Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Amino Acid Substitutions in KdpA, the K+-Binding and -Translocating Subunit of the KdpFABC Complex of Escherichia coli

ABSTRACT When grown under K+ limitation, Escherichia coli induces the K+-translocating KdpFABC complex. The stimulation of ATPase activity by NH4+ ions was shown for the first time. Substitutions in KdpA, which is responsible for K+ binding and translocation, revealed that enzyme complexes KdpA:G232A and KdpA:G232S have completely lost their cation selectivity.
Saccharomyces cerevisiae Dmc 1 Protein Promotes Renaturation of Single-strand DNA ( ssDNA ) and Assimilation of ssDNA into Homologous Supercoiled Duplex DNA *

Dmc1 and Rad51 are eukaryotic RecA homologues that are involved in meiotic recombination. The expression of Dmc1 is limited to meiosis, whereas Rad51 is expressed in mitosis and meiosis. Dmc1 and Rad51 have unique and overlapping functions during meiotic recombination. Here we report the purification of the Dmc1 protein from the budding yeast Saccharomyces cerevisiae and present basic characterization of its biochemical activity. The protein has a weak DNA-dependent ATPase activity and binds both single-strand DNA (ssDNA) and double-strand DNA. Electrophoretic mobility shift assays suggest that DNA binding by Dmc1 is cooperative. Dmc1 renatures linearized plasmid DNA with first order reaction kinetics and without requiring added nucleotide cofactor. In addition, Dmc1 catalyzes strand assimilation of ssDNA oligonucleotides into homologous supercoiled duplex DNA in a reaction promoted by ATP or the non-hydrolyzable ATP analogue AMP-PNP.
Effect of Dietary Energy Level on Nutrient Utilization, Insulin-like Growth Factor-I and Insulin-like Growth Factor Binding Protein-3 in Plasma, Liver and Longissimus dorsi Muscle in Growing-finishing Pigs Using Soybean Oil as an Energy Source

Two experiments were carried out to study the effects of dietary energy level on nutrient digestion, nitrogen (N) utilization, growth performance, insulin-like growth factor-I (IGF-I), and insulin-like growth factor binding protein-3 (IGFBP-3) in plasma, liver and longissimus dorsi muscle in growing-finishing pigs. In experiment 1 (Exp 1), 15 castrated male pigs (Duroc×Landrace ×Large White) (Body weight, BW, 55.6±1.8 kg) were divided into three groups and fed rations containing 13.33, 14.87 and 17.35 MJ digestible energy (DE)/kg as treatments I, II and III, respectively, using soybean oil as an energy source. The experiment lasted 8 days and faecal and urinary samples were collected during the last 3 days. The results showed that the digestibility of dry matter (DM), energy and N was increased from treatments I to III (p 0.05). In experiment 2 (Exp 2), 36 female pigs (Duroc×Landrace×Large White) (BW 41.5±3.8 kg) were divided into three groups. The pigs were fed with the same three rations used in Exp 1 for 60 days. At the end of Exp 2, eight pigs were selected from each group for blood sampling and 4 pigs for slaughter trial. The results indicated that average daily feed intake (ADFI) and N-intake were significantly decreased (p<0.01), and DE intake (p<0.01) and average daily gain (ADG) (p<0.05) were increased. IGF-I and IGFBP-3 in plasma were increased (p<0.05). No significant differences in IGF-I and IGFBP-3 in liver and longissimus dorsi muscle were found between different treatments. It was concluded that higher dietary DE level improved nutrient digestibility, ADG and feed/gain ratio when soybean oil was used as an energy source in the ration of growing-finishing pigs. No significant differences were found in N- retention and IGF-I and IGFBP-3 in liver and longissimus dorsi muscle between different treatments. (Key Words : Dietary Energy, IGF-I, IGFBP-3, Pigs, Soybean Oil)
Cytomegalovirus polymerase chain reaction viraemia in patients receiving ganciclovir maintenance therapy for retinitis

