Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunohistochemical characterization of early and advanced knee osteoarthritis by NF‐κB and iNOS expression

This study was performed to determine the differences in grade of synovitis and expression of NF‐κB and iNOS in knee synovial membrane between early and advanced stage of osteoarthritis (OA). Thirty synovial membrane intra‐operative biopsies of patients (ten controls, ten with early and ten with advanced OA according to Kellgren–Lawrence radiological score) were immunohistochemically (NF‐κB and iNOS) and hystologically (Krenn synovitis score) analyzed and correlated to WOMAC clinical score and pain duration. Krenn synovitis score of patients with radiologically early OA was significantly higher than in patients with advanced OA (p < 0.001). NF‐κB expression in both synovial intima (p < 0.001) and subintima (p < 0.001) was also higher in early OA. iNOS expression in subintima was significantly higher in early than in advanced OA (p < 0.001), while in intima iNOS showed no statistical difference between groups (p = 0.07). The lymphocytic nodules, located in synovial subintima, were significantly higher in advanced OA when compared to early OA (p = 0.006) and the control group (p < 0.001). These results suggest that in early OA, there is a localized inflammation of the synovial membrane with high expression of NF‐κB and iNOS. In advanced OA, number of expressed factors is reduced, with the exception of intima cells that highly express iNOS, reflecting the ongoing localized inflammatory process of lower degree. In advanced OA, the density of the resident cells is reduced and lymphocytic nodules appear, confirming the important role of adaptive immunity in later OA stage. Clinical significance of this study is better understanding possibilities of preventive measures for synovitis and OA advancement. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:1990–1997, 2017.
Comment on: urinary tract infections in general practice patients: diagnostic tests versus bacteriological culture.

1. Kern WV, Steib-Bauert M, de With K. Comment on: Hospital consumption of antibiotics in 15 European countries: results of the ESAC Retrospective Data Collection (1997–2002). J Antimicrob Chemother 2006; 58: doi:10.1093/jac/dkl344. 2. Vander Stichele RH, Elseviers MM, Ferech M et al. Hospital consumption of antibiotics in 15 European countries: results of the ESAC Retrospective Data Collection (1997–2002). J Antimicrob Chemother 2006; 58: 159–67.
An Information System for Judicial and Public Administration Using Artificial Intelligence and Geospatial Data

The adoption of information technology in judicial and public administration has become a major need nowadays with the rapid growth of information regarding managerial issues. This paper presents an advanced methodology developed by using Information and Communication Technologies (ICT) and artificial intelligence to support decision making in public and judicial administration. A prototype Management Information System for public administration (MISPA) was developed to provide a computerized way of managing geospatial urban, environmental and crime data of an urban area. This system was developed by using several programming languages, a Database Management System (DBMS) and other technologies and programming tools. The proposed system was developed aiming at the systemization and modernization of public, judicial and police authorities that are associated with issues that have to be dealt by studying urban data regarding crime and environmental data and supports decision making based on crime forecasting.
Causal inference by using invariant prediction: identification and confidence intervals

What is the difference between a prediction that is made with a causal model and that with a non‐causal model? Suppose that we intervene on the predictor variables or change the whole environment. The predictions from a causal model will in general work as well under interventions as for observational data. In contrast, predictions from a non‐causal model can potentially be very wrong if we actively intervene on variables. Here, we propose to exploit this invariance of a prediction under a causal model for causal inference: given different experimental settings (e.g. various interventions) we collect all models that do show invariance in their predictive accuracy across settings and interventions. The causal model will be a member of this set of models with high probability. This approach yields valid confidence intervals for the causal relationships in quite general scenarios. We examine the example of structural equation models in more detail and provide sufficient assumptions under which the set of causal predictors becomes identifiable. We further investigate robustness properties of our approach under model misspecification and discuss possible extensions. The empirical properties are studied for various data sets, including large‐scale gene perturbation experiments.
Response Patterns of Single Neurons in the Tortoise Olfactory Epithelium and Olfactory Bulb

