Miracle-dz/UniFAR-FTUs huggingface dataset:
NeuroD2 and neuroD3: distinct expression patterns and transcriptional activation potentials within the neuroD gene family

We have identified two new genes, neuroD2 and neuroD3, on the basis of their similarity to the neurogenic basic-helix-loop-helix (bHLH) gene neuroD. The predicted amino acid sequence of neuroD2 shows a high degree of homology to neuroD and MATH-2/NEX-1 in the bHLH region, whereas neuroD3 is a more distantly related family member. neuroD3 is expressed transiently during embryonic development, with the highest levels of expression between days 10 and 12. neuroD2 is initially expressed at embryonic day 11, with persistent expression in the adult nervous system. In situ and Northern (RNA) analyses demonstrate that different regions of the adult nervous system have different relative amounts of neuroD and neuroD2 RNA. Similar to neuroD, expression of neuroD2 in developing Xenopus laevis embryos results in ectopic neurogenesis, indicating that neuroD2 mediates neuronal differentiation. Transfection of vectors expressing neuroD and neuroD2 into P19 cells shows that both can activate expression through simple E-box-driven reporter constructs and can activate a reporter driven by the neuroD2 promoter region, but the GAP-43 promoter is preferentially activated by neuroD2. The noncongruent expression pattern and target gene specificity of these highly related neurogenic bHLH proteins make them candidates for conferring specific aspects of the neuronal phenotype.
Curcumin alleviates ischemia reperfusion-induced acute kidney injury through NMDA receptor antagonism in rats

Abstract Objective: The present study investigated the role of N-methyl-d-aspartate (NMDA) receptors in curcumin-mediated renoprotection against ischemia reperfusion (I/R)-induced acute kidney injury (AKI) in rats. Methods: Rats were subjected to bilateral renal I/R (40 min I, 24 hours R) to induce AKI. Kidney injury was assessed by measuring creatinine clearance, blood urea nitrogen, plasma uric acid, potassium level, fractional excretion of sodium, and macroproteinuria. Oxidative stress in renal tissues was assessed by measuring myeloperoxidase activity, thiobarbituric acid reactive substances, superoxide anion generation, and reduced glutathione content. Hematoxylin & eosin staining was done to assess histological changes in renal tissues. Curcumin (30 and 60 mg/kg) was administered one hour before subjecting rats to AKI. In separate groups, NMDA receptor agonists, glutamic acid (200 mg/kg), and spermidine (20 mg/kg) were administered prior to curcumin treatment in rats followed by AKI. Results: I/R-induced AKI was demonstrated by significant change in plasma and urine parameters along with marked increase in oxidative stress and histological changes in renal tissues that were aggravated with pretreatment of glutamic acid and spermidine in rats. Administration of curcumin resulted in significant protection against AKI. However, glutamic acid and spermidine pretreatments prevented curcumin-mediated renoprotection. Conclusion: It is concluded that NMDA receptor antagonism significantly contributes towards curcumin-mediated protection against I/R-induced AKI.
Serological Profiles of Urate, Paraoxonase-1, Ferritin and Lipid in Parkinson’s Disease: Changes Linked to Disease Progression

Background: Oxidative stress plays a role in the pathogenesis of neuronal death. Serum levels of urate or lipid were associated with the incidence of Parkinson’s disease (PD). Objective: We compared urate, paraoxonase-1 (PON1), iron, ferritin and lipid in sera of 119 PD patients and 120 healthy controls matched by age, sex and body mass index. We aimed to elucidate whether those serological data are correlated with disease progression. Results: Mean age (SD) of PD patients was 73.4 (8.7) years. Mean Yahr stage (SD) was 3.2 (0.9). Mean disease duration (SD) was 6.9 (5.1) years. Mean dose of L-DOPA (SD) was 355 (157) mg/day. As compared to controls, serum levels of total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), urate and PON1 activity were significantly reduced, and serum ferritin levels were significantly increased in male and female PD patients. Serum urate levels and PON1 activities were inversely related, and serum ferritin levels were correlated with Yahr stage and PD duration in men and women. Serum levels of TC and LDL-C were inversely related to Yahr stage or PD duration in female patients. Conclusions: Our studies indicated serological profiles of urate, PON1, ferritin, TC and LDL-C in PD patients. These serological changes were linked to PD progression. Metabolism of lipid, oxidant- and antioxidant-related substances may contribute to the pathogenesis and the progression of PD.
Daytime levels of melatonin in patients with age‐related macular degeneration

