Miracle-dz/UniFAR-FTUs huggingface dataset:
Introduction of Viral Hemorrhagic Septicemia Virus into Freshwater Cultured Rainbow Trout Is Followed by Bursts of Adaptive Evolution

ABSTRACT Viral hemorrhagic septicemia virus (VHSV), a rhabdovirus infecting teleost fish, has repeatedly crossed the boundary from marine fish species to freshwater cultured rainbow trout. These naturally replicated cross-species transmission events permit the study of general and repeatable evolutionary events occurring in connection with viral emergence in a novel host species. The purpose of the present study was to investigate the adaptive molecular evolution of the VHSV glycoprotein, one of the key virus proteins involved in viral emergence, following emergence from marine species into freshwater cultured rainbow trout. A comprehensive phylogenetic reconstruction of the complete coding region of the VHSV glycoprotein was conducted, and adaptive molecular evolution was investigated using a maximum likelihood approach to compare different codon substitution models allowing for heterogeneous substitution rate ratios among amino acid sites. Evidence of positive selection was detected at six amino acid sites of the VHSV glycoprotein, within the signal peptide, the confirmation-dependent major neutralizing epitope, and the intracellular tail. Evidence of positive selection was found exclusively in rainbow trout-adapted virus isolates, and amino acid combinations found at the six sites under positive selection pressure differentiated rainbow trout- from non-rainbow trout-adapted isolates. Furthermore, four adaptive sites revealed signs of recurring identical changes across phylogenetic groups of rainbow trout-adapted isolates, suggesting that repeated VHSV emergence in freshwater cultured rainbow trout was established through convergent routes of evolution that are associated with immune escape. IMPORTANCE This study is the first to demonstrate that VHSV emergence from marine species into freshwater cultured rainbow trout has been accompanied by bursts of adaptive evolution in the VHSV glycoprotein. Furthermore, repeated detection of the same adaptive amino acid sites across phylogenetic groups of rainbow trout-adapted isolates indicates that adaptation to rainbow trout was established through parallel evolution. In addition, signals of convergent evolution toward the maintenance of genetic variation were detected in the conformation-dependent neutralizing epitope or in close proximity to disulfide bonds involved in the structural conformation of the neutralizing epitope, indicating adaptation to immune response-related genetic variation across freshwater cultured rainbow trout.
Development of value added products based on barley (Hordeum vulgare) and their nutritional evaluation

1. Title of the thesis : Development of value added products based on barley and their nutritional evaluation 2. Full name of the degree holder : Alka Vasan 3. Admission No. : 2010HS67D 4. Title of degree : DOCTOR OF PHILOSOPHY 5. Name and address of Major Advisor : Dr. (Mrs.) Pinky Boora Professor and Head Department of Foods and Nutrition CCS Haryana Agricultural University Hisar -125001, India 6. Degree awarding University : CCS, Haryana Agricultural University, Hisar 7. Year of award of degree : 2015 8. Major subject : Foods and Nutrition 9. Total Number of pages in thesis : 151 + ix + I 10. Number of words in the abstract : Approx. 478
Formation of micro-structural banding in hot-rolled medium-carbon steel

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Are age and gender suitable matching criteria in organ dose reconstruction using surrogate childhood cancer patients’ CT scans?

