Miracle-dz/UniFAR-FTUs huggingface dataset:
Deformability of Density Separated Red Blood Cells in Normal Newborn Infants and Adults

Summary: The deformability of neonatal and adult red blood cells (RBC) was studied using both unseparated and density (i.e., age) fractionated RBC. Blood samples were obtained from 10 normal newborn infants (placental blood) and 10 adults. Deformability was measured by direct microscopic observation of RBC subjected to shear stresses of 2.5–500 dynes/cm2 using a counter-rotating Rheoscope. There was no significant difference in deformability between unseparated neonatal and adult RBC at any shear stress. The 3% least dense (“youngest”) RBC showed significantly decreased hemoglobin concentrations (MCHC), increased volumes (MCV) and elevated deformability at any shear stress when compared to the 3% most dense (“oldest”) cells, with the values for the unseparated RBC lying between these two extremes. The least dense neonatal RBC had a significantly lower MCHC and higher deformability than the least dense adult cells; however, the most dense neonatal RBC had lost more volume than the adult cells (33 versus 17%), had a higher MCHC, and were less deformable than the most dense adult cells. This indicates that the accelerated decrease in deformability of aging neonatal RBC is related to the more pronounced increase in MCHC, which is the principal determinant of the internal viscosity of the RBCSpeculation: The shortened survival time of neonatal red blood cells (RBC) is probably the consequence of accelerated aging of neonatal RBC. Differences in biochemical composition and a decrease in some RBC activities, which are important for the maintenance of membrain integrity, cell volume, and deformability might be responsible for the faster loss of membrane fragments and deformability of neonatal RBC when compared to adult cells. These alterations presumably impede the ability of aging neonatal RBC to pass the narrow splenic slits, thus promoting their eventual destruction by macrophages.
Apnea-Induced Cortical BOLD-fMRI and Peripheral Sympathoneural Firing Response Patterns of Awake Healthy Humans

End-expiratory breath-holds (BH) and Mueller manoeuvres (MM) elicit large increases in muscle sympathetic nerve activity (MSNA). In 16 healthy humans (9♀, 35±4 years) we used functional magnetic resonance imaging with blood oxygen level-dependent (BOLD) contrast to determine the cortical network associated with such sympathoexcitation. We hypothesized that increases in MSNA evoked by these simulated apneas are accompanied by BOLD contrast changes in the insular cortex, thalamus and limbic cortex. A series of 150 whole-brain images were collected during 3 randomly performed 16-second end-expiratory BHs and MMs (-30 mmHg). The identical protocol was repeated separately with MSNA recorded from the fibular nerve. The time course of the sympathoexcitatory response to both breathing tasks were correlated with whole-brain BOLD signal changes. Brain sites demonstrating both positive (activation) and negative (deactivation) correlations with the MSNA time course were identified. Sympathetic burst incidence increased (p<0.001) from 29±6 (rest) to 49±6 (BH) and 47±6 bursts/100 heartbeats (MM). Increased neural activity (Z-scores) was identified in the right posterior and anterior insular cortices (3.74, 3.64), dorsal anterior cingulate (3.42), fastigial and dentate cerebellar nuclei (3.02, 3.34). Signal intensity decreased in the left posterior insula (3.28) and ventral anterior cingulate (3.01). Apnea both activates and inhibits elements of a cortical network involved in the generation of sympathetic outflow. These findings identify a neuroanatomical substrate to guide future investigations into central mechanisms contributing to disorders characterized by elevated basal MSNA and exaggerated sympathetic responses to simulated apneas such as sleep apnea and heart failure.
Sensitive and inexpensive digital DNA analysis by microfluidic enrichment of rolling circle amplified single-molecules

