Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the number and information content of fluorescent-labeled SSR markers for rice germplasm characterization.

The use of genetic resources for rice has been suggested as the most relevant alternative to raise the productivity levels achieved by modern cultivars (Brondani et al. 2003). However, before using these resources, it is fundamental to compile in depth knowledge on the existing genetic variability in these accessions to identify genotypes that could ultimately contribute effectively to genetic gains for traits of interest in rice breeding programs. It is estimated that over 200.000 accessions are stored in rice germplasm banks all over the
SelfSampling Versus Physicians' Sampling for Cervical Cancer Screening Agreement of Cytological Diagnoses.

BACKGROUND A major problem with cervical cancer screening in countries which have no organized national screening program for cervical cancer is suboptimal participation. Implementation of selfsampling method may increase the coverage. OBJECTIVE We determined the agreement of cytological diagnoses made on samples collected by women themselves (selfsampling) versus samples collected by physicians (Physician sampling). MATERIALS AND METHODS We invited women volunteers to undergo two procedures; cervical selfsampling using the Evalyn brush and physician sampling using a Cervex brush. The women were shown a video presentation on how to take their own cervical samples before the procedure. The samples taken by physicians were taken as per routine testing (Gold Standard). All samples were subjected to Thin Prep monolayer smears. The diagnoses made were according to the Bethesda classification. The results from these two sampling methods were analysed and compared. RESULTS A total of 367 women were recruited into the study, ranging from 22 to 65 years age. There was a significant good agreement of the cytological diagnoses made on the samples from the two sampling methods with the Kappa value of 0.568 (p=0.040). Using the cytological smears taken by physicians as the gold standard, the sensitivity of selfsampling was 71.9% (95% CI:70.972.8), the specificity was 86.6% (95% CI:85.7 87.5), the positive predictive value was 74.2% (95% CI:73.375.1) and the negative predictive value was 85.1% (95% CI: 84.286.0). Selfsampling smears (22.9%) allowed detection of microorganisms better than physicians samples (18.5%). CONCLUSIONS This study shows that samples taken by women themselves (selfsampling) and physicians have good diagnostic agreement. Selfsampling could be the method of choice in countries in which the coverage of women attending clinics for screening for cervical cancer is poor.
Distinct organ-dependent mechanisms for the control of murine cytomegalovirus infection by natural killer cells

Antiviral mechanisms by which natural killer (NK) cells control murine cytomegalovirus (MCMV) infection in the spleens and livers of C57BL/6 mice were measured, revealing different mechanisms of control in different organs. Three days postinfection, MCMV titers in the spleens of perforin 0/0 mice were higher than in those of perforin +/+ mice, but no elevation of liver titers was found in perforin 0/0 mice. NK cell depletion in MCMV-infected perforin 0/0 mice resulted only in an increase in liver viral titers and not in spleen titers. Depletion of gamma interferon (IFN-gamma) in C57BL/6 mice by injections with monoclonal antibodies to IFN-gamma resulted in an increase of viral titers in the liver but not in the spleen. Analyses using IFN-gamma-receptor-deficient mice, rendered chimeric with C57BL/6 bone marrow cells, indicated that in a recipient environment where IFN-gamma cannot exert its effects, the depletion of NK cells caused an increase in MCMV titers in the spleens but had little effect in the liver. IFN-gamma has the ability to induce a variety of cells to produce nitric oxide, and administrating the nitric oxide synthase inhibitor N(omega)-monomethyl-L-arginine into MCMV-infected C57BL/6 mice resulted in MCMV titer increases in the liver but not in the spleen. Taken together, these data suggest that in C57BL/6 mice, there is a dichotomy in the mechanisms utilized by NK cells in the regulation of MCMV in different organs. In the spleen NK cells exert their effects in a perforin-dependent manner, suggesting a cytotoxic mechanism, while in the liver the production of IFN-gamma by NK cells may be a predominant mechanism in the regulation of MCMV synthesis. These results may explain why the Cmv-lr locus, which maps closely to genes regulating NK cell cytotoxic function, confers an NK cell-dependent resistance to MCMV infection in the spleen but not in the liver.
Self-reported Knowledge, Attitude and Consumption of Sugar-sweetened Beverages among Undergraduate Oral Health Students at a University in South Africa