PURPOSE The purpose of this work was to assess the feasibility of using surrogate CT scans of matched patients for organ dose reconstructions for childhood cancer (CC) survivors, treated in the past with only 2D imaging data available instead of 3D CT data, and in particular using the current literature standard of matching patients based on similarity in age and gender. METHODS Thirty-one recently treated CC patients with abdominal CT scans were divided into six age- and gender-matched groups. From each group, two radiotherapy plans for Wilms' tumor were selected as reference plans and applied to the age- and gender-matched patients' CTs in the respective group. Two reconstruction strategies were investigated: S1) without field adjustments; S2) with manual field adjustments according to anatomical information, using a visual check in digitally reconstructed radiographs. To assess the level of agreement between the reconstructed and the reference dose distributions, we computed (using a collapsed cone algorithm) and compared the absolute deviation in mean and maximum dose normalized by the prescribed dose (i.e., normalized errors |NEmean | and |NE2cc |) in eight organs at risk (OARs): heart, lungs, liver, spleen, kidneys, and spinal cord. Furthermore, we assessed the quality of a reconstruction case by varying acceptance thresholds for |NEmean | and |NE2cc |. A reconstruction case was accepted (i.e., considered to pass) if the errors in all OARs are smaller than the threshold. The pass fraction for a given threshold was then defined as the percentage of reconstruction cases that were classified as a pass. Furthermore, we consider the impact of allowing to use a different CT scan for each OAR. RESULTS Slightly smaller reconstruction errors were achieved with S2 in multiple OARs than with S1 (P < 0.05). Among OARs, the best reconstruction was found for the spinal cord (average |NEmean | and |NE2cc | ≤ 4%). The largest average |NEmean | was found in the spleen (18%). The largest average |NE2cc | was found in the left lung (26%). Less than 30% of the reconstruction cases (i.e., pass fraction) meet the criteria that |NEmean | < 20% and |NE2cc | < 20% in all OARs when using age and gender matching and a single CT to do reconstructions. Allowing other matchings and combining reconstructions for OARs from multiple patients, the pass fraction increases substantially to more than 60%. CONCLUSIONS To conclude, reconstructions with small deviations can be obtained by using CC patients' CT scans, making the general approach promising. However, using age and gender as the only matching criteria to select a CT scan for the reconstruction is not sufficient to guarantee sufficiently low reconstruction errors. It is therefore suggested to include more features (e.g., height, features extracted from 2D radiographs) than only age and gender for dose reconstruction for CC survivors treated in the pre-3D radiotherapy planning era and to consider ways to combine multiple reconstructions focused on different OARs.
Assessment of man-portable robots for law enforcement agencies

This project has involved testing a Packbot Scout within a SWAT-unit for five months. This was done to explore the tactical benefits of the system and to test the robot's technical performance with end users. Another objective was to compare earlier results -- obtained by investigating military during training -- with results from deployment during true risk. The SWAT-team, equipped with and trained to use the robot, set a standard to bring it with them on regular missions. Using the robot during negotiation proved to be the most beneficial application. Other uses would be for long-term surveillances and deploying non-lethal weapons. Early results indicate that the Stockholm SWAT-unit, consisting of 80 active officers, could deploy the robot at least 20 times a year.
Role of Hepcidin in Dysregulation of Iron Metabolism and Anemia of Chronic Diseases

Iron is an essential element and its correct balance is necessary for good health and normal cellular functioning [1]. Hepcidin is the iron-regulatory hormone of hepatic origin. It is a defensin-like low-molecular-weight peptide that plays an important role in iron metabolism. Hepcidin and its receptor ferroportin play most important role in controlling the dietary absorption and tissue distribution of iron. Recently discovered hepcidin molecule has been recognized as the main hormone behind the pathogenesis of anemia of chronic disease.
Encapsulation of biological active phenolic compounds extracted from wine wastes in alginate-chitosan microbeads

Abstract Grapes (Vitis vinifera) are produced in large amounts worldwide and mostly are used for winemaking. Their untreated wastes are rich in valuable secondary metabolites, such as phenolics. Thus, in this study, white and red wine wastes (Malagouzia and Syrah variety) were investigated for their added value phenolics, which were analysed by high performance liquid chromatography (HPLC) and electrospray ionisation-mass spectrometry (ESI/MS) and subsequently encapsulated in several polymers. Extracts from all wastes gave high amounts of total phenolics (13 ± 2.72–22 ± 2.69 mg g−1) and possessed high antioxidant activity (67–97%). In addition to their significant antibacterial activity against gram-negative and gram-positive bacteria, interesting results were also obtained from their anti-inflammatory and antiplatelet activity, in vitro. Encapsulation of the extracts was selective, leaving out most of sugars and other organic compounds when alginate-chitosan was used. Encapsulation efficiency recorded for all extracts ranged from 55% to 79%. Release studies were also performed in several solutions aiming in their commercial use in food and pharmaceutical industries.
Mapping the Structural and Dynamical Features of Multiple p53 DNA Binding Domains: Insights into Loop 1 Intrinsic Dynamics