Objectives:To determine whether recurrence of polymerase chain reaction (PCR) viraemia during maintenance ganciclovir for cytomegalovirus (CMV) retinitis correlates with (i) CMV disease at a new anatomical site, (ii) progression of the presenting retinitis, or (iii) acquisition of genetic changes in gene UL97 associated with resistance to ganciclovir. Design:A previously described cohort of 45 patients presenting with first episode retinitis was followed clinically using ophthalmoscopy and serial tests for PCR viraemia for a median of 7 months. CMV viral load and genetic markers of ganciclovir resistance were measured in PCR-positive samples. Methods:PCR amplification of the glycoprotein B region of CMV and quantitative competitive PCR assays were employed. Genetic changes in UL97 were identified by sequencing/point mutation assay. Results:PCR viraemia correlated significantly with new episodes of CMV disease (P = 0.011) and a trend was seen for the association with progression of retinitis (P = 0.07). Amongst the 14 patients PCR-positive during maintenance ganciclovir, 10 (71%) had genetic markers of resistance. None of these patients became PCR-negative in blood after reinduction ganciclovir therapy compared with three out of four without markers of resistance (P = 0.022). Conclusions:CMV PCR viraemia correlated strongly with the development of new episodes of CMV disease. Most patients with progression of retinitis remained PCR-negative in blood, consistent with therapeutic failure due to poor intraocular penetration of ganciclovir. However, the minority who were PCR-positive in blood may have reinfected their eye, and frequently had markers of ganciclovir resistance. The implications of these findings for the management of patients with CMV disease are discussed. © 1998 Lippincott-Raven Publishers
Characteristics of organic acid profiles in 16 species of wild growing edible mushrooms

ABSTRACT The aim of study was to determine 9 organic acids in nine aboveground and seven wood-growing wild edible mushroom species originated from an area under the direct influence of a busy trunk road in Poland. The organic acids in the extracts of samples were identified by reversed-phase column liquid chromatography (RPLC). The presented results show that all the mushroom species were characterized by high variation in the profile and content of the analyzed acids. Each of mushroom species contained oxalic acid, the profiles of the other acids strictly depended on mushroom species. Among aboveground species, the highest total content of organic acids was found in Lepista gilva (267.5 ± 26.6 mg g−1 dry weight (DW)), while Laccaria amethystina was characterized by the lowest content (37.7 ± 6.5 mg g−1 DW). Within wood-growing species, the highest content of organic acids was determined in Flammulina velutipes (171.9 ± 26.7 mg g−1 DW), whereas the lowest content (34.2 ± 2.9 mg g−1 DW) of the studied acids was observed in Grifola frondosa.
Polychlorinated biphenyls

Millions of pounds of polychlorinated biphenyl (PCB) compounds have been produced in multiple countries for industrial applications over the last several decades. PCB exposure induces various adverse health effects in animals and humans. Environmental and occupational exposures to PCBs have been associated with liver, kidney, endocrine, and neurodevelopmental adverse effects. We have collected and reviewed animal and human data cited in the US National Library of Medicine from 2000 to 2010. In brief, our review shows new evidence, that is, in animal studies, exposure to one of the PCBs, A1221, induces a significant alteration of serum luteinizing hormone. The effects were more profound in the F2 generation, particularly with respect to fluctuations in hormones and reproductive tract tissues across the estrous cycle. Morphological analyses of brain tissue from rats exposed to A1254 confirmed the results of an earlier work which showed that the relative size of the intra- and infrapyramidal (II-P) mossy fibers was smaller than that in the controls and also reduction in growth was selective for the II-P mossy fibers. PCB exposure increased anogenital distance and prostate size but decreased epididymal weight, epididymal sperm count, and motile epididymal sperm count. No effects were observed on testicular weight or size. The epidemiological data showed an association between diabetes mellitus prevalence and elevated concentrations of PCB 153. Additionally, prenatal PCB exposure studies were associated with a smaller thymic index at birth and could adversely affect immune responses to childhood vaccinations and resistance to respiratory infections. PCB exposure was also reported to adversely affect enamel development in children in a dose-dependent manner. Because PCBs and their metabolites are potential health hazards, understanding the risk factors associated with individual PCBs, PCB mixtures, and PCB metabolites is important. PCB exposures of vulnerable populations (pregnant women, fetuses, infants, and children) are of particular concern because of heightened sensitivity during this period of brain development.
Angle Illusion in a Straight Road