Aims and Objectives: This study assessed the knowledge, attitude and consumption of sugar-sweetened beverages (SSBs) and its association with body mass index (BMI) among undergraduate oral health students. Materials and Methods: A cross-sectional design was used and the study was conducted at a South African dental university. Undergraduate dental and oral hygiene students (n = 344) registered in 2015 were invited to participate. A self-administered questionnaire was used to elicit the necessary information. Data analysis included frequencies and correlations using Chi-square tests. Statistical significance was set at P < 0.05. Results: The response rate was 88% (301) and the mean age was 22.3 years (range: 17–42; standard deviation ±3.2). The majority were female (72%) and 70% of respondents had an acceptable level of knowledge on the types of SSBs and possible health conditions if consumed excessively. Almost half (46%) had a positive attitude toward the consumption of SSBs. Clinical students had a significantly higher level of knowledge compared to nonclinical students (P = 0.03). Participants consumed an average of six teaspoons (±9.5) of sugar from SSBs daily. Those with poor knowledge and attitude consumed significantly more SSBs (P < 0.01) than those with higher levels of knowledge and attitude. Males were significantly more obese and overweight than females (P < 0.01). There was no association between the amount of sugar consumed from SSBs and the BMI. Conclusions: The knowledge and attitude toward SSBs was acceptable. Although sugar consumption from SSBs was relatively high, there was no significant correlation between the consumption of SSBs and the BMI.
Genome structure‐based screening identified epigenetically silenced microRNA associated with invasiveness in non‐small‐cell lung cancer

MicroRNA (miRNA) expression is frequently altered in human cancers. To search for epigenetically silenced miRNAs in non‐small‐cell lung cancer (NSCLC), we mapped human miRNAs on autosomal chromosomes and selected 55 miRNAs in silico. We treated six NSCLC cell lines with the DNA methylation inhibitor 5‐aza‐2′‐deoxycytidine (5‐aza‐CdR) and determined the expressions of the 55 miRNAs. Fourteen miRNAs were decreased in the cancer cell lines and were induced after 5‐aza‐CdR treatment. After a detailed DNA methylation analysis, we found that mir‐34b and mir‐126 were silenced by DNA methylation. Mir‐34b was silenced by the DNA methylation of its own promoter, whereas mir‐126 was silenced by the DNA methylation of its host gene, EGFL7. A chromatin immunoprecipitation assay revealed H3K9me2 and H3K9me3 in mir‐34b and EGFL7, and H3K27me3 in EGFL7. The overexpression of mir‐34b and mir‐126 decreased the expression of c‐Met and Crk, respectively. The 5‐aza‐CdR treatment of lung cancer cell line resulted in increased mir‐34b expression and decreased c‐Met protein. We next analyzed the DNA methylation status of these miRNAs using 99 primary NSCLCs. Mir‐34b and mir‐126 were methylated in 41 and 7% of all the cases, respectively. The DNA methylation of mir‐34b was not associated with c‐Met expression determined by immunohistochemistry, but both mir‐34b methylation (p = 0.007) and c‐Met expression (p = 0.005) were significantly associated with lymphatic invasion in a multivariate analysis. The DNA methylation of mir‐34b can be used as a biomarker for an invasive phenotype of lung cancer.
Development of an Outpatient Native Kidney Biopsy Service in Low-Risk Patients: A Multidisciplinary Approach