The transcription factor p53 regulates cellular integrity in response to stress. p53 is mutated in more than half of cancerous cells, with a majority of the mutations localized to the DNA binding domain (DBD). In order to map the structural and dynamical features of the DBD, we carried out multiple copy molecular dynamics simulations (totaling 0.8 μs). Simulations show the loop 1 to be the most dynamic element among the DNA-contacting loops (loops 1-3). Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart). Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. We propose (1) a novel mechanism underlying the dynamics of loop 1 and the possible tread-milling of p53 on DNA and (2) possible mutations on loop 1 residues to restore the transcriptional activity of an oncogenic mutation at a distant site.
Various aspects, patterns and risk factors in breast cancer patients of Balochistan.

PURPOSE Breast cancer is the commonest malignancy of females throughout the world with one million new cases each year. In Pakistan, the burden of breast cancer disease is high with late stage presentation being a common feature, more than half being stage III or stage IV. The objective of this study was to study various aspects, patterns and risk factors in breast cancer patients of Balochistan. METHOD Present study was performed on 134 patients of breast cancer who were registered in CENAR. The patients were interviewed by providing a questionnaire. Informed consent was taken from all the patients who took part in this study after explanation of the study aims. Body mass index (BMI) was calculated andbiopsy reports were obtained from patients files. All the cases were classified with respect to age, gender, ethnic group (Baloch, Pashtoon, Punjabi, Afghani, Hazara) BMI, cancer type, cancer grade, hormonal status, side of the cancer, fertility and marital status. RESULTS Out of 134 patients, the most common ethnic group was Pashtoon with a total of 42 and the common age group was 41-50 years with a total of 51. Invasive ductal carcinoma (IDC) was the most common type, accounting for in 128 patients (95.5%) followed by invasive lobular carcinoma (ILC). CONCLUSION Pashtoon was the most common ethnic group, IDC was common type and most of the patients had an ER/PR positive hormonal status.
Adaptor protein 1 B mu subunit does not contribute to the recycling of kAE1 protein in polarized renal epithelial cells

Abstract Mutations in the gene encoding the kidney anion exchanger 1 (kAE1) can lead to distal renal tubular acidosis (dRTA). dRTA mutations reported within the carboxyl (C)-terminal tail of kAE1 result in apical mis-targeting of the exchanger in polarized renal epithelial cells. As kAE1 physically interacts with the μ subunit of epithelial adaptor protein 1 B (AP-1B), we investigated the role of heterologously expressed μ1B subunit of the AP-1B complex for kAE1 retention to the basolateral membrane in polarized porcine LLC-PK1 renal epithelial cells that are devoid of endogenous AP-1B. We confirmed the interaction and close proximity between kAE1 and μ1B using immunoprecipitation and proximity ligation assay, respectively. Expressing the human μ1B subunit in these cells decreased significantly the amount of cell surface kAE1 at the steady state, but had no significant effect on kAE1 recycling and endocytosis. We show that (i) heterologous expression of μ1B displaces the physical interaction of endogenous GAPDH with kAE1 WT supporting that both AP-1B and GAPDH proteins bind to an overlapping site on kAE1 and (ii) phosphorylation of tyrosine 904 within the potential YDEV interaction motif does not alter the kAE1/AP-1B interaction. We conclude that μ1B subunit is not involved in recycling of kAE1.
Autogenous Bone Graft Versus Bovine Bone Graft in Association With Platelet-Rich Plasma for the Reconstruction of Alveolar Clefts: A Pilot Study