We report a new angle illusion observed when viewing a real scene involving a straight road. The scene portrays two white lines which outline a traffic lane on a road and converge to a vanishing point. In experiment 1, observers estimated the angle created by these converging lines in this scene or in its image projected onto a screen. Results showed strong underestimation of the angle, ie over 50% for observations of both the real scene and its projected image. Experiment 2 assessed how depth cues in projected images influence the angle illusion. Results showed that this angle illusion disappeared when scene information surrounding convergent lines was removed. In addition, the illusion was attenuated with projection of an inverted scene image. These findings are interpreted in terms of a misadoption of depth information in the processing of angle perception in a flat image; in turn, this induces a massive angle illusion.
Adaptive Learning Algorithms for Transferable Visual Recognition

Author(s): Hoffman, Judith | Advisor(s): Darrell, Trevor | Abstract: Understanding visual scenes is a crucial piece in many artificial intelligence applications ranging from autonomous vehicles and household robotic navigation to automatic image captioning for the blind. Reliably extracting high-level semantic information from the visual world in real-time is key to solving these critical tasks safely and correctly. Existing approaches based on specialized recognition models are prohibitively expensive or intractable due to limitations in dataset collection and annotation. By facilitating learned information sharing between recognition models these applications can be solved; multiple tasks can regularize one another, redundant information can be reused, and the learning of novel tasks is both faster and easier.In this thesis, I present algorithms for transferring learned information between visual data sources and across visual tasks - all with limited human supervision. I will both formally and empirically analyze the adaptation of visual models within the classical domain adaptation setting and extend the use of adaptive algorithms to facilitate information transfer between visual tasks and across image modalities.Most visual recognition systems learn concepts directly from a large collection of manually annotated images/videos. A model which detects pedestrians requires a human to manually go through thousands or millions of images and indicate all instances of pedestrians. However, this model is susceptible to biases in the labeled data and often fails to generalize to new scenarios — a detector trained in Palo Alto may have degraded performance in Rome, or a detector trained in sunny weather may fail in the snow. Rather than require human supervision for each new task or scenario, this work draws on deep learning, transformation learning, and convex-concave optimization to produce novel optimization frameworks which transfer information from the large curated databases to real world scenarios.
A Comparison of Metal and Plastic Cannulae for Vacuum Aspiration

A comparative study of the safety and effectiveness of metal (Purandare) versus plastic (Karman) cannulae for first trimester abortion was conducted on 400 women. Two hundred vacuum aspiration procedures were performed using each type of cannula. All aspirations were performed by a single physician, and patient follow‐up was performed by a second physician. The complication rates, amount of retained tissue, rates of cannula obstruction and procedure times of the two cannulae were compared. Our findings showed no significant difference in any of these evaluation criteria for the metal and plastic cannulae.
Fractures of the hyoid bone and thyroid cartilage in suicidal hanging.

OBJECTIVE To analyze the frequency of hyoid bone and thyroid cartilage fractures caused by suicidal hanging in Thai people and compare the different methods of visualizing the those fractures. Results could be used for forensic purposes. MATERIAL AND METHOD A prospective study of hyoid bone and thyroid cartilage fractures in Thai people who died from suicidal hanging between November 2008 and August 2009. The authors confirmed suicides, based on history, crime scene investigation, autopsy reports, and other police information, visual and palpatory examination, and stereomicroscopy with or without 1% Toluidine. Neck dissection was performed following the protocol of Prinsloo and Gordon. Results and data analysis were performed via SPSS version 16. RESULTS Twenty male cases of suicidal hanging were reviewed. Fractures of the hyoid bone and/or thyroid cartilage were found in five cases (25%). Two cases ofthe hyoid bone fracture, two cases of thyroid cartilage fracture, and one case was both bone fractures. Mean age of all cases, non-fracture, and fracture cases were 42.40, 35.93, and 61.80 years, respectively The knot was at the back of the neck in most cases (12 cases, 60%) and at the left, front, and right in four, two, and two cases, respectively. However there was no relation between location ofthe knot at the neck and fractures of hyoid bone and thyroid cartilage (p=1). Incomplete and complete hanging were found in 11 and nine cases. Five cases with fractures of the hyoid bone and/or thyroid cartilage were incomplete hanging. The visual and palpatory examination did not detect the fracture of hyoid bone in all 20 cases but stereomicroscopy and stereomicroscopy with Toluidine blue stain detected fracture in three cases. For detecting thyroid cartilage fractures, all three methods had the same result. CONCLUSION Fractures of the hyoid bone and thyroid cartilage in 25% of Thais who died of suicidal hanging were related with older ages and incomplete hanging but not related with location of the knot. The stereomicroscopic method is fast and effective in detecting fractures of the hyoid bone and thyroid cartilage.
Frequency Support From a Fixed-Pitch Type-2 Wind Turbine in a Diesel Hybrid Mini-Grid