Purpose: Melatonin (N‐acetyl‐5‐methoxytryptamine) (MT) is a hormone that acts as an antioxidant. It is produced by the pineal gland and within the retina; its release is blocked by light entering the eye. We examined whether MT daytime levels differ between pseudophakic patients with age‐related macular degeneration (ARMD) and pseudophakic subjects without any ocular pathology of the same age.
Postnatal delay of myelin formation in brains from Down syndrome infants and children.

Myelination up to the age of 6 years was studied in two groups consisting of 129 Down syndrome (DS) 17/129 fetuses and 112/129 postnatal) and 73 non-DS cases (10/73 fetuses and 63/73 postnatal). In both groups studied a similar number of congenital heart disease (CHD), gastrointestinal (GI) malformations and infections were diagnosed. Paraffin or celloidin brain sections were stained with Klüver-Barrera, Heidenhain or Loyez method. The myelination was found to be delayed in 29/129 (22.5%) DS and only in 5/73 (6.8%) non-DS cases. Myelination in fetuses and newborns in the DS and non-DS groups was not delayed. In DS the myelination was delayed between ages 2 months-6 years (17/29; 58.6%) up to 12 months, and 12/29 (41.4%) aged 2-6 years, while in non-DS aged 2-6 months only. The myelination delay affected tracts with late beginning and slow cycle of myelination, mainly the associated and intercortical fibers of the fronto-temporal lobes. In 3/7 of DS cases (ages 3, 4, 6 years) less advanced myelination of U fibers was noted. In both groups the myelination delay seemed also to depend on the systemic diseases which affected the subjects during the time of myelination. In DS where CHD was present the myelination delay was found in 14/29 (48.2%) in contrast to 3/5 (60%) non-DS. Also, in 28/129 (23%) DS cases dates regarding the developmental milestones were available and some correlation was found between developmental and myelination delay. (ABSTRACT TRUNCATED AT 250 WORDS)
Trajectory Analysis of the Campus Serial Rapist Assumption.

IMPORTANCE Rape on college campuses has been addressed recently by a presidential proclamation, federal legislation, advocacy groups, and popular media. Many initiatives assume that most college men who perpetrate rape are serial rapists. The scientific foundation for this perspective is surprisingly limited. OBJECTIVE To determine whether a group of serial rapists exists by identifying cohesive groups of young men, indicated by their trajectories of rape likelihood across high school and college. DESIGN, SETTING, AND PARTICIPANTS Latent class growth analysis of the 2 largest longitudinal data sets of adolescent sexual violence on college campuses using 2 distinct groups of male college students. The first group was used for derivation modeling (n = 847; data collected from August 1990 through April 1995) and the second for validation modeling (n = 795; data collected from March 2008 through May 2011). Final data analyses were conducted from February 16, 2015, through February 20, 2015. MAIN OUTCOMES AND MEASURES Rape perpetration assessed using the Sexual Experiences Survey. RESULTS Across samples, 178 of 1642 participants (10.8%) reported having perpetrated at least 1 rape from 14 years of age through the end of college. A 3-trajectory model best fit both the derivation and validation data sets. Trajectories reflected low or time-limited (92.6% of participants), decreasing (5.3%), and increasing (2.1%) rape patterns. No consistently high trajectory was found. Most men who perpetrated a rape before college were classified in the decreasing trajectory. During college, the increasing trajectory included 14 men (15.2%) who reported having perpetrated a rape, the decreasing trajectory included 30 men (32.6%), and the low or time-limited included 48 men (52.2%). No participant in the low or time-limited trajectory reported perpetrating a rape during more than 1 period. Most men (67 [72.8%]) who committed college rape only perpetrated rape during 1 academic year. CONCLUSIONS AND RELEVANCE Although a small group of men perpetrated rape across multiple college years, they constituted a significant minority of those who committed college rape and did not compose the group at highest risk of perpetrating rape when entering college. Exclusive emphasis on serial predation to guide risk identification, judicial response, and rape-prevention programs is misguided. To deter college rape, prevention should be initiated before, and continue during, college. Child and adolescent health care professionals are well positioned to intervene during the early teenage years by informing parents about the early onset of nonconsensual sexual behavior.
N,N-Diethyl-2-hydroxyethanaminium 5-(5-chloro-2,4-dinitrophenyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate hemihydrate