Abstract Single molecule quantification assays provide the ultimate sensitivity and precision for molecular analysis. However, most digital analysis techniques, i.e. droplet PCR, require sophisticated and expensive instrumentation for molecule compartmentalization, amplification and analysis. Rolling circle amplification (RCA) provides a simpler means for digital analysis. Nevertheless, the sensitivity of RCA assays has until now been limited by inefficient detection methods. We have developed a simple microfluidic strategy for enrichment of RCA products into a single field of view of a low magnification fluorescent sensor, enabling ultra-sensitive digital quantification of nucleic acids over a dynamic range from 1.2 aM to 190 fM. We prove the broad applicability of our analysis platform by demonstrating 5-plex detection of as little as ∼1 pg (∼300 genome copies) of pathogenic DNA with simultaneous antibiotic resistance marker detection, and the analysis of rare oncogene mutations. Our method is simpler, more cost-effective and faster than other digital analysis techniques and provides the means to implement digital analysis in any laboratory equipped with a standard fluorescent microscope.
Xenobiotic Metabolizing Gene Variants and Renal Cell Cancer: A Multicenter Study

Background: The countries of Central and Eastern Europe have among the highest worldwide rates of renal cell cancer (RCC). Few studies have examined whether genetic variation in xenobiotic metabolic pathway genes may modify risk for this cancer. Methods: The Central and Eastern Europe Renal Cell Cancer study was a hospital-based case–control study conducted between 1998 and 2003 across seven centers in Central and Eastern Europe. Detailed data were collected from 874 cases and 2053 controls on demographics, work history, and occupational exposure to chemical agents. Genes [cytochrome P-450 family, N-acetyltransferases, NAD(P)H:quinone oxidoreductase I (NQO1), microsomal epoxide hydrolase (mEH), catechol-O-methyltransferase (COMT), uridine diphosphate-glucuronosyltransferase (UGT)] were selected for the present analysis based on their putative role in xenobiotic metabolism. Haplotypes were calculated using fastPhase. Odds ratios and 95% confidence intervals were estimated by unconditional logistic regression adjusted for country of residence, age, sex, smoking, alcohol intake, obesity, and hypertension. Results: We observed an increased risk of RCC with one SNP. After adjustment for multiple comparisons it did not remain significant. Neither NAT1 nor NAT2 slow acetylation was associated with disease. Conclusion: We observed no association between this pathway and renal cell cancer.
Antigenic and immunogenic properties of recombinants from Salmonella typhimurium and Salmonella minnesota rough mutants expressing in their lipopolysaccharide a genus-specific chlamydial epitope

Rough mutants from Salmonella typhimurium and Salmonella minnesota were transformed with a plasmid containing a 6.5-kilobase insert of DNA from Chlamydia trachomatis assumed to encode a glycosyltransferase. Transformation resulted in the expression of a genus-specific chlamydial epitope on the lipopolysaccharide (LPS) of the recombinant strains. Proteinase K-digested whole-cell lysates of the recombinants and of controls were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by silver staining or Western blot analysis. Two LPS populations were detected in the recombinants, the parent LPS and a faster-migrating component. The latter stained with monoclonal antibody against the genus-specific chlamydial epitope and was not seen in the controls. LPS was extracted and purified from recombinants of S. minnesota R595 and R4 and characterized by the passive hemolysis and passive hemolysis inhibition assays and by hydrolysis kinetics. Different antigenic determinants could be distinguished from each other by the passive hemolysis inhibition test with monospecific antigen-antibody reactions. Rabbits were immunized with heat-killed recombinant bacteria to study the immunogenic properties of the recombinants. In all animals, antibodies were raised against the parent core specificity and against the chlamydia-specific epitope. The data show that the recombinant bacteria are useful as immunogens to prepare polyclonal antisera against chlamydiae and that LPS isolated from them exhibits the same antigenic determinants as chlamydial LPS and may thus be used as a substitute for chlamydial LPS in serological assays.
Is Income Inequality ‘Toxic for Mental Health’? An Ecological Study on Municipal Level Risk Factors for Depression

Most inequality research on the relationship between inequality and mental health has focused on cross-country variation. Findings from within-country data are mixed. We examined whether changes in municipal Gini index or in the share of people living in relative poverty were linked to changes in the use of antidepressants in several Finnish municipalities between 1995 and 2010. We found that more young adult females used antidepressants in municipalities where relative poverty had increased. Changes in municipal-level Gini index were not positively associated with changes in the use of antidepressants in the municipalities between 1995 and 2010. However, fewer elderly females used antidepressants in municipalities where the Gini index increased. In addition, more young adults used antidepressants in municipalities where the number of those not being educated or trained had also increased. An increase in the number of persons over 65 years of age living alone was positively associated with an increase in the use of antidepressants among elderly females.
Real time clustering of tweets using adaptive PSO technique and MapReduce