Frequency stability is an important issue in small diesel hybrid autonomous power systems (mini-grids) with high penetration of wind power. With large variations of wind power and load demand, the rate of change of frequency (ROCOF) and frequency excursions tend to increase what can lead to load shedding and tripping of renewable energy generators. The power required from the grid-forming diesel engine generator sets (gen-sets) to balance the system tends to vary more, resulting in increased unit cycling. These problems can be mitigated with costly energy storage units and sophisticated wind turbines (WTs) that provide frequency support via active power control. This paper presents an approach for introducing a power (P) versus frequency (f) droop characteristic in a low-cost fixed-pitch wound rotor induction generator (WRIG)-based WT that allows it to provide frequency support. The effectiveness of the proposed technique in reducing frequency and power demand variations from the diesel power plant is demonstrated by means of simulations.
Analysis of 5518 unique, productively rearranged human VH3-23*01 gene sequences reveals CDR-H3 length-dependent usage of the IGHD2 gene family

Clear and accurate understanding of diversity in antibody complementarity-determining regions (CDRs) is critical for antibody discovery and engineering. Previous observations of antibody CDR-H3 diversity were based on analyzing available antibody sequences in the public databases. The results may not accurately reflect that of natural antibody repertoire due to erroneous species annotation and the presence of man-made CDR loop diversity in public antibody sequence databases. In this study, in a precisely controlled germline context, we explored the relationship between amino acid composition and CDR-H3 length using 5518 unique productively rearranged human VH3-23*01 gene sequences. CDR-H3 length-dependent usage of the Cys-Xn-Cys motif is reported here.
Gabapentin decreases morphine consumption and improves functional recovery following total knee arthroplasty.

BACKGROUND Moderate to severe pain after total knee arthroplasty often interferes with postoperative rehabilitation and delays discharge from hospital. The present study examined the effects of a four-day postoperative gabapentin (GBP) regimen versus placebo on opioid consumption, pain scores and knee flexion, as well as adverse effects, after total knee arthroplasty. METHODS After obtaining research ethics board approval and informed consent, 40 patients were enrolled in a randomized, single-blind, placebo-controlled, open-label study. Patients were assigned to one of five groups - preoperative placebo/postoperative placebo (G1), preoperative GBP 600 mg/postoperative placebo (G2), preoperative GBP 600 mg/postoperative GBP 100 mg three times per day (G3), preoperative GBP 600 mg/ postoperative GBP 200 mg three times per day (G4) and preoperative GBP 600 mg/postoperative GBP 300 mg three times per day (G5). Postoperative GBP or placebo was continued for four days after surgery. Two hours before surgery, all patients received celecoxib 400 mg. Based on the above groupings, patients in G1 received placebo medication, whereas patients in G2, G3, G4 and G5 received gabapentin 600 mg 2 h preoperatively. All patients received femoral and sciatic nerve blocks, followed by spinal anesthesia. Beginning in the postanesthetic care unit, all patients received a regimen of celecoxib 200 mg every 12 h for four days and a patient-controlled morphine analgesia pump for 48 h. RESULTS Thirty-six patients (G1, n=7; G2, n=7; G3, n=8; G4, n=7; G5, n=7) completed the study. Data were analyzed by one-way ANOVA followed by a contrast comparing patients who received postoperative GBP (G3, G4 and G5) (n=22) with patients who received placebo postoperatively (G1 and G2) (n=14). Patients who received GBP postoperatively used significantly less patient-controlled morphine analgesia at 24 h, 36 h and 48 h (P<0.05). The postoperative GBP patients had significantly better active assisted knee flexion on postoperative days 2 and 3, with a trend toward better flexion on postoperative day 4. Patients who received GBP postoperatively reported less pruritus than patients who received placebo. There were no differences in pain scores. CONCLUSIONS These results support the use of GBP in the acute postoperative period. Further trials are needed to delineate the optimal dose, timing and duration of GBP use following surgery.
A qualitative study of an electronic health record : perspective on planning objectives and implementation at King Faisal Specialist Hospital & Research Centre (KFSH & RC), Saudi Arabia