Objective: To compare the outcomes of 2 different bone graft materials: autogenous bone grafts from mandibular symphysis and bovine bone grafts associated with platelet-rich plasma (PRP). Methods: Twenty individuals met the inclusion criteria and accepted to participate in the study. Group A patients underwent alveolar bone grafting using autologous bone and group B patients using a bovine bone graft associated with PRP. Cone beam computed tomography scans were taken and reconstructed 3-dimensionally for all patients preoperatively and 1 year postoperatively. Results: A significant reduction was detected for area and volume within group A and group B. Between groups, no significant difference was found for area or volume. Conclusions: Bovine grafts associated with PRP are a good option for the reconstruction of alveolar clefts and provide good results such as autologous bone grafts.
Outage Performance for Dynamic Power Allocation in Hybrid Non-Orthogonal Multiple Access Systems

In this letter, we propose a novel dynamic power allocation scheme for hybrid non-orthogonal multiple access (DH-NOMA). The exact expressions for the outage probabilities and their asymptotic approximations at high signal-to-noise ratio are derived in DH-NOMA systems. Both Monte Carlo simulations and analytical results are used to compare the proposed scheme with the existing works, such as NOMA based on fixed power allocation (F-NOMA) and cognitive radio inspired NOMA (CR-NOMA). The provided results demonstrate that the DH-NOMA scheme can always achieve better outage performance than the traditional orthogonal multiple access, and achieve a more balanced tradeoff between the two user individual rates than F-NOMA and CR-NOMA.
Design, Synthesis, Characterization, QSAR, Docking, Anti-inflammatory and Analgesic Evaluation of Some New Phthalazinediones.

BACKGROUND phthalazine derivatives were reported to possess anticonvulsant , cardiotonic , antibacterial, analgesic , anti-inflammatory, and anti-microbial activity. In the current study, we applied the QSAR for prediction of newly phthalazinediones incorporating thioamide moiety aiming to reach a more potent anti-inflammatory and Analgesic agent. METHODS Phthalazinediones 10-15 have been synthesized through condensation of dibenzobarallene 3 with thiosemicarbazides 4-8. One equation was predicted using quantitative structure activity relationship (QSAR) and regression analysis for the anti-inflammatory activity with a regression correlation (R) close to unity. The docking studies were performed to investigate the biological trends of the organic compounds (thiol form) against cyclooxygenas- 2 enzyme, which is a responsible inflammation mediator by using Molgro Virtual Docker (MVD) software. The anti-inflammatory activity and analgesic effect of the thioamides 10-15 were determined by collagen II-adjuvant induced paw edema test in rats. RESULTS Compounds 10, 11, 12, and 14, exhibited promising anti-inflammatory activity. Furthermore, in the pain scoring, compounds 10, 11 and 12 were found to be more effective than piroxicam and the order of the analgesic effect of the investigated compounds is as followed 14 >12 > 10 > 11 > 15. CONCLUSION It is clear from the foregoing that the compound 14 is a promising compound if future pharmacological detailed studies. This is consistent with what has been predictable equation 1 in this study.
Radiographic evaluation of the effect of obesity on alveolar bone in rats with ligature-induced periodontal disease

There is evidence that the lack of metabolic control of obese patients may accelerate periodontitis. The aim of this study was to evaluate radiographically the effect of cafeteria-diet-induced obesity on alveolar bone loss in rats subjected to periodontal disease. Twenty male Wistar rats were randomly divided into four groups: 1) control group, 2) control and ligature group; 3) cafeteria group; and 4) cafeteria and ligature group. The animals were evaluated for obesity and euthanized, and the mandible of each rat was removed to perform a radiographic evaluation of alveolar bone loss and its effect on diet-induced obesity. The results showed greater alveolar bone loss in the mice in Group 4 (P<0.01). Thus, we concluded that obese mice, on average, showed greater radiographic evidence of alveolar bone loss than mice undergoing induction of obesity.
Evaluation of the aerosol indirect effect in marine stratocumulus clouds : droplet number, size, liquid water path, and radiative impact