The asymmetric unit of the title salt, C6H16NO+·C10H4ClN4O7 −·0.5H2O, contains two cations, two anions and one water molecule. In one independent anion, one nitro group is rotationally disordered over two orientations in a 0.657 (8):0.343 (8) ratio. In the crystal, intermolecular N—H⋯O and O—H⋯O hydrogen bonds link all the components into ribbons extending along [100].
Escherichia coli’s physiology can turn membrane voltage dyes into actuators

The electrical membrane potential (Vm) is one of the components of the electrochemical potential of protons across the biological membrane (proton motive force), which powers many vital cellular processes, and Vm also plays a role in signal transduction. Therefore, measuring it is of great interest, and over the years a variety of techniques has been developed for the purpose. In bacteria, given their small size, Nernstian membrane voltage probes are arguably the favourite strategy, and their cytoplasmic accumulation depends on Vm according to the Nernst equation. However, a careful calibration of Nernstian probes that takes into account the trade-offs between the ease with which the signal from the dye is observed, and the dyes’ interactions with cellular physiology, is rarely performed. Here we use a mathematical model to understand such trade-offs and, based on the knowledge gained, propose a general work-flow for the characterization of Nernstian dye candidates. We demonstrate the work-flow on the Thioflavin T dye in Escherichia coli, and identify conditions in which the dye turns from a Vm probe into an actuator. SIGNIFICANCE STATEMENT The phospholipid bilayer of a biological membrane is virtually impermeable to charged molecules. Much like in a rechargeable battery, cells harness this property to store an electrical potential that fuels life reactions but also transduces signals. Measuring this electrical potential, also referred to as membrane voltage, is therefore of great interest and a variety of techniques have been employed for the purpose, starting as early as the 1930s. For the case of bacteria, which are smaller in size and possess a stiffer cell wall, arguably the most popular approach to measuring membrane voltage are Nernstian probes that accumulate across the bacterial membrane according to the Nernst potential. The present study characterizes the undesired effects Nernstian probes can have on cell physiology, which can be crucial for the accurate interpretation of experimental results. Using mathematical modelling and experiments, the study provides a general, simple workflow to characterise and minimise these effects.
The effects of empathy and circadian preference on cyberbullying of adolescents in Turkey

ABSTRACT In this study, the relationships among empathic tendency and circadian preference on cyberbullying and cybervictimization of adolescents in Turkey were examined. The study group included 1540 adolescents (861 female, 679 male), and anonymous and voluntary participation was sought in forming the study group. Data were collected from each participant by assessing a demographic questionnaire, the Composite Scale of Morningness for circadian preference, Empathy, Cyberbully and Victim Scales. The most important result was that gender, empathy, and Composite Scale of Morningness scores were the predictors for cyberbullying and cybervictimization, and as a consequence, male and evening-oriented adolescents scored higher on cyberbullying and cybervictimization. Additionally, it was observed that cyberbullying and empathy were inversely correlated in adolescents.
Principal Component Analysis Based on L1-Norm Maximization