The responses to odor stimulation of 40 single units in the olfactory mucosa and of 18 units in the olfactory bulb of the tortoise (Gopherus polyphemus) were recorded with indium-filled, Pt-black-tipped microelectrodes. The test battery consisted of 27 odorants which were proved effective by recording from small bundles of olfactory nerve. Two concentrations of each odorant were employed. These values were adjusted for response magnitudes equal to those for amyl acetate at –2.5 and –3.5 log concentration in olfactory twig recording. Varying concentrations were generated by an injection-type olfactometer. The mucosal responses were exclusively facilitory with a peak frequency of 16 impulses/sec. 19 mucosal units responded to at least one odorant and each unit was sensitive to a limited number of odorants (1–15). The sensitivity pattern of each unit was highly individual, with no clear-cut types, either chemical or qualitative, emerging. Of the 18 olfactory bulb units sampled, all responded to at least one odorant. The maximum frequency observed during a response was 39 impulses/sec. The bulbar neurons can be classified into two types. There are neurons that respond exclusively with facilitation and others that respond with facilitation to some odorants and with inhibition to others. Qualitatively or chemically similar odorants did not generate similar patterns across bulbar units.
Microscale Quantitative Analysis of Polyhydroxybutyrate in Prokaryotes Using IDMS

Poly(3-hydroxybutyrate) (PHB) is an interesting biopolymer for replacing petroleum-based plastics, its biological production is performed in natural and engineered microorganisms. Current metabolic engineering approaches rely on high-throughput strain construction and screening. Analytical procedures have to be compatible with the small scale and speed of these approaches. Here, we present a method based on isotope dilution mass spectrometry (IDMS) and propanolysis extraction of poly(3-hydroxybutyrate) from an Escherichia coli strain engineered for PHB production. As internal standard (IS), we applied an uniformly labeled 13C-cell suspension, of an E. coli PHB producing strain, grown on U-13C-glucose as C-source. This internal 13C-PHB standard enables to quantify low concentrations of PHB (LOD of 0.01 µg/gCDW) from several micrograms of biomass. With this method, a technical reproducibility of about 1.8% relative standard deviation is achieved. Furthermore, the internal standard is robust towards different sample backgrounds and dilutions. The early addition of the internal standard also enables higher reproducibility and increases sensitivity and throughput by simplified sample preparation steps.
Pleistocene geochronology and palaeothermometry from protein diagenesis in ostrich eggshells: implications for the evolution of modern humans.

Proteinaceous residues incorporated within the crystal structure of ostrich eggshells (OES) are retained without loss over geological time exceeding 10 million years. Degradation of the polypeptides, including hydrolysis to smaller peptide fragments and eventual release of free amino acids, decomposition, and racemization and epimerization occur at regular, predictable rates dependent on ambient temperature. The extent of isoleucine epimerization (aIle/Ile ratio) in OES follows linear first-order reversible kinetics in controlled-temperature laboratory simulations of time up to an aIle/Ile ratio in excess of 1.0. The hydrolysis of leucine also follows a predictable pattern, but deviates from first-order kinetics. A nonlinear mathematical model has been developed that adequately describes the pattern of leucine hydrolysis through a wide temperature range. Arrhenius parameters were derived from laboratory experiments combined with rate constant values found for 14C-dated OES from stratified caves in southern Africa. These parameters for isoleucine epimerization and leucine hydrolysis differ by ca. 10%, allowing the simultaneous solution of the two equations for temperature, independent of sample age. Although the uncertainty of the simultaneous temperature is relatively high (+/- 10 degrees C), it provides an effective means of identifying burned samples. If sample age is known, palaeotemperatures (the integrated thermal history experienced by an eggshell as opposed to an 'instantaneous' temperature) can be calculated with a precision of better than +/- 1 degrees C. The ages of levels at Border Cave, South Africa, from which anatomically modern human skeletal remains have been recovered, are dated by the extent of isoleucine epimerization in associated OES. (ABSTRACT TRUNCATED AT 250 WORDS)
A defensin‐like gene expressed in the black‐legged tick, Ixodes scapularis

