Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of the Homodimeric Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803 Suggests a Mechanism for Redox Regulation*

Background: Glycine decarboxylase (P-protein) is essential for many vital processes, including nucleotide biosynthesis and photosynthesis. Results: Disulfide formation drives conformational changes that inactivate the cyanobacterial P-protein, a model for plant and human glycine decarboxylase. Conclusion: Glycine decarboxylase activity is regulated by cellular redox homeostasis. Significance: This is the first molecular model for redox regulation of glycine decarboxylase. Glycine decarboxylase, or P-protein, is a pyridoxal 5′-phosphate (PLP)-dependent enzyme in one-carbon metabolism of all organisms, in the glycine and serine catabolism of vertebrates, and in the photorespiratory pathway of oxygenic phototrophs. P-protein from the cyanobacterium Synechocystis sp. PCC 6803 is an α2 homodimer with high homology to eukaryotic P-proteins. The crystal structure of the apoenzyme shows the C terminus locked in a closed conformation by a disulfide bond between Cys972 in the C terminus and Cys353 located in the active site. The presence of the disulfide bridge isolates the active site from solvent and hinders the binding of PLP and glycine in the active site. Variants produced by substitution of Cys972 and Cys353 by Ser using site-directed mutagenesis have distinctly lower specific activities, supporting the crucial role of these highly conserved redox-sensitive amino acid residues for P-protein activity. Reduction of the 353–972 disulfide releases the C terminus and allows access to the active site. PLP and the substrate glycine bind in the active site of this reduced enzyme and appear to cause further conformational changes involving a flexible surface loop. The observation of the disulfide bond that acts to stabilize the closed form suggests a molecular mechanism for the redox-dependent activation of glycine decarboxylase observed earlier.
Genetic Map Position of the Gluconate-6-Phosphate Dehydrogenase Gene in Salmonella typhimurium

Gluconate-6-phosphate dehydrogenase (GND) is genetically determined in Salmonella typhimurium by a locus (gnd) mapping between the somatic antigen (rfb) and histidine (his) operons. The enzyme is constitutive. Strains of Salmonella carrying an F′ genetic element which contains the gnd+ gene have GND activity two to three times that of the wild type. This gene dosage effect was used to determine that the GND reaction is not rate-limiting for the metabolism of glucose by the pentose shunt in S. typhimurium.
USE OF THE PRESSURE JUMP BOUNDARY CONDITION IN THE HIGH SPEED RAREFIED GAS FLOWS

The simulation of rarefied gas flow in hypersonic aerodynamics is important for the design of space and re-entry vehicles. Computer simulations can provide the necessary aerodynamic data at less cost and for cases where experiments are difficult to conduct. Therefore, there is a constant effort to develop newer numerical methods and to improve the existing ones based on appropriate physical modeling, so as to make the computer simulations closer to reality. CFD methods are preferred for rarefied flows in the continuum and slip flow regime. The range 0.001 ≤ Kn ≤ 0.01 is called the slip regime, where the no-slip conditions are no longer applicable. The no-slip boundary conditions are replaced in this regime with slip velocity and temperature-jump boundary conditions.
A new species of nocturnal gecko , genus Paroedura , from the karstic Tsingy de Bemaraha formation in western Madagascar

We describe the new gecko species Paroedura neglecta sp. n. from the Tsingy de Bemaraha National Park in western Madagascar, belonging to the P. bastardi/tanjaka clade. The species in this clade are characterized by three light dorsal crossbands on the dorsum of juveniles and subadults whereas all other Paroedura species have four such bands. The new species differs from all species in the P. bastardi complex in having the nostril in contact with the rostral scale. It is most similar to the sympatric P. tanjaka, from which it differs by the presence of prominent dorsal tubercles arranged in regular longitudinal rows (versus rather irregular rows of dorsal tubercles), smaller size, details of the dorsal colour pattern and strong genetic divergence.
Grasped Element Position Recognition and Robot Pose Adjustment during Assembly