Received 9 June 2004; revised 24 September 2004; accepted 10 February 2005; published 20 April 2005. [1] Data from nine stratocumulus clouds in the northeastern Pacific Ocean were analyzed to determine the effect of aerosol particles on cloud microphysical and radiative properties. Seven nighttime and two daytime cases were included. The number concentration of below-cloud aerosol particles (>0.10 mm diameter) was highly correlated with cloud droplet number concentration. Droplet number concentrations were typically about 75% of particle number concentration in the range of particle concentrations studied (� 400 cm � 3 ). Particle number was anticorrelated with droplet size and with liquid water content in drizzle-sized drops. Radiative impact also depends upon cloud liquid water content and geometric thickness. Although most variability in these macroscopic properties of the clouds could be attributed to variability in the large-scale environment, a weak anticorrelation between particle concentration and cloud geometric thickness was observed. Because of these variations, no correlation between calculated cloud optical thickness or albedo and particle concentration was detectable for the data set as a whole. For regions with comparable liquid water contents in an individual cloud, higher particle concentrations did correspond to increased cloud optical thickness. These results verify that higher particle concentrations do directly affect the microphysics of stratiform clouds. However, the constant liquid water path assumption usually invoked in the Twomey aerosol indirect effect may not be valid.
Global Impact of Rotavirus Vaccination on Childhood Hospitalizations and Mortality From Diarrhea

In 2006, 2 rotavirus vaccines were licensed. We summarize the impact of rotavirus vaccination on hospitalizations and deaths from rotavirus and all-cause acute gastroenteritis (AGE) during the first 10 years since vaccine licensure, including recent evidence from countries with high child mortality. We used standardized guidelines (PRISMA) to identify observational evaluations of rotavirus vaccine impact among children <5 years of age that presented at least 12 months of pre- and post-vaccine introduction surveillance data. We identified 57 articles from 27 countries. Among children <5 years of age, the median percentage reduction in AGE hospitalizations was 38% overall and 41%, 30%, and 46% in countries with low, medium, and high child mortality, respectively. Hospitalizations and emergency department visits due to rotavirus AGE were reduced by a median of 67% overall and 71%, 59%, and 60% in countries with low, medium, and high child mortality, respectively. Implementation of rotavirus vaccines has substantially decreased hospitalizations from rotavirus and all-cause AGE.
The Effect of Diacutaneous Fibrolysis on Patellar Position Measured Using Ultrasound Scanning in Patients With Patellofemoral Pain Syndrome.

CONTEXT Tightness or lack of flexibility of several muscles of the thigh has been associated with patellofemoral joint pain. A tight iliotibial band can lead to laterally located patella and an abnormal patellar tracking pattern. Diacutaneous fibrolysis (DF) is commonly used to reduce muscle tightness, but no studies have evaluated the effects of this technique in the treatment of patients with patellofemoral pain syndrome. OBJECTIVE To assess the effect of DF on patellar position in patients with patellofemoral pain syndrome. DESIGN A single-group, pretest-posttest clinical trial. SETTING University of Zaragoza. PARTICIPANTS A total of 46 subjects with patellofemoral pain (20 males, 26 females; age: 27.8 [6.9] y). INTERVENTION Three sessions of DF. MAIN OUTCOME MEASURES Patellar position measurement using real-time ultrasound scanning; pain intensity measured with visual analog scale and function measured with the Anterior Knee Pain Scale. RESULTS The application of 3 sessions of DF significantly increased the patellar position at posttreatment evaluation (P < .001) and at 1-week follow-up (P < .001). There was not a significant difference on patellar position between posttreatment and follow-up measurements (P = .28). There were also a statistically significant decrease in pain and increase in function at posttreatment and at 1-week follow-up measurements (P < .001). CONCLUSION This study found that patellar position, pain intensity, and function were significantly improved after 3 sessions of DF and at 1-week follow-up.