Background: In the US, native kidney biopsies are usually inpatient procedures. We developed an outpatient biopsy protocol for low-risk patients and assessed its safety and efficacy. Methods: Patients with an SBP <140 mm Hg and a BMI ≤35 who were not taking anticoagulants, ASA and NSAIDS in the preceding week were included. Biopsies were performed under ultrasound guidance using a 15-gauge needle that changed to a 14-gauge needle during the study. Patients were discharged after 5 h of observation if there were no signs of bleeding. Complications were carefully recorded. Results: Between November 2008 and April 2011, 105 patients underwent outpatient renal biopsies. A 15-gauge needle was used in 43 patients (group A) while a 14-gauge needle was used in 62 (group B). A median of 25 (range 4–64) glomeruli were obtained in group A versus 39 (range 0–107) in group B (p < 0.001). Complications requiring admission for observation occurred in 7 patients (16%) in group A versus 5 patients (8%) in group B (p = 0.22). One patient in group B had bleeding requiring intervention, while all other complications were minor. Nine complications occurred during the observation period, while 3 patients presented >48 h after biopsy. The mean cost per patient for each outpatient biopsy was USD 976 versus USD 5,489 for inpatients. Conclusions: In a selected low-risk population, outpatient renal biopsy is safe with low complication rates and results in significant cost savings relative to elective inpatient biopsies. The use of a 14-gauge biopsy needle resulted in a greater yield of glomeruli without increased complications.
Efficiency of part lactation test day records for genetic evaluations using fixed and random regression models

The efficiency of part lactation test day (TD) records in first parity for the genetic evaluation of bulls and cows using a random regression model (RRM) and a fixed regression model (FRM) was studied, modelling the random and fixed lactation curves by Legendre polynomials. The data set consisted of 9 242 783 TD records for first lactation milk yield of 1 134 042 Holstein Friesian heifers. The efficiency of both models with part lactation TD records was examined by comparing predicted transmitting abilities (PTAs) for 305-day milk yield for 114 bulls and their 4697 daughters, from analyses where the maximum number of TD records of these daughters was restricted to the initial 2, 4 or 6 TDs with those estimated from 10 TDs. The correlations of PTAs estimated from 2, 4 or 6 TDs with those from 10 TDs computed for cows and bulls within each model were very similar. A rank correlation of 0·91 (0·92 FRM) was obtained for cows between PTAs based on 2 TDs and those from 10 TDs. The correlation increased to 0·96 with 4 TDs and 0·98 with 6 TDs. For bulls, correlations between PTAs estimated from 4 or 6 TDs with those estimated from 10 TDs were high at 0·98 and 0·99 respectively. With 2 TDs, the correlation was 0·95. The average under-prediction of PTAs with 2, 4 or 6 TDs relative to 10 TDs was generally higher and more variable with a FRM compared with a RRM for highly persistent cows and bulls. A similar trend was observed for mean over-prediction of PTAs, except for the initial predictions based on 2 TDs when the RRM gave a higher mean overprediction for bulls and their daughters with low persistency but high initial TD records. The range of over and under-predictions were large (up to 200 kg milk) for some bulls when only 2 TDs were included in both models. A moderate correlation of 0·64 was obtained between persistency evaluations estimated from 10 TDs with those estimated from 2 TDs. The correlation increased to 0·71 with 4 TDs included and 0·85 with 6 TDs. The moderately high correlation between 6 TDs and 10 TDs of 0·85 was unexpected given the high correlation of 0·99 between PTAs for yield estimated from 6TDs with those estimated from 10 TDs.
The Efficiency of Pollution Removal From Domestic Wastewater in Constructed Wetland Systems With Vertical Flow With Common Reed and Glyceria Maxima

The paper presents the results of research on the effects of removing pollution from domestic wastewater in two beds of constructed wetland systems with vertical flow. Bed I was planted with common reed (Phragmites australis Cav. Trin. Ex Steud.), whereas bed II with Glyceria maxima (Glyceria aquatica L.). The surface of each of the beds amounted to 30 m2, and the hydraulic load of each of them amounted to 0.033 m3·m-2·d-1. The study showed very good results in the removal of most of the analyzed indicators of contamination, which were similar in both analyzed beds. They were, respectively: 91 and 93% – for total suspended solids, 96 and 98% – for BOD5, 96 and 94% – for CODCr, 88 and 86% – for ammonia nitrogen and 87 and 88% – for total phosphorus. Much smaller effects were reported with regard to total nitrogen removal – 55% in bed I with common reed and 54% in bed II with Glyceria maxima. The tested beds also eliminated the number of coliform bacteria and faecal coliform bacteria quite effectively. Average effects of the removal of coliform bacteria in bed I and II were 99.74%, in the case of faecal coliform 98.06% and 97.94% respectively. Values of basic indicators of contamination (total suspended solids, BOD5 and CODCr) in the wastewater discharged from the analyzed beds met the requirements of the Regulation of the Minister of the Environment of 2014. The test results obtained in the first year of operation of the analyzed beds show that neither of the applied plants significantly improves the results of contaminant removal.
Fusarium species associated with vanilla stem rot in Indonesia