– Upgrading building envelopes with fully prefabricated 2D modules requires high accuracy during the manufacturing process with tolerances lower than 1 mm. In the research described in this paper, computer designed and accurately manufactured objects have been assembled with robotic arms. However, in previous phases, it was detected that during the assembly process, the placement differed from the planned location due to undesired deviations of the object while being grasped and placed by the robotic tool. The experiments presented in this paper imply correcting this deviation by localizing the grasped object’s position and recalculating the path and final pose of the assembly process. For localizing the deviated grasped object’s location, an intermediate pose was planned. During this pose, the location of the grasped object was estimated by two different means. For the first solution, visual markers have been placed on a known corner of the objects and these have been recognized with a camera. For the second solution, the coordinates of the objects were measured by a digital theodolite. The location of the deviated object was calculated and compared to the planned location so the robot could divert from its original path. The measurable parameter in the experiments was the assembly accuracy. The results in the two experiments have been analyzed and compared. According to the results, the solutions could be implemented not only in the factory, but at on-site processes as well.
Achieving Safety

Conceptualizations of safer sex practices among young gay men (YGM) are frequently structured around communication between partners and the subsequent utilization or absence of condoms in a sexual encounter. Drawing on a sample of 34 in-depth interviews with YGM, ages 18 to 24, the authors explore the ways in which conceptualizations and definitions of safer sex are discussed and enacted. Placing attention on their safer sex practices, the authors analyze the conversations that do and do not occur among YGM and their partners, including the strategies (e.g., negotiated safety, condom communication and negotiation) that are commonly perceived as most useful by YGM. The authors provide recommendations regarding how to craft safer sex messages for YGM by considering their competing demands.
Reexamining Real Interest Rate Parity

Much research has investigated the real interest rate parity (RIRP) hypothesis that argues that real interest rates should equalize across countries. However, the empirical findings have been mixed. Early results, assuming stationarity of real rates, rejected the hypothesis. However, more recent tests that assume real rates to be nonstationary have found more support for RIRP. The objective of this paper is to consider whether the inconclusive results of previous RIRP tests may stem from the different approaches used in constructing real interest rates. The results for six different methods for calculating the real interest rate indicate that unit root results are very sensitive to how the real interest rate is computed. Testing 36 different bivariate combinations of the real interest rates in four OECD countries we find very limited support for the RIRP hypothesis. Furthermore, we also find very limited support for the existence of a world interest rate when we test the real rates jointly as a group.
SCENARIO BASED GROUND MOTION SIMULATIONS FOR ASSESSING THE SEISMIC HAZARD IN İZMIR, TURKEY

Collision of the Arabian and African plates with Eurasia forces the Anatolian micro-plate to move west-wards. In the Aegean Sea, the Anatolian micro-plate rotates counter-clockwise and extends due to the subduction zone along the Hellenic Arc. This deformation results in reactivation of faults on the west coast of Turkey, which results in destructive earthquakes. İzmir, the third largest city in Turkey, has been destroyed by (large) earthquakes several times in recent history, latest in 1778. In this study, a deterministic seismic hazard analysis is conducted based on ground motion simulations for nine different earthquake rupture scenarios for recognized faults in the area surrounding İzmir. The method adopted is a hybrid broad-band ground motion simulation technique, which has previously been validated. The earthquake scenarios are based on existing knowledge of source parameters, local as well as regional. Among the various faults surrounding İzmir, the largest peak ground motions are associated with two faults, the İzmir fault (normal) which lies underneath the city and the Tuzla fault (strike-slip) which lies southwest of the city. The results indicate that a rupture on the 42 kilometer long İzmir fault can produce ground acceleration as high as 0.3 g on bedrock level in the center of İzmir. Considering the site effect potential in the area, this value needs to be treated as the lower threshold. The simulation results indicate that the historic events that have caused severe destruction in İzmir most likely have occurred on either the İzmir or the Tuzla faults. Furthermore the attenuation of the simulated ground motions agrees well with empirical relations as far as peak ground accelerations are concerned.
Locally testable cyclic codes