These days large amount of data is generated by social media such as Twitter, Facebook and YouTube etc. These kinds of data have very complicated structures which causes difficulty with respect to capturing, storing, analyzing, clustering and visualization of data. Recently, clustering of such data has caught the attention of researchers. For this, distinct algorithms such as K-Means are suggested to cluster the data. There is a need for an algorithm that is able to cluster the data in a lesser amount of time, in case of data stream. Hence the need to use a parallel and distributed environment using map-reduce framework. Likewise particle swarm optimization techniques are preferable for clustering problem, since it scales very well as data, dimensions increase. The paper implements PSO algorithm for clustering Twitter data using Hadoop's map-reduce framework. The outcome illustrates that parallel PSO performs very well compared to K-Means algorithm. The results show that the F-Measure is increasing with increase in number of particles. Also the optimum number of nodes required is illustrated with experimental result.
NMDA Receptors of Gastric-Projecting Neurons in the Dorsal Motor Nucleus of the Vagus Mediate the Regulation of Gastric Emptying by EA at Weishu (BL21)

A large number of studies have been conducted to explore the efficacy of electroacupuncture (EA) for the treatment of gastrointestinal motility. While several lines of evidence addressed the basic mechanism of EA on gastrointestinal motility regarding effects of limb and abdomen points, the mechanism for effects of the back points on gastric motility still remains unclear. Here we report that the NMDA receptor (NMDAR) antagonist kynurenic acid inhibited the gastric emptying increase induced by high-intensity EA at BL21 and agonist NMDA enhanced the effect of the same treatment. EA at BL21 enhanced NMDAR, but not AMPA receptor (AMPAR) component of miniature excitatory postsynaptic current (mEPSC) in gastric-projecting neurons of the dorsal motor nucleus of the vagus (DMV). In sum, our data demonstrate an important role of NMDAR-mediated synaptic transmission of gastric-projecting DMV neurons in mediating EA at BL21-induced enhancement of gastric emptying.
Relationships between vitamin A, iron status and helminthiasis in Bangladeshi school children

Abstract Objective To explore the relationships between biochemical indicators of vitamin A and iron status and the intestinal helminths Ascaris lumbricoides and hookworm in primary school children. Setting Two rural governmental schools in northwestern Bangladesh. Design Cross-sectional study. Subjects The sample consisted of 164 children in grades 3–5. Methods Serum retinol and β-carotene (by high-performance liquid chromatography, HPLC), haemoglobin (HemoCue), ferritin (enzyme-linked immunoadsorbent assay, ELIZA) and height and weight were measured. Dietary intake of vitamin A was assessed using a food frequency questionnaire and faecal analyses were done using Stoll's egg-count technique. Results The mean serum retinol was 26.8 μg dl−1 and 20% had a level of <20 μg dl−1, the cut-off value for low vitamin A status. There was a strong positive association between serum β-carotene and serum retinol (r = 0.44, P <0.001), suggesting those with higher retinol levels had a higher carotene intake. Thirty-one per cent were anaemic (Hb <11.5 g dl−1), 30% had iron deficiency (serum ferritin <12.0 μg l−1) and 14% were suffering from iron deficiency anaemia. Children with a serum retinol level of 20 μg dl−1 had significantly lower ferritin (14.0 compared to 26.0 μg l−1, P = 0.005) and Hb levels (11.7 compared to 12.4 g dl−1, P = 0.005) than those with higher levels. The proportion of iron deficiency anaemia was significantly greater among children with hookworm. Our data suggest that hookworm exerts its impact on iron status independently of the vitamin A status of the host. Conclusions Programmes to improve iron status should consider including both vitamin A prevention programmes and deworming.
F-scan: An approach to functional RTL scan for assignment decision diagrams

This paper presents a new methodology for functional Register Transfer Level (RTL) scan, in which existing functional elements and paths can be maximally utilized. The approach is called F-scan, which primarily aims to reduce the total area overhead due to augmentation for testing. Since the method allows for parallel scanning of test vectors, test application time is also made to be at the minimum. The case study shows the effectiveness of our approach compared to full scan design1.
Spatiotemporal Gating of Sensory Inputs in Thalamus during Quiescent and Activated States