Indonesia is one of the world’s leading producers of vanilla, an important cash crop for smallholders. Stem rot disease is a major constraint to vanilla production in Indonesia and has caused significant economic losses over the last decade. Previous reports of vanilla stem rots in the Asia-Pacific region include those caused by Fusarium, Colletotrichum and Phytophthora species. In this paper, we report Fusarium species associated with the disease. Seven major vanilla-producing provinces were surveyed for disease incidence and 850 samples were collected. Isolates were recovered from diseased stem tissues using a selective medium. Pure cultures on carnation leaf-piece agar and potato dextrose agar were identified based on morphological criteria. Some ambiguous species were verified based on DNA sequences of the translation elongation factor gene.Atotal of 542 Fusarium isolates were recovered, comprising 12 species, namely F. decemcellulare, F. fujikuroi, F. graminearum, F. mangiferae, F. napiforme, F. oxysporum, F. polyphialidicum, F. proliferatum, F. pseudocircinatum, F. semitectum, F. solani and F. subglutinans. F. oxysporum was the most commonly isolated species from all areas surveyed, followed by F. solani and F. semitectum. F. oxysporum, F. solani and F. semitectum were tested for pathogenicity to vanilla but only F. oxysporum was shown to be pathogenic. The vanilla stem rot pathogen in Indonesia is verified to be F. oxysporum f. sp. vanillae.
Identification of patients in medical publications: need for informed consent.

In medical journals patients are sometimes identified through clinical photographs or detailed descriptions of their sex, age, accommodation, occupation, etc. Occasionally, such details are relevant for the scientific message; sometimes they are included only because of a tradition of painstaking presentation of details in clinical reporting. How often a patient's identity is unduly disclosed is not known. Recent studies contain only a few examples. `'5 We have encountered several disclosures in our journals, which have caused reaction in patients and relatives, despite longstanding policies of masking the eyes and removing superfluous social details. To investigate current editorial opinion on this subject we approached several editors of medical journals and asked them to describe their policies and to comment on the possible need for a set ofguidelines.
A Shallow Network with Combined Pooling for Fast Traffic Sign Recognition

Traffic sign recognition plays an important role in intelligent transportation systems. Motivated by the recent success of deep learning in the application of traffic sign recognition, we present a shallow network architecture based on convolutional neural networks (CNNs). The network consists of only three convolutional layers for feature extraction, and it learns in a backward optimization way. We propose the method of combining different pooling operations to improve sign recognition performance. In view of real-time performance, we use the activation function ReLU to improve computational efficiency. In addition, a linear layer with softmax-loss is taken as the classifier. We use the German traffic sign recognition benchmark (GTSRB) to evaluate the network on CPU, without expensive GPU acceleration hardware, under real-world recognition conditions. The experiment results indicate that the proposed method is effective and fast, and it achieves the highest recognition rate compared with other state-of-the-art algorithms.
d-Propoxyphene is a Potent Inhibitor of Debrisoquine, but Not S-Mephenytoin 4‐Hydroxylation In Vivo

The debrisoquine and S-mephenytoin 4-hydroxylation phenotyping tests were performed in 14 healthy subjects. All were extensive metabolizers of both drugs. After at least 4 weeks, they received a 150 mg tablet of d-propoxyphene and 5 h later the debrisoquine-mephenytoin test was repeated. This single dose of d-propoxyphene caused no change in mephenytoin S/R ratio, but increased the debrisoquine metabolic ratio (MR) in each subject (p < 0.025). The four subjects with a relatively high MR (5.1–8.3) in the first test had an MR of debrisoquine in the second test ranging between 22 and 40, falsely classifying them as "poor metabolizers" of debrisoquine. This shows that d-propoxyphene is a potent inhibitor of debrisoquine, but not of S-mephenytoin 4-hydroxylase in vivo. A previous in vitro study has shown that d-propoxyphene inhibits the hydroxylation of desipramine, which is a substrate of the debrisoquine hydroxylase.
Flare Activity and Magnetic Helicity Injection by Photospheric Horizontal Motions