Abstract. The black‐legged tick Ixodes scapularis Linnaeus (Acari: Ixodidae) is an important vector of microbial pathogens. Knowledge of the tick's innate immune response, particularly defensin and other antimicrobial peptides, is important for understanding how microbes survive in this tick. A defensin gene (slnA) from I. scapularis was obtained by reverse transcription–polymerase chain reaction (RT–PCR) using mRNA extracted from tissues of female ticks. RT–PCR indicated the gene was expressed in the midgut, haemocytes, and fat‐body, although no evidence of a peptide was found. Sequencing a cloned cDNA fragment revealed a 225 bp open reading frame encoding a 74 amino acid pre‐prodefensin, including the putative 38 amino acid mature peptide. Similarity between the defensin amino acid sequences of I. scapularis and Dermacentor variabilis (Say) (Acari: Ixodidae) was 62.2% for the pre‐prodefensin region; for the mature defensins from these two species the similarity was 78.9%, with the six cysteine residues being located in the same relative position. PCR amplification and sequencing of chromosomal DNA suggests that slnA, along with vsnA, the defensin gene from D. variabilis, does not contain any introns. This is in contrast to the defensins described for the soft tick, Ornithodoros moubata (sensu Walton) (Acari: Argasidae). The role of defensin in the innate immune response of I. scapularis following microbial invasions is discussed.
Double mutant MRL‐lpr/lpr‐gld/gld cells fail to trigger lpr‐graft‐versus‐host disease in syngeneic wild‐type recipient mice, but can induce wild‐type B cells to make auto‐antibody

Lethally irradiated mice reconstituted with histocompatible stem cells from Fas‐deficient MRL/lpr mice develop a wasting syndrome reminiscent of chronic graft‐versus‐host disease. However, reconstitution with double Fas‐/Fas ligand (FasL)‐deficient stem cells does not result in wasting disease, demonstrating that FasL expression is an important component of the effector mechanisms leading to this syndrome. In the absence of wasting disease double‐deficient T cells can induce wild‐type B cells to make autoantibodies. These data indicate that autoantibody production is regulated by FasL‐expressing T cells, and that Fas‐sufficient wild‐type B cells differ from Fas‐deficient lpr cells only with regard to their sensitivity to FasL.
Parameters of pulmonary injury after total or partial cardiopulmonary bypass.

BACKGROUND We have established that thromboxane B2 (TX) blood levels increase across the pulmonary circulation after total cardiopulmonary bypass (CPB) but not after partial CPB. In the present study, we used the same model and examined the parameters of pulmonary injury after total or partial CPB. METHODS AND RESULTS Fourteen anesthetized sheep were placed on total CPB (n = 7), without ventilation and with occlusion of the pulmonary artery, or partial CPB (n = 7), with ventilation and an open pulmonary artery. After 90 minutes, the sheep were separated from CPB, and the pulmonary artery was perfused normally. After 30 minutes, we elevated left atrial pressure in all sheep. Plasma TX, plasma leukotriene B4, platelet counts, white blood cell counts, and plasma protein concentration were measured before CPB and every 15 minutes after CPB for 1 hour. The right and left atrial blood samples were obtained simultaneously. Pulmonary arterial pressure, left atrial pressure, and pulmonary arterial flow were measured. Pulmonary vascular resistance (PVR) was calculated for 30 minutes after CPB. Lung lymph protein, TX, leukotriene B4, and flow were measured before CPB and every 30 minutes after CPB for 1 hour. Pulmonary biopsies and bronchoalveolar lavage fluid were obtained before CPB and at the end of the experiment. After total CPB, levels of TX across the pulmonary circulation increased significantly, but leukotriene B4 remained constant. Platelets and white blood cells were consumed across the pulmonary circuit after total CPB but not after partial CPB. PVR increased by 170%, lymph flow increased by 233%, lung water content increased by 15%, and the ratio of lymph to plasma protein decreased by 20% after total CPB, but similar changes did not occur after partial CPB. CONCLUSIONS During total CPB, the lungs are totally dependent on oxygen supply provided by nonpulsatile bronchial arterial flow. Lung injury seen with restoration of pulmonary artery flow and ventilation may be the result of an inflammatory response associated with TX elevation after a period of relative pulmonary ischemia. Pulmonary injury was not seen after less severe pulmonary arterial flow deprivation, with maintenance of ventilation (partial CPB). Although the specific cause is undetermined from these data, the occurrence of elevated TX levels and lung damage after total CPB is clearly established.
Methods Paper : An improved surface sterilization technique for introducing leaf , nodal and seed explants of Aquilaria malaccensis from field sources into tissue culture