The main role of the thalamus is to relay sensory inputs to the neocortex according to the regulations dictated by behavioral state. Hence, changes in behavioral state are likely to transform the temporal and spatial properties of thalamocortical receptive fields. We compared the receptive fields of single cells in the ventroposterior medial thalamus (VPM) of urethane-anesthetized rats during quiescent states and during aroused (activated) states. During quiescent states, VPM cells respond to stimulation of a principal whisker (PW) and may respond modestly to one or a few adjacent whiskers (AWs). During either generalized forebrain activation or selective thalamic activation caused by carbachol infusion in the VPM, the responses to AWs enhance so that VPM receptive fields become much larger. Such enlargement is not observed at the level of the principal trigeminal nucleus, indicating that it originates within the thalamus. Interestingly, despite the increase in AW responses during activation, simultaneous deflection of the PW and AWs produced VPM responses that resembled the PW response, as if the AWs were not stimulated. This nonlinear summation of sensory responses was present during both quiescent and activated states. In conclusion, the thalamus suppresses the excitatory surround (AWs) of the receptive field during quiescent states and enlarges this surround during arousal. But, thalamocortical cells represent only the center (PW) of the receptive field when the center (PW) and surround (AWs) are stimulated simultaneously.
Ion Conduction through the hERG Potassium Channel

The inward rectifier voltage-gated potassium channel hERG is of primary importance for the regulation of the membrane potential of cardiomyocytes. Unlike most voltage-gated K+-channels, hERG shows a low elementary conductance at physiological voltage and potassium concentration. To investigate the molecular features underlying this unusual behavior, we simulated the ion conduction through the selectivity filter at a fully atomistic level by means of molecular dynamics-based methods, using a homology-derived model. According to our calculations, permeation of potassium ions can occur along two pathways, one involving site vacancies inside the filter (showing an energy barrier of about 6 kcal mol−1), and the other characterized by the presence of a knock-on intermediate (about 8 kcal mol−1). These barriers are indeed in accordance with a low conductance behavior, and can be explained in terms of a series of distinctive structural features displayed by the hERG ion permeation pathway.
Complete System for Text Line Extraction Using Convolutional Neural Networks and Watershed Transform

We present a novel Convolutional Neural Network based method for the extraction of text lines, which consists of an initial Layout Analysis followed by the estimation of the Main Body Area (i.e., the text area between the baseline and the corpus line) for each text line. Finally, a region-based method using watershed transform is performed on the map of the Main Body Area for extracting the resulting lines. We have evaluated the new system on the IAM-HisDB, a publicly available dataset containing historical documents, outperforming existing learning-based text line extraction methods, which consider the problem as pixel labelling problem into text and non-text regions.
Upregulation of miR-21 in Cisplatin Resistant Ovarian Cancer via JNK-1/c-Jun Pathway

Cisplatin has been the most accepted drug for the treatment of ovarian cancer for almost 40 years. Although the majority of patients with ovarian cancer respond to front-line platinum combination chemotherapy, many patients will develop cisplatin-resistance disease, which is extremely rapid and fatal. Although various mechanisms of cisplatin resistance have been postulated, the key molecules involved in such resistance have not been identified. MiRNAs are endogenously expressed small non-coding RNAs, which are evolutionarily conserved and function as post-transcriptional regulators of gene expression. Dysregulation of miRNAs have been associated with cancer initiation, progression and drug resistance. The oncogenic miRNA-21, one of the best-studied miRNAs, is upregulated in almost all human cancers. However, the regulation of miR-21 in cisplatin resistant ovarian cancer cells has not been assessed. In this study, we measured the miR-21 expression by real-time PCR and found upregulation of miR-21 in cisplatin resistant compared with cisplatin sensitive ovarian cancer cells. Chromatin immunoprecipitation studies demonstrated the association of the c-Jun transcription factor to the pri-mir-21 DNA promoter regions. Blocking the JNK-1, the major activator of c-Jun phosphorylation, reduced the expression of pre-mir-21 and increased the expression of its well-known target gene, PDCD4. Overexpression of miR-21 in cisplatin sensitive cells decreased PDCD4 levels and increased cell proliferation. Finally, targeting miR-21 reduced cell growth, proliferation and invasion of cisplatin resistant ovarian cancer cells. These results suggest that the JNK-1/c-Jun/miR-21 pathway contributes to the cisplatin resistance of ovarian cancer cells and demonstrated that miR-21 is a plausible target to overcome cisplatin resistance.
Recurrence of venous thromboembolism in patients with familial thrombophilia.