We present observational evidence that the occurrence of homologous flares in an active region is physically related to the injection of magnetic helicity by horizontal photospheric motions. We have analyzed a set of 1 minute cadence magnetograms of NOAA AR 8100 taken over a period of 6.5 hr by the Michelson Doppler Imager on board the Solar and Heliospheric Observatory. During this observing time span, seven homologous flares took place in the active region. We have computed the magnetic helicity injection rate into the solar atmosphere by photospheric shearing motions and found that a significant amount of magnetic helicity was injected during the observing period. In a strong M4.1 flare, the magnetic helicity injection rate impulsively increased and peaked at the same time as the X-ray flux. The flare X-ray flux integrated over the X-ray emission time strongly correlates with the magnetic helicity injected during the flaring interval. The integrated X-ray flux is found to be a logarithmically increasing function of the injected magnetic helicity. Our results suggest that injection of helicity and abrupt increase of helicity magnitude play a significant role in flare triggering.
STK15 Gene Overexpression, Centrosomal Amplification, and Chromosomal Instability in the Absence of STK15 Mutations in Laryngeal Carcinoma

Centrosomes regulate cell division by forming bipolar mitotic spindles and, thus, play an essential role in the maintenance of chromosomal stability. Centrosomal amplification has been found commonly among tumor cells. Previous studies have suggested that a STK15 (serine/threonine kinase 15) gene can induce centrosomal amplification, chromosomal instability, and cell transformation. To investigate the role of STK15 gene abnormalities in the occurrence of centrosomal amplification and chromosomal instability, a combinatory approach has been taken to investigate the expression level and point mutations of the STK15 and centrosomal/chromosomal aberrations among 72 cases of laryngeal squamous cell carcinoma and a representative Hep-2 cell line. Although no mutation was detected within its exons 6 or 7, overexpression of STK15 has been found in 47 cases (65 percent) as well as in the Hep-2 cell line; for the latter apparent centrosomal amplification also has been noted, with the number of centrosomes within a single cell varying between 1 and 7 and the proportion of cells with amplified centrosomes reaching 11∼ 23 percent. Karyotype analysis of Hep-2 cell line has suggested common occurrence of chromosomal aberrations, with the number of chromosomes ranging between 43 and 84, modal number between 69 and 74, and structural aberrations, represented by 13 marker chromosomes, including translocations, deletions, and isochromosomes found in various subclones. Our results suggest that in Hep-2 cell line overexpression of STK15 gene may cause centrosomal amplification thereby result in chromosomal instability through abnormal mitosis. Detection of STK15 overexpression in laryngeal carcinoma has led us to propose that the above may be one of the mechanisms underlying laryngeal carcinogenesis.
Superior fatigue resistance of elite black South African distance runners.

Black athletes currently dominate long-distance running events in South Africa. In an attempt to explain an apparently superior running ability of black South African athletes at distances > 3 km, we compared physiological measurements in the fastest 9 white and 11 black South African middle-to long-distance runners. Whereas both groups ran at a similar percentage of maximal O2 uptake (%VO2max) over 1.65-5 km, the %VO2max sustained by black athletes was greater than that of white athletes at distances > 5 km (P < 0.001). Although both groups had similar training volumes, black athletes reported that they completed more exercise at > 80% VO2max (36 +/- 18 vs. 14 +/- 7%: P < 0.005). When corrections were made for the black athletes' smaller body mass, their superior ability to sustain a high %VO2max could not be explained by any differences in VO2max, maximal ventilation, or submaximal running economy. Superior distance running performance of the black athletes was not due to a greater (+/- 50%) percentage of type I fibers but was associated with lower blood lactate concentrations during exercise. Time to fatigue during repetitive isometric muscle contractions was also longer in black runners (169 +/- 65 vs. 97 +/- 69 s; P < 0.05), but whether this observation explains the superior endurance or was due to the lower peak muscle strength (46.3 +/- 10.3 vs. 67.5 +/- 18.0 Nm/l lean thigh volume; P < 0.01) remains to be established.