Cyclic linear codes of block length n over a finite field F/sub q/ are the linear subspaces of F/sub q//sup n/ that are invariant under a cyclic shift of their coordinates. A family of codes is good if all the codes in the family have constant rate and constant normalized distance (distance divided by block length). It is a long-standing open problem whether there exists a good family of cyclic linear codes based on F.J. MacWilliams and N.J.A. Sloane (1977). A code C is r-testable if there exist a randomized algorithm which, given a word x /spl isin/ F/sub q//sup n/, adaptively selects r positions, checks the entries of x in the selected positions, and makes a decision (accept or reject x) based on the positions selected and the numbers found, such that (i) if x /spl isin/ C then x is surely accepted; (ii) if dist(x,C) /spl ges/ /spl epsi/n then x is probably rejected (dist refers to Hamming distance). A family of codes is locally testable if all members of the family are r-testable for some constant r. This concept arose from holographic proofs/PCPs. O. Goldreich and M. Sudan (2002) asked whether there exist good, locally testable families of codes. In this paper we address the intersection of the two questions stated.
Chapter 13 Specialized Surgical Platforms

A large fraction of the burden of disease comprises conditions that are potentially amenable to surgical intervention (chapters 1 and 2) (Bickler and others 2015; Mock and others 2015). The proportion is higher in lowand middle-income countries (LMICs) (Shrime, Sleemi, and Ravilla 2014). Because of difficulties in access to surgical care—often due to issues of cost, transportation, infrastructure, and a lack of providers (Chao and others 2012; Ilbawi, Einterz, and Nkusu 2013; Knowlton and others 2013; Linden and others 2012)—this surgical burden is sometimes borne by the international charitable sector. Historically, first-level hospitals in LMICs have tended primarily to treat conditions associated with a low disability-adjusted life year (DALY) burden. These hospitals have done so with a high loss to follow-up; patients scheduled for surgeries often do not return for their operations (Ilbawi, Einterz, and Nkusu 2013), especially as the complexity and up-front costs of the surgeries increase. Meanwhile, charitable sector involvement has grown rapidly: the charitable sector in the United States, which includes many international charitable surgical organizations, has grown at a pace exceeding the growth of gross domestic product by 20 percent and is currently larger than its counterpart agriculture, construction, transportation, and utilities sectors (Casey 2007). Médecins Sans Frontières (also known as Doctors Without Borders) alone has an annual budget of more than US$700 million, much of which comes from private funders (McCoy, Chand, and Sridhar 2010). This review focuses specifically on the charitable sector’s role in the delivery of surgical care in LMICs. This chapter uses the World Health Organization’s (WHO’s) six geographical regions: African Region, Region of the Americas, South-East Asia Region, European Region, Eastern Mediterranean Region, and Western Pacific Region.
Circulating levels of adiponectin and leptin in patients with prostate cancer

Prostate cancer (PCa) is one of the major health care problems in males. It is known that red and processed meat consumption, fat intake and obesity are risk factors for PCa development. Adiponectin and leptin are adipokines that are synthesized in visceral adipose tissue and associated with obesity. Up to date, the association of serum adiponectin and leptin with PCa largely remains unexplored. Therefore, we studied the concentration of adiponectin and leptin in PCa patients in Chinese population. 92 prospective cases of prostate cancer and 92 matched healthy controls were enrolled in this study. Serum adiponectin and leptin levels were detected by enzymelinked immunosorbent assays (ELISA) technique. No statistically significant differences were observed in age, bodymass index (BMI), prostate specific antigen (PSA), fasting blood glucose (FBG), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), total cholesterol (TC), triglycerides (TG), creatinine (CRE), and blood urea nitrogen (BUN) in the paired groups. Both serum adiponectin and leptin levels were significantly higher in patients with PCa compared to healthy controls (P<0.001 for both). Subsequently, there was a positive correlation between adiponectin and PSA (r=0.285, P<0.001). Positive significant correlations between BMI, PSA, TG and leptin were also observed in whole group (r=0.270, P<0.001; r=0.348, P<0.001; r=0.170, P=0.021, respectively). However, the serum adiponectin and leptin levels were not related to the Gleason score of PCa. Receiver operating characteristic curves analysis of the investigated serum adiponectin differentiated cancer patients from the healthy individuals with a sensitivity of 87%, specificity of 56%. Leptin levels also distinguished patients from the healthy controls with a sensitivity of 69%, specificity of 68%. Our study shows that the serum levels of adiponectin and leptin in PCa patients were higher than healthy controls. Adiponectin and leptin may be important markers of PCa. For validation, further studies including large cohort studies would be required.
Molecular cloning of CLC chloride channels in Oreochromis mossambicus and their functional complementation of yeast CLC gene mutant.