A method of principal component analysis (PCA) based on a new L1-norm optimization technique is proposed. Unlike conventional PCA which is based on L2-norm, the proposed method is robust to outliers because it utilizes L1-norm which is less sensitive to outliers. It is invariant to rotations as well. The proposed L1-norm optimization technique is intuitive, simple, and easy to implement. It is also proven to find a locally maximal solution. The proposed method is applied to several datasets and the performances are compared with those of other conventional methods.
Moderate Ingestion of Alcohol Is Associated With Acute Ethanol‐Induced Suppression of Circulating CTX in a PTH‐Independent Fashion

The “J shape” curve linking the risk of poor bone health to alcohol intake is now well recognized from epidemiological studies. Ethanol and nonethanol components of alcoholic beverages could influence bone remodeling. However, in the absence of a solid underlying mechanism, the positive association between moderate alcoholic intake and BMD remains questionable because of confounding associated social factors. The objective of this work was to characterize the short‐term effects of moderate alcohol consumption on circulating bone markers, especially those involved in bone resorption. Two sequential blood‐sampling studies were undertaken in fasted healthy volunteers (age, 20–47 yr) over a 6‐h period using beer of different alcohol levels (<0.05–4.6%), solutions of ethanol or orthosilicic acid (two major components of beer), and water ± calcium chloride (positive and negative controls, respectively). Study 1 (24 subjects) assessed the effects of the different solutions, whereas study 2 (26 subjects) focused on ethanol/beer dose. Using all data in a “mixed effect model,” we identified the contributions of the individual components of beer, namely ethanol, energy, low‐dose calcium, and high‐dose orthosilicic acid, on acute bone resorption. Markers of bone formation were unchanged throughout the study for all solutions investigated. In contrast, the bone resorption marker, serum carboxy terminal telopeptide of type I collagen (CTX), was significantly reduced after ingestion of a 0.6 liters of ethanol solution (>2% ethanol; p ≤ 0.01, RM‐ANOVA), 0.6 liters of beer (<0.05–4.6% ethanol; p < 0.02), or a solution of calcium (180 mg calcium; p < 0.001), but only after calcium ingestion was the reduction in CTX preceded by a significant fall in serum PTH (p < 0.001). Orthosilicic acid had no acute effect. Similar reductions in CTX, from baseline, were measured in urine after ingestion of the test solutions; however, the biological variability in urine CTX was greater compared with serum CTX. Modeling indicated that the major, acute suppressive effects of moderate beer ingestion (0.6 liters) on CTX were caused by energy intake in the early phase (∼0–3 h) and a “nonenergy” ethanol component in the later phase (∼3 to >6 h). The early effect on bone resorption is well described after the intake of energy, mediated by glucagon‐like peptide‐2, but the late effect of moderate alcohol ingestion is novel, seems to be ethanol specific, and is mediated in a non–calcitonin‐ and a non–PTH‐dependent fashion, thus providing a mechanism for the positive association between moderate alcohol ingestion and BMD.
Optimum conditions for preparation of bio-calcium from blood cockle and golden apple snail shells and characterization

Research on the utilization of calcium compounds from seashells has attracted much interest in diverse applications. However, the optimum temperature and time for preparation of calcium compounds from shells remains unknown. These factors have a direct effect on the purity of the obtained calcium phases. In this study, the influence of calcination temperature and holding time on the phase transformations of CaCO3 from sea shells and freshwater shells, i.e., blood cockle and golden apple snail shells, was studied. High purity and crystalline CaCO3 and CaO was produced from both types of shells by calcination at 600 °C and 800 °C, respectively. Overall both blood cockle and golden apple snail shells could be used to produce calcium compounds with 95–98% pure calcium with trace amounts of As, Cd, Hg, and Pb. Phase transformation of CaCO3 depends on calcination temperature and holding time. The calcium content in CaCO3 and CaO from golden apple snail shells was higher than that from blood cockle shells. This result also indicated that the calcium compounds from blood cockle shell were easier to grind than those from golden apple snail shells primarily due to an early transformation of the calcium phase of golden apple snail shells.
THE PRESENCE OF POLYCYCLIC AROMATIC HYDROCARBONS (PAH) IN OIL OBTAINED AT PYROLYSIS OF JORDAN OIL SHALE