The patient health record is an essential information source for management and delivery of patient care services. Paper-based records are problematic with the issues, such as illegibility, missing data, double data entry, and difficulty with information retrieval. Thanks to the advent of the Health Insurance Portability and Accountability Act (HIPAA), which the Kingdom of Saudi Arabia introduces as part of healthcare reform, the local healthcare system employed Electronic Health Record (EHR) in order to enhance accountability and efficiency. The King Faisal Specialist Hospital & Research Centre (KFSH & RC) was the first organization to implement the EHR. The article explored the actual impact of EHR within KFSH & RC, as well as the issues surrounding the implementation of EHR. It evaluated the role of senior managers in the EHR planning. Qualitative research was chosen using interpretative phenomenology as the selected methodology. Information for the study was collected using semi-structured interviews with four senior managers and six patients. Three focus group interviews were also conducted with six healthcare provider middle managers in each group. The total sample was twenty eight participants. The study identified three categories of impact, including positive and negative issues affecting the staff, patients, and KFSH&RC organization.
Nitric Oxide Releases Calcitonin-Gene-Related Peptide from Rat Dura mater Encephali Promoting Increases in Meningeal Blood Flow

Nitric oxide (NO) and calcitonin-gene-related peptide (CGRP) are implicated in the pathophysiology of vascular headaches. We studied the interaction of these two vasodilatory mediators in an animal model and suggest that NO may increase meningeal blood flow not only by its direct vasodilatory action but also by stimulating CGRP release. First, CGRP release from the rat cranial dura mater was measured in vitro using an enzyme immunoassay. Hemisected skulls with adhering dura mater were filled with synthetic interstitial fluid and stimulated with the NO donor diethylamine-NONOate (10–5–10–3M) or with NO gas (1,000 ppm), which caused concentration-dependent increases in CGRP release up to 166.8%. Second, meningeal blood flow was recorded in vivo in the exposed dura mater using laser Doppler flowmetry. Topical application of the NO donors NONOate, S-nitroso-N-acetylpenicillamine and N-ethyl-2-(1-ethyl-2-hydroxy-2-nitrosohydrazino)-ethenamine (10–5–10–3M) caused concentration-dependent increases in blood flow. These increases were significantly reduced by local preliminary application of the CGRP receptor antagonist CGRP8–37 (10–4M). We conclude that NO stimulates the release of CGRP from dural afferents. The blood-flow-increasing effect of NO seems to be partly mediated by CGRP. The interaction of NO and CGRP may be relevant for the development of vascular headaches.
Lung infections in cystic fibrosis: deriving clinical insight from microbial complexity

Lower respiratory tract bacterial infections, such as those associated with cystic fibrosis lung disease, represent a major healthcare burden. Treatment strategies are currently informed by culture-based routine diagnostics whose limitations, including an inability to isolate all potentially clinically significant bacterial species present in a sample, are well documented. Some advances have resulted from the introduction of culture-independent molecular assays for the detection of specific pathogens. However, the application of bacterial community profiling techniques to the characterization of these infections has revealed much higher levels of microbial diversity than previously recognized. These findings are leading to a fundamental shift in the way such infections are considered. Increasingly, polymicrobial infections are being viewed as complex communities of interacting organisms, with dynamic processes key to their pathogenicity. Such a model requires an analytical strategy that provides insight into the interactions of all members of the infective community. The rapid advance in sequencing technology, along with protocols that limit analysis to viable bacterial cells, are for the first time providing an opportunity to gain such insight.