We have cloned two members of the CLC chloride channel family (OmCLC-3 and OmCLC-5) from gill cDNA libraries of the euryhaline tilapia Oreochromis mosammbicus. At the amino acid level, OmCLC-3 is 90.5% identical to rat CLC-3 and OmCLC-5 is 79.2% identical to rat CLC-5. Ribonuclease protection assay revealed that OmCLC-5 was mainly expressed in the gill, kidney, and intestine in both freshwater- (FW) and seawater- (SW) adapted tilapia. Although the mRNA of OmCLC-3 was broadly expressed in tissues of FW- and SW-adapted tilapia, the most intense signals were observed in the gill, kidney, intestine, and brain. Injection of OmCLC-3 and OmCLC-5 cRNAs into Xenopus oocytes did not elicit chloride currents, but these clones did functionally complement the gef1 phenotype of YPH250(gef), a yeast strain in which a single CLC channel (GEF1) has been disrupted by homologous recombination. These results clearly indicated that CLC channels closely related to the mammalian CLC-3, -4, and -5 subfamily exist also in tilapia and that OmCLC-3 and OmCLC-5 function as intracellular chloride channels.
A 5-Year Epidemiological Study of Nosocomial Bloodstream Infections in a Neurosurgery Department

The characteristics of nosocomial bloodstream infections (BSIs) in a neurosurgical department were studied over a 5-year period. The rate of nosocomial BSI was 3.0%. Gram-negative bacteria were the most commonly isolated pathogens (65.9% of isolates). For all the pathogens isolated, the rate of resistance to commonly used antimicrobial agents was high. Of the 101 patients with nosocomial BSI, 50 (49.5%) died during their stay at the Department of Neurosurgery. At the same time, overall mortality rate among neurosurgical inpatients without nosocomial BSI was 5.4% (ie, 175 of 3,216 patients died).
N 94-16 03 : t Evaluation of a Distributed Catchment Scale Water Balance Model

The validit,, of some of the simplifying assumptions in a conceptual ,,_ater balance model is investigated b,, comparing simulation results from the conceptual model with simulation results from a three-dimensional physically based numerical model and vdth field observations. We examine, in particular, assumptions and simplilications related to water table d,,namics, vertical soil moisture and pressure head distributions+ and subsurface flow contributions to stream discharge. The conceptual model relies on a topographic index to predict saturation excess runoff" and on Philip's infiltration equation to predict infiltration excess runoff. The numerical model solves the three-dimensional Richards equation describing flow in variably saturated porous media, and handles seepage face boundaries, infiltration excess and saturation excess runoff production, and soil driven and atmosphere driven surface fluxes. The study catchments (a 7.2-km 2 catchment and a 0.64-km z subcatchment) are located in the North Appalachian ridge and valley region of eastern Pennsylvania. Hydrologic data collected during the M+*CHYDRO90 field experiment are used to calibrate the models and to evaluate simulation results. It is found that water table dynamics as predicted by the conceptual model are close to the observations in a shallow water well and therefore, that a linear relationship between a topographic index and the local water table depth is found to be a reasonable assumption for catchment scale modeling. However, the hydraulic equilibrium assumption is not valid for the upper 100 cm layer of the unsaturated zone and a conceptual model that incorporates a root zone is suggested. Furthermore. theoretical subsurface flow characteristics from the conceptual model are found to be different from field observations, numerical simulation results, and theoretical baseflow recession characteristics based on Boussinesq's groundwater equation.
Data Mining Performance in Identifying the Risk Factors of Early Arteriovenous Fistula Failure in Hemodialysis Patients