The presence of polycyclic aromatic hydrocarbons (PAH) in the oil obtained at pyrolysis of Jordan oil shale in a fluidised-bed reactor in the atmosphere of nitrogen and nitrogen/steam has been investigated. The final pyrolysis temperature was 520 °C, at which the maximum oil yield was established. The derived oils were fractionated into chemical classes using mini-column liquid chromatography followed by analysis using capillary column gas chromatography with mass spectrometry (GC/MS) for identification and quantification of PAH. The derived oils were found to contain significant amounts of PAH, mainly naphthalene, fluorene and phenanthrene and their alkylated derivatives, and lower amounts of fluoranthrene, pyrene and chrysene. Some of the PAH found in the derived oils are known to be carcinogenic and/or mutagenic, and consequently the oils may represent a significant environmental and health hazard. The PAH have probably formed via Diels-Alder type reactions or via gas-phase cracking of aliphatic compounds.
Modeling and analyzing spike timing dependent plasticity with linear hybrid automata

We propose a model for synaptic plasticity according to the Spike Timing Dependent Plasticity (STDP) theory using Linear Hybrid Automata (LHA). We first present a compositional LHA model in which each component corresponds to some process in STDP. We then abstract this model into a monolithic LHA model in order to enable formal analysis using hybrid model checking. We discuss how the availability of an LHA model as well as its formal analysis using the tool PHAVer can support a better understanding of the dynamics of STDP.
Data Mining Techniques Based Students Achievements Analysis

In this work, data mining techniques are used to determine the students’ achievements in Mathematic class. In other words, we use the data mining techniques to determine if there is any link between the student achievement and various student related data such as student grades, demographic, social information and school related data. Data mining techniques, Decision Tree (DT), Discriminant Analysis (DA), Support Vector Machines (SVM), k-nearest neighbor (K-NN) and ensemble learner are used in prediction purposes. A publicly available dataset is considered in experimental works. Experimental works, on computer environment are carried out to validate the data mining techniques. All data mining methodologies are simulated on MATLAB environment with 5-fold cross-validation technique. The classification performance is measured by accuracy and root mean square error (RMSE) criterions. Three experimental setups and for each setup, three scenarios are considered during experimentation. The obtained results are encouraging and the comparison with some of the existing achievements shows the superiority of our work.
Evaluation of ADAM-12 as a Diagnostic Biomarker of Ectopic Pregnancy in Women with a Pregnancy of Unknown Location

Background Ectopic pregnancy (EP) remains the most life-threatening acute condition in modern gynaecology. It remains difficult to diagnose early and accurately. Women often present at emergency departments in early pregnancy with a ‘pregnancy of unknown location’ (PUL) and diagnosis/exclusion of EP is challenging due to a lack of reliable biomarkers. Recent studies suggest that serum levels of a disintegrin and metalloprotease protein-12 (ADAM-12) can be used differentiate EP from viable intrauterine pregnancy (VIUP). Here we describe a prospective study evaluating the performance of ADAM-12 in differentiating EP from the full spectrum of alternative PUL outcomes in an independent patient cohort. Methodology/Principal Findings Sera were collected from 120 patients at their first clinical presentation with a PUL and assayed for ADAM-12 by ELISA. Patients were categorized according to final pregnancy outcomes. Serum ADAM-12 concentrations were increased in women with histologically-confirmed EP (median 442 pg/mL; 25%–75% percentile 232–783 pg/mL) compared to women with VIUP (256 pg/mL; 168–442 pg/mL) or miscarriage (192 pg/mL; 133–476 pg/mL). Serum ADAM-12 did not differentiate histologically-confirmed EP from spontaneously resolving PUL (srPUL) (416 pg/mL; 154–608 pg/mL). The diagnostic potential of ADAM-12 was only significant when ‘ambiguous’ PUL outcomes were excluded from the analysis (AROC = 0.6633; P = 0.03901). Conclusions/Significance When measured in isolation, ADAM-12 levels had limited value as a diagnostic biomarker for EP in our patient cohort. The development of a reliable serum biomarker-based test for EP remains an ongoing challenge.