BACKGROUND Treatment of patients with deep vein thrombosis and an antithrombin or protein C or S deficiency is based on case reports and personal experience. OBJECTIVE To systematically assess the risk for recurrence of venous thromboembolism after a first episode in patients with these deficiencies, a literature review and retrospective family cohort study were performed. METHODS For the literature review, the annual incidence of a first recurrent venous thromboembolism was assessed for each deficiency by dividing the number of venous thromboembolic events by the number of years at risk. For the family cohort study, 1- and 5-year cumulative incidences of first recurrence were calculated based on medical histories taken in relatives of consecutive patients in whom venous thromboembolism and a deficiency were diagnosed. RESULTS For the literature review, the annual incidence of a first recurrent venous thromboembolism in patients with antithrombin or protein S deficiency ranged from 13% to 17% and 14% to 16%, respectively. For the family cohort study, the 1- and 5-year cumulative incidences of recurrent venous thromboembolism were 10% (95% confidence interval, 1%-19%) and 23% (95% confidence interval, 10%-36%), respectively. Warfarin sodium (Coumadin) prophylaxis was associated with 2 venous thromboembolic events in 141 years at risk (1.4% per year), in contrast with 19 events in 709 years at risk (2.7% per year) without prophylaxis (difference, -1.3%; 95% confidence interval, -3.5% to 1.0%). CONCLUSIONS The annual incidence of recurrent venous thromboembolism is high during the first years following a first episode, but seems to decline thereafter. Therefore, our results challenge current practice of prescribing lifelong warfarin therapy after a first or second episode of venous thromboembolism in patients with antithrombin or protein C or S deficiency.
Immunohistochemical analysis of chronic discoid and subacute cutaneous lupus erythematosus—relation to immunopathological mechanisms

An immunohistochemical analysis of skin biopsies was performed in 18 patients with cutaneous lupus erythematosus (LE), using the alkaline phosphatase and monoclonal anti‐alkaline phosphatase method (APAAP). The study group was subdivided on the basis of clinical criteria into 10 patients with chronic discoid LE (CDLE) and eight patients with subacute cutaneous LE (SCLE).
Vitamin D3 and 25-hydroxyvitamin D3 in pork and their relationship to vitamin D status in pigs

Abstract The content of vitamin D in pork produced in conventional systems depends on the vitamin D concentration in the pig feed. Both vitamin D3 and 25-hydroxyvitamin D3 (25(OH)D3) are essential sources of dietary vitamin D; however, bioavailability assessed by serum 25(OH)D3 concentration is reported to be different between the two sources. Furthermore, the relationship between serum 25(OH)D3 level and the tissue content of vitamin D3 and 25(OH)D3 is unknown. The objective of this study was to investigate the potential of increasing the content of vitamin D in different pig tissues by increasing the levels of vitamin D3 and 25(OH)D3 in the pig feed for 49 d before slaughter. Concurrently, the 25(OH)D3 level in serum was investigated as a biomarker to assess the content of vitamin D3 and 25(OH)D3 in pig tissues. Adipose tissue, white and red muscle, the liver and serum were sampled from pigs fed feed containing either vitamin D3 or 25(OH)D3 at 5, 20, 35 or 50 µg/kg feed for 7 weeks before slaughter. The tissue 25(OH)D3 level was significantly higher in the pigs fed 25(OH)D3 compared with those fed vitamin D3, while the tissue vitamin D3 level was higher in the pigs fed vitamin D3 compared with those fed 25(OH)D3. The content of 25(OH)D3 in the different tissues fully correlated with the serum 25(OH)D3 level, whereas the correlation between the tissue content of vitamin D3 and serum 25(OH)D3 was dependent on the source of the ingested vitamin D3.