* Author for correspondence: Rozi Mohamed, Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. Tel. : 60-3-8946 7183 (Office), Fax: 60-3-8943 2514. Email: rozimohd@putra. upm.edu. my. Abstract. A critical stage in the introduction of plants into tissue culture is to obtain cultures free from microbial contamination. This study investigated different sterilization regimes for leaf and nodal explants from Aquilaria malaccensis grown in the shade house under natural environmental conditions, and for seeds from wild mature trees. We found that pre-sterilization using 0.2% Benomyl for 15 minutes improved the number of ‘clean and alive’ individuals of all types of explants, especially when followed by surface sterilization using mercury chloride (HgCl2). Treatment with 0.1 % HgCl2 for 15 and 30 seconds yielded the best results for leaf and nodal explants, respectively. Maximum percentage of ‘clean and alive’ seeds was observed when using 0.2 % HgCl2 for 12 minutes. Treatment with Clorox® bleach (5.25% sodium hypochlorite as the active ingredient) even at high concentration (50% Clorox®) alone was not sufficient to control fungal and bacterial contamination in the explants. We conclude that HgCl2 coupled with Benomyl pre-treatment produced a highly efficient sterilization method producing 83 – 90% ‘clean’ leaf, nodal and seed explants of A. malaccensis from natural sources after fourteen days in culture.
Who Participates in the Dutch Chlamydia Screening? A Study on Demographic and Behavioral Correlates of Participation and Positivity

Background: In the Netherlands, an Internet-based Chlamydia Screening Implementation was initiated in 3 regions, aiming to reduce population prevalence by annual testing and treatment of people aged 16 to 29 years. We studied who was reached in the first screening round by relating participation and chlamydia positivity to sociodemographic and sexual risk factors. Methods: Data from the 2008/2009 screening round were analyzed (261,025 screening invitations, 41,638 participants). Participation rates were adjusted for the sexually active population. Sociodemographic and behavioral correlates of screening participation and positivity were studied by (multilevel) logistic regression models. Results: The overall adjusted participation rate in the first screening round was 19.5% (95% confidence interval, 19.4–19.7) among sexually active people (women, 25%; men, 13%). Sociodemographic factors associated with lower participation were male gender (odds ratio [OR], male 1 vs. female 1.8), young age (OR, 16–19 1 vs. older groups 1.7–2.1), non-Dutch origin (OR between 0.7–0.9), lower education (OR, low 1 vs. high 1.4), high community risk level (0.8), and low socioeconomic status (0.9). Behavioral factors associated with lower participation were a long-standing relationship (0.7) and no reported history or symptoms of sexually transmitted infections (no symptoms, 0.4–0.6) . Factors most strongly related to higher Ct positivity were young age (OR, 1 vs. older groups 0.5–0.8), non-Dutch origin (1.4–2.8), non-Dutch steady partner (1.9–2.7), residence in a high-risk area (1.4–1.5), lower education (high, 0.3–0.5), and a history or symptoms of sexually transmitted infection (no symptoms, 0.4–0.6). Conclusions: Sociodemographic factors associated with lower participation were also associated with higher Ct positivity, showing that high-risk demographic groups are more difficult to mobilize than low-risk groups. Independent of this, higher behavioral risk levels were associated with higher participation rates, suggesting self-selection for screening based on the persons' risk (perception) in both low- and high community risk groups. Our study shows the complexity of the process, including individual and community factors that also interact, when screening for chlamydia.
A comparison of pregnant subgroups with positive 50-gram glucose challenge test results to those with negative results in terms of obstetric and perinatal outcomes.