Background and Objectives: Arteriovenous fistula is a popular vascular access method for surgical treatment of hemodialysis patients. The method, however, is associated with a high rate of early failure varying in the range of 20-60%. Predicting early Arteriovenous fistula failure and its risk factors can help reduce its incidence, its hospitalization rate, and associated costs. In this study, we examined performance of data mining in the prediction of early AVF failure and identification of its risk factors. Methods: The data of 193 patients who underwent homodialysis in Hasheminejad Kidney Center were explored. Eight common attributes of the patients including age, sex, hypertension level, Diabetes Mellitus state, hemoglobin level, smoking behavior, location of Arteriovenous fistula, and thrombosis state were used in the machine learning process. Two learning operators including W-Simple Cart and WJ48 tree were used in data mining process. Findings: Smoking was identified as a factor influencing the relationship between the outcome of vascular access surgery and hemoglobin level. Prediction accuracy varied within the range of 69.15-85.11%. Conclusions: According to our results smoking is a crucial risk factor for early Arteriovenous fistula failure, even at normal levels of hemoglobin. Our results provide further supports for the notion that data mining can help medical decision-making process by deciphering the complex interactions between various biological variables and translating the hidden patterns in data into detailed decision-making criteria.
A novel hybrid first-line therapy for H . pylori eradication : results of a pilot study

Helicobacter pylori (H. pylori) eradication remains challenging in clinical practice. Current European guidelines recommend bismuth-based quadruple therapy for 10-14 days in geographic areas with a high prevalence of primary antibiotic resistance (> 20% for clarithromycin, or > 40% for metronidazole, or > 15% for dual resistance), such as Italy [1]. However, a large number of tablets are required for this therapy administered for 10-14 days: indeed, as many as 14 capsules daily are necessary, even if using the Pylera® package (bismuth subcitrate potassium 140 mg, metronidazole 125 mg, and tetracycline 125 mg). Moreover, some trials found that Pylera® causes side-effects leading to an earlier interruption more frequently than other regimens [2-4]. A shorter quadruple regimen might decrease the side-effects, but the efficacy might be reduced. Therefore, by loaning the concept of sequential therapy [5], a short course of amoxicillin-based dual therapy could prevent efficacy reduction of a short course of Pylera® therapy. Since this is a prospective, open-label, pilot study, a total of 30-40 patients are sufficient [6]. Consecutive adults complaining of dyspeptic symptoms referred for upper endoscopy between February and November 2018 were considered for recruitment into the study. Patients diagnosed for the first time with H. pylori infection at the histological assessment of gastric mucosa were invited to participate. A 10day hybrid therapy with esomeprazole 40 mg and amoxicillin 1 g, both b.i. d, was administered for the first 5 days, followed by esomeprazole 40 mg b.i. d. and Pylera 3 tablets q.i. d (after breakfast, lunch, dinner and before bedtime) for the following 5 days. Patients were instructed that the possible darkness of stools as well as the metallic taste during therapy were clinically irrelevant. At the end of the treatment, patients were invited for a visit to assess the compliance to therapy and the incidence of side-effects by a personal interview. Bacterial eradication LETTERS TO THE EDITOR
ANALYTICAL AND NUMERICAL INVESTIGATION OF DYNAMICALLY EXCITED DAMS WITH ICE-COVERED RESERVOIRS

This paper examines the dynamic response of a concrete dam impounding an ice-covered reservoir and subjected to forced vibration testing. The analytical research presented is a follow-up to an extensive dynamic testing program carried out on an 84-m high concrete gravity dam located in northeastern Quebec, Canada, under harsh winter conditions, including a 1.0 to 1.5-m-thick ice sheet covering the reservoir. One of the major challenges encountered when analyzing ice–dam–reservoir–foundation interaction is modelling the complex nature of the ice and the boundary conditions governing the icecovered reservoir motion. The problem is further complicated because there are little or no appropriate observational evidence relevant to ice–dam interaction processes. Some of these challenges are addressed herein using a two-dimensional analytical approach, which investigates the effect due to ice cover, the influence of water compressibility, foundation flexibility, and reservoir bottom absorption. A frequency domain substructure method technique is used and a new boundary condition along the ice-cover– reservoir interface is proposed. The technique developed is implemented in a finite element code specialized in the seismic analysis of concrete dams.