Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of nitrogen converters in membrane bioreactor

In this study, the activity and diversity of nitrogen converters, ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), ammonia-oxidizing archaea (AOA) and Anammox bacteria in a pilot-scale membrane bioreactor (MBR) were investigated and monitored using amoA and 16S rDNA-based molecular tools. The pilot-scale MBR (100 m3/day) was located inside the full-scale Pasakoy Advanced Wastewater Treatment Plant (WWTP), and operated for approximately 5 months without sludge purge. During 148 days of operation, volatile suspended solids (VSS) concentration increased from 2,454 mg/L to 10,855 mg/L and the average organic carbon and ammonia nitrogen removal rates were 92% and 99%, respectively. Real-time PCR results indicated that the fraction of AOB increased from 2.94% to 4.05% when VSS concentration reached to 3,750 mg/L throughout 148 days of operation. At higher VSS concentrations, the fraction of AOB declined gradually to 1.15% while the fraction of Nitrospira population was varied between 8.23 and 13.01%. However, significant change or any positive and negative correlations between VSS concentration and Nitrospira population were not observed in this period. The phylogenetic analysis revealed that MBR harbored diverse AOB community which was related to the Nitrosomonas and Nitrosospira lineage. Candidatus Nitrospira defluvii was the only detected NOB in this study.
Neonatal Antibiotic Treatment Is a Risk Factor for Early Wheezing

OBJECTIVE. The use of antibiotics in infancy and subsequent changes in the intestinal bacterial flora have been discussed as risk factors for the development of asthma. However, it has been difficult to exclude the possibility that antibiotics have been given in early episodes of wheezing. As a result, there has been a risk of reverse causation. To minimize the risk of reverse causation, we have focused on the effect of antibiotics that are already administered on the neonatal ward. METHODS. In a cohort study of infants born in western Sweden in 2003, we studied the development of wheezing. The families of the infants were randomly selected and sent a questionnaire at child ages 6 and 12 months. The response rate was 68.5% to the 6-month questionnaire and 68.9% to the 12-month questionnaire. RESULTS. At 12 months, 20.2% of infants had had 1 or more episodes of wheezing, and 5.3% had had 3 or more episodes. Inhaled corticosteroids had been taken by 4.1% of the infants. Independent risk factors for wheezing disorder treated with inhaled corticosteroids were neonatal antibiotic treatment, male gender, gestational age of <37 weeks, having a mother with asthma, having a sibling with asthma or eczema, and breastfeeding for <5 months. CONCLUSIONS. Treatment with antibiotics in the neonatal period was an independent risk factor for wheezing that was treated with inhaled corticosteroids at 12 months of age. These results indirectly support the hypothesis that an alteration in the intestinal flora can increase the risk of subsequent wheezing.
On the assembly of 3D higher-order Nedelec curl-conforming tetrahedral elements

In previous publications, the authors have proposed a methodology for the practical implementation of the Nedelec's (1980) first family of curl-conforming tetrahedral elements. The implementations corresponding to orders higher than one exhibit important differences with respect to those appeared in the literature. This paper deals with the assembly of the higher-order finite elements thus obtained. In particular, two different options are proposed to define the degrees of freedom associated to the faces of neighboring elements. Both options allow one to perform the computations over the parent element, while providing the tangential continuity through elements when utilizing the conventional finite element assembly procedure. The advantages and disadvantages of the two options are compared.
Novel Pan-Genomic Analysis Approach in Target Selection for Multiplex PCR Identification and Detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia Complex Species: a Proof-of-Concept Study

ABSTRACT Burkholderia pseudomallei, Burkholderia thailandensis, and the Burkholderia cepacia complex differ greatly in pathogenicity and epidemiology. Yet, they are occasionally misidentified by biochemical profiling, and even 16S rRNA gene sequencing may not offer adequate discrimination between certain species groups. Using the 23 B. pseudomallei, four B. thailandensis, and 16 B. cepacia complex genome sequences available, we identified gene targets specific to each of them (a Tat domain protein, a 70-kDa protein, and a 12-kDa protein for B. pseudomallei, B. thailandensis, and the B. cepacia complex, respectively), with an in-house developed algorithm. Using these targets, we designed a robust multiplex PCR assay useful for their identification and detection from soil and simulated sputum samples. For all 43 B. pseudomallei, seven B. thailandensis, and 20 B. cepacia complex (B. multivorans, n = 6; B. cenocepacia, n = 3; B. cepacia, n = 4; B. arboris, n = 2; B. contaminans, B. anthina, and B. pyrrocinia, n = 1 each; other unnamed members, n = 2) isolates, the assay produced specific products of predicted size without false positives or negatives. Of the 60 soil samples screened, 19 (31.6%) and 29 (48.3%) were positive for B. pseudomallei and the B. cepacia complex, respectively, and in four (6.7%) soil samples, the organisms were codetected. DNA sequencing confirmed that all PCR products originated from their targeted loci. This novel pan-genomic analysis approach in target selection is simple, computationally efficient, and potentially applicable to any species that harbors species-specific genes. A multiplex PCR assay for rapid and accurate identification and detection of B. pseudomallei, B. thailandensis, and the B. cepacia complex was developed and verified.
Anti-Oxidative, Metal Chelating and Radical Scavenging Effects of Protein Hydrolysates from Blue-spotted Stingray

Purpose: To evaluate protein hydrolysates and membrane ultrafiltration fractions of blue-spotted stingray for metal chelating and radical scavenging activities, as well as protection against oxidative protein damage. Methods: Stingray protein isolates were hydrolysed with alcalase, papain and trypsin for 3 h. Alcalase hydrolysate was fractionated by membrane ultrafiltration to yield 10 kDa fractions. Peptide contents, iron and copper chelating activity, 2, 2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) and hydroxyl radical scavenging activities, and protection against oxidative protein damage were evaluated. Results: Three-hour alcalase hydrolysate (3AH) had the highest peptide content and the lowest half maximal effective concentration (EC50) for ABTS radical scavenging (793.9 µg/mL), hydroxyl radical scavenging (6.93 mg/mL), iron chelating (116.4 µg/mL) and copper chelating activity (2136.9 µg/mL) among the hydrolysates. Among the fractions of 3AH, 10 kDa fraction showed the best copper chelating activity. The < 3 kDa and 3 - 10 kDa fractions had similar levels of hydroxyl radical scavenging activity to reduced glutathione. The protective effects of 3AH and < 3 kDa fraction against oxidative protein damage were comparable to that of reduced glutathione. Conclusion: Alcalase is the best protease for producing hydrolysates with metal chelating and antioxidant activities from stingray proteins. Alcalase hydrolysate, specifically its < 3 kDa fraction, has potential for future applications in antioxidant therapy and health food formulation.
Incidental Asymptomatic Orbital Calcifications

Objective To use modern computed tomography (CT) imaging to quantify the incidence of asymptomatic incidental orbital calcifications and describe their histological features. Materials and Methods One hundred orbital CT scans were reviewed. In addition, patients who had orbital calcification(s) detected on a brain CT scan were examined by the ophthalmology service. Results Of the orbital CT scans, 2% had bilateral drusen of the optic nerve head, 3% had calcified scleral plaques anterior to the medial or lateral rectus muscles, and 3% had bilateral ossification of the trochlear apparatus. Routine brain CT scans detected asymptomatic calcifications of the sclera and dura surrounding the proximal optic nerves. Conclusion Incidental asymptomatic orbital calcifications are commonly encountered on modern high-resolution CT images of the brain and orbit. This article should help the clinician to confidently distinguish these densities from foreign bodies or pathological calcifications.
Antimicrobial activity of Piper arboreum and Piper tuberculatum (Piperaceae) against opportunistic yeasts.

In the scope of our ongoing research on bioactive agents from natural sources, 24 extracts and fractions obtained from Piper arboreum Aub. and Piper tuberculatum Jacq. (Piperaceae) were screened for antifungal activity by using broth microdilution method. The current investigation reveals that P. arboreum extracts and fractions were more effective against Candida krusei and Candida parapsilosis than Cryptococcus neoformans. The growth of Candida albicans was weakly affected by all the tested extracts and fractions. The strongest effects were observed for hexane and ethyl acetate fractions from leaves of P. arboreum, with MIC values (in ig/ml) of 15.6 and 31.2 ig/ml against C. krusei, respectively. Additionally, phytochemical investigation of the hexane fraction of P. arboreum leaves furnished 3 pyrrolidine amides; piperyline, 4,5-dihydropiperyline and tetrahydropiperyline, which could be responsible, at least in part for the observed antifungal activity. The most active compound, tetrahydropiperyline, displayed MIC values of 15.6 ig/ml against C. krusei, C. parapsilosis and C. neoformans.
Changes in brainstem auditory evoked potentials among North Indian females with Type 2 diabetes mellitus

Background: Diabetes mellitus is a complex metabolic disorder whose detrimental effects on various organ systems, including the nervous system are well known. Aim: This study was conducted to determine the changes in the brainstem auditory evoked potentials (BAEP) in patients with type 2 diabetes mellitus. Materials and Methods: In this case-control study, 116 females with type 2 diabetes and 100 age matched, healthy female volunteers were selected. The brainstem auditory evoked potentials (BAEP) were recorded with RMS EMG EP Marc-II Channel machine. The measures included latencies of waves I, II, III, IV, V and Interpeak latencies (IPL) I-III, III-V and I-V separately for both ears. Data was analysed statistically with SPSS software v13.0. Results: It was found that IPL I-III was significantly delayed (P = 0.028) only in the right ear, while the latency of wave V and IPL I-V showed a significant delay bilaterally (P values for right ear being 0.021 and 0.0381 respectively while those for left ear being 0.028 and 0.016 respectively), in diabetic females. However, no significant difference (P > 0.05) was found between diabetic and control subjects as regards to the latencies of waves I, II, III, IV and IPL III-V bilaterally and IPL I-III unilaterally in the left ear. Also, none of the BAEP latencies were significantly correlated with either the duration of disease or with fasting blood glucose levels in diabetics. Conclusions: Therefore, it could be concluded that diabetes patients have an early involvement of central auditory pathway, which can be detected quite accurately with the help of auditory evoked potential studies.
A major gibberellic Acid-induced barley aleurone cysteine proteinase which digests hordein : purification and characterization.

We previously described the purification and characterization of a 37,000 M(r) cysteine proteinase, designated EP-A, from gibberellic acid (GA(3))-induced barley (Hordeum vulgare L.) aleurone layers (S Koehler, T-HD Ho [1988] Plant Physiol 87: 95-103). A second, more abundant protease has now been purified from this tissue. This protease, designated EP-B, has an apparent M(r) of 30,000 on 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). It resolves into two bands during native isoelectric focusing with pl of 4.6 to 4.7. The analysis of hemoglobin digestion products by both gradient SDS-PAGE and Bio-Gel P2 chromatography, the inhibition of protease activity by E-64, leupeptin, iodoacetate, and p-hydroxymercuribenzoate, and N-terminal amino acid sequence analysis all indicate that EP-B is a cysteine proteinase. The first 22 amino acids at the N terminus of EP-B have been determined, and their sequence is 90% similar to that of EP-A. EP-B has properties similar to EP-A; however, EP-B is much more sensitive to high pH during gel electrophoresis and therefore is not detectable on native activity gels used to detect EP-A. Its pH optimum against azocasein and hemoglobin is 4.5 to 4.6. Both of these proteinases digest hordeins enriched for the B and D fractions into similar peptides of 25,000 to 2,000 M(r) as determined by gradient SDS-PAGE.
Partial protection against muscle damage by eccentric actions at short muscle lengths.

PURPOSE This study investigated the hypothesis that maximal eccentric actions at a short muscle length would fail to confer a protective effect against muscle damage induced by maximal eccentric exercise at a long muscle length. METHODS Eleven males performed 24 maximal eccentric actions of the nondominant elbow flexors over a short extension range from an elbow joint angle of 0.87-1.74 rad (S-ECC) followed 4 wk later by eccentric actions at a long range of 2.27-3.14 rad (L-ECC). A second group of 11 males performed L-ECC on two occasions using the nondominant arm separated by 4 wk. Changes in maximal isometric strength, range of motion, upper arm circumference, muscle soreness, plasma creatine kinase and aspartate aminotransferase activities, and B-mode ultrasound images were compared between bouts and between groups by two-way repeated measures ANOVA. RESULTS All measures changed significantly (P < 0.01) after the first bout; however, the effects were significantly (P < 0.01) smaller after S-ECC compared with L-ECC. The second bout resulted in significantly (P < 0.01) reduced changes in all measures compared with the first bout in the subjects who performed L-ECC on both occasions. The subjects who performed S-ECC in the first bout displayed significantly smaller changes after L-ECC than those seen after L-ECC alone, with the degree of attenuation being around 50-70%. CONCLUSION Contrary to the hypothesis, S-ECC provided partial but effective protection against L-ECC. This result suggests adaptations associated with the repeated bout effect were also produced after S-ECC, but the degree of adaptations was not as strong as that by L-ECC. Eccentric exercise at a short extension range can be used as a strategy to present severe muscle damage.
Crystal structures of three 3-chloro-3-methyl-2,6-diarylpiperidin-4-ones

The syntheses and crystal structures of 3-chloro-3-methyl-r-2,c-6-diphenylpiperidin-4-one and two of its derivatives are described. In each structure, the piperidine ring adopts a chair conformation. In the crystals, molecules are linked into C(6) chains by weak N—H⋯O hydrogen bonds and C—H⋯π interactions are also observed.
Safety and Pharmacokinetics of Ribavirin for the Treatment of La Crosse Encephalitis

Background: La Crosse viral encephalitis (LACVE) is associated with residual epilepsy and neurocognitive deficits in survivors. This report summarizes 3 phases of clinical studies of children treated with intravenous (IV) ribavirin (RBV), each one exploring a different phase (I, IIA, IIB) of clinical trial development. Methods: In phase I, 7 children with life-threatening LACVE were treated with emergency use RBV using a moderate IV dose (8.33 mg/kg/dose q 8 hours day 1, 5 mg/kg/dose q 8 hours days 2–10). In phase IIA, 12 children with severe LACVE were enrolled: 8 treated with RBV (same dose as phase I) and 4 with placebo. In phase IIB an escalated dose was used (33 mg/kg dose 1, then 16 mg/kg/dose q 6 hours for 4 days, and 8 mg/kg/dose q 8 hours for 3 days). Results: In a group of 15 children treated in phase I and phase IIA, RBV appeared safe at moderate dose, but based on steady-state RBV levels of 9.3 &mgr;M, estimated cerebrospinal fluid levels were less than 20% of the EC50 of RBV for LACVE. At the escalated dose used in phase IIB, adverse events occurred, likely related to RBV, and therefore the trial was discontinued. Nevertheless, valuable pharmacokinetic (PK) and safety data were obtained at moderate dose, with potential treatment implications for other indications. Conclusions: Although the results do not support the use of RBV for LACVE, this nevertheless is the largest study of antiviral treatment for LACVE to date and the largest pharmacokinetic analysis of IV RBV in children for any indication.
Interplay of transcription factors in T‐cell differentiation and function: the role of Runx

Over the past years, increasing numbers of distinct subsets have been discovered and identified for a T lymphocytes’ entity. Differentiation and function of each T cell subset are controlled by a specific master transcription factor. Importantly, Runt‐related transcription factors, particularly Runx1 and Runx3, interplay with these master regulators in various aspects of T cells’ immunity. In this review article, we first explain roles of Th‐Pok and Runx3 in differentiation of CD4 versus CD8 single positive cells, and later focus on cross‐regulation of Th‐Pok and Runx3 and their relationship with other factors such as TCR strength. Next, we provide evidences for the direct interplay of Runx1/3 with T‐bet and GATA3 during Th1 versus Th2 commitment to activate or silence transcription of signature cytokine genes, IFNγ and IL4. Lastly, we explain feed‐forward relationship between Runx1 and Foxp3 and discuss roles of Runx1 in regulatory T cells’ suppressive activity. This review highlights an essential importance of Runx molecules in controlling various T cell subsets’ differentiation and functions through molecular interplay with the master transcription factors in terms of protein‐protein interaction as well as regulation of gene expression.
A new discrepancy of HPA‐3 genotyping because of a rare HPA‐27bw polymorphism

Dear Sir, Foetal/neonatal alloimmune thrombocytopenia (FNAIT) results from maternal alloimmunisation against foetal platelet antigens. To date, 29 human platelet antigens (HPAs) have been described (database of the European Bioinformatics Institute: http://www.ebi.ac.uk/ipd/hpa/table1.html). Diagnosing FNAIT is important for both the management of the index case and antenatal management in subsequent pregnancies. Laboratory diagnosis relies on the detection of maternal alloantibodies and identification of the offending antigen by HPA typing. Because of the scarcity of phenotyping reagents in platelet immunology, most laboratories perform genotyping, but a number of uncharacterised mutations and single nucleotide polymorphisms located near the HPA polymorphism have been reported to cause false genotyping results (Bertrand et al., 2010; Nogues et al., 2013). Here, we report the case of a 28-year-old woman from Angola, third pregnancy/second delivery (one voluntary abortion), who gave birth to a severely thrombocytopenic boy at 39 weeks of gestation (WG) (newborn platelet count at delivery: 50·109/L; Fig. 1a). The father was from Congo. During the pregnancy, gestational thrombocytopenia was