AIM To compare the pregnant subgroups with positive 50-gram glucose challenge test results to those with negative results in terms of obstetric and perinatal outcomes. METHODS A total number of 977 pregnant women were included in the study. A glucose challenge test was performed for all pregnant women. Subsequently, 3 hours 100 gram oral glucose tolerance test was performed for the patients who had a positive test. According to 50-gram glucose challenge test 1st hour glucose values, the patients were categorized into 5 subgroups (less 140, 140-159, 160-179, 180-199 and ≥200). Also, the patients, whose 3 hours 100 gram oral glucose tolerance tests were positive, as well as those diagnosed with impaired glucose tolerance, were included in Group 5. All the groups were compared in terms of obstetric and perinatal outcomes. RESULTS Cut-off scores of 50-gram glucose challenge test were found to be 153.5 mg/dl. It was observed that the glycemic values increased as the mean of delivery week decreased. The differences between all groups were found to be statistically significant with regard to macrosomia, large for gestational age, presentation anomalies, polyhydramnios, ablatio placentae, preeclampsia and gestational hypertension. Increase in the rate ratio was observed for the glycemic values, they got higher. The results showed statistically significant differences between all groups in terms of neonatal hospitalizations after birth and observation rates. CONCLUSION The patients with a 50-gram glucose challenge test 1st hour glucose values of 180 mg/dl or higher are associated with poor perinatal and fetal outcomes.
Noni (Morinda citrifolia) Modulates the Hypothalamic Expression of Stress- and Metabolic-Related Genes in Broilers Exposed to Acute Heat Stress

Heat stress (HS) adversely affects growth performance and inflicts heavy economic losses to the poultry industry. There is, therefore, a critical need to identify new alternative strategies to alleviate the negative effects induced by HS. The tropic medicinal plant, Morinda citrifolia (Noni), is being used in livestock nutrition, however the literature is limited and conflicting for its impact on growth performance. The present study aimed to determine the effect of Noni on feeding and drinking behavior as well as on the hypothalamic expression of stress- and metabolic-related genes in broiler chickens exposed to acute HS. A total of 480 1 day-old male broiler chicks were randomly assigned to 12 controlled environmental chambers. Birds were subjected to two environmental conditions (TN, 25°C vs. HS, 35°C for 2 h) and fed two diets (control vs. 0.2% Noni) in a 2 × 2 factorial design. Feed intake and core body temperature (BT) were recorded during HS period. Blood was collected and hypothalamic tissues were harvested for target gene and protein analyses. Acute HS-broilers exhibited higher BT (~1°C), spent less time eating with a significant decrease in feed intake, and spent more time drinking along with higher drinking frequency compared to those maintained under TN conditions. Although Noni supplementation did not improve feed intake, it significantly delayed (~30 min) and reduced the BT-induced by HS. At molecular levels and under HS conditions, Noni supplementation down regulated the hypothalamic expression of HSP90 and its related transcription factors HSF1, 2, and 4, increased orexin mRNA levels, and decreased the phosphorylation levels of AMPKα1/2Thr172 and mTORSer2481. Together, these data indicated that Noni supplementation might modulate HS response in broilers through central orexin-AMPK-mTOR pathways.
bFGF Stimulates GAP-43 Phosphorylation at Ser41 and Modifies Its Intracellular Localization in Cultured Hippocampal Neurons

Cultured hippocampal neurons have been used to study GAP-43 phosphorylation and subcellular distribution. By immunofluorescence, GAP-43 was found associated with adherent membrane patches that remained attached to the substratum after in situ permeabilization with Nonidet-NP40. This association increases during neuronal development and is stabilized by the actin cytoskeleton. Basic fibroblast growth factor (bFGF) promotes GAP-43 translocation from the cytosol to adherent membrane patches and, at the same time, stimulates GAP-43 phosphorylation, mainly at the protein kinase C (PKC) site (Ser41). Inhibition of PKC prevented bFGF-stimulated GAP-43 phosphorylation and translocation, while activation by phorbol esters mimicked bFGF effects, suggesting that phosphorylation at Ser41 regulates GAP-43 subcellular localization. Using biochemical fractionation and phosphorylation analysis, it was found that Ser41 phosphorylation was highest in cytoskeleton-associated GAP-43 and lowest in membrane-associated GAP-43. It is proposed that GAP-43 is continuously cycling between intracellular compartments depending on its phosphorylation state and could be taking part in initial adhesive complexes assembled during growth cone advance.