in the analysis. The 3-month abstinence was 23.4% and significantly associated with older age, being married, and presenting with lower (≤ 10 ppm) baseline carbon monoxide (CO) levels. On a multivariable level, lower CO levels, a higher income (relative to the lowest income group), being older, and reporting severe dependence (relative to dependence reported as 'somewhat' or 'not') were significant predictors of higher odds of abstinence at three months. Reasons for failing to quit included not being able to handle withdrawal and seeing no value in quitting. Long- term ARs did not reach 7%. CONCLUSIONS In a sample of Jordanian smokers (>9CPD) with cancer and receiving smoking cessation treatment, ARs were low and further declined with time. Results underscore the need for more aggressive patient management and rigorous follow-up during and after smoking cessation treatment, particularly when this takes place in challenging settings. Observed reasons for failure to abstain should be used to tailor counseling practices.
Cytogenetic analyses of human oocytes provide new data on non-disjunction mechanisms and the origin of trisomy 16.

BACKGROUND Nowadays, oocyte donation is an extended practise in IVF programmes. However, to date, little information on aneuploidy frequency in oocytes from donors is available. Aneuploidy is one of the major causes of embryo and fetal wastage as well as of congenital mental and developmental disabilities. It is known that most aneuploidies are due to non-disjunction events occurring in the maternal germ line. Linkage studies have associated abnormal patterns of meiotic recombination to the origin of the non-disjunction event in many aneuploid conditions. METHODS AND RESULTS In the present study, we analyse the frequency of chromosome imbalances in a series of metaphase I (MI; n = 44) and metaphase II (MII; n = 103) oocytes from 140 young donors (aged from 18 to 35 years, mean age 26.6) after hormone-induced superovulation. The aneuploidy frequency found in MII oocytes was 12.6%, and both whole-chromosome non-disjunction (1.94%) and premature separation of sister chromatids (PSSC) (12.6%) have been found. The chromosomes involved have been identified by multiplex fluorescent in situ hybridization (FISH). Achiasmate chromosomes have been identified in MI oocytes (9.1%), with most of them corresponding to chromosome 16 (6.8%). For this reason, the meiotic recombination pattern of chromosome 16 has been analysed in prophase I oocytes (n = 81) by immunofluorescence staining against MLH1 protein and subsequent FISH with specific probes. Our results show a percentage of oocytes with non-crossover bivalent 16 (2.5%) and a high percentage of bivalents 16 with a single exchange (19.8%). CONCLUSIONS In the present study, we report the finding of a considerable frequency of aneuploidy in oocytes from young donors, with the frequency of PSSC being higher than the frequency of whole-chromosome non-disjunction. In addition, we report vulnerable patterns of meiotic recombination in chromosome 16 that may be at risk of leading to a non-disjunction event. This gives new data on the susceptibility of the control population to conceive a trisomic 16 embryo.
An Amish founder mutation disrupts a PI(3)P-WHAMM-Arp2/3 complex–driven autophagosomal remodeling pathway

The actin assembly machinery coordinates a variety of membrane-remodeling processes. This paper shows that an inherited mutation in the WHAMM gene causes severe defects in autophagy and that the WHAMM protein normally binds to PI(3)P and nucleates actin to promote LC3 incorporation during autophagosome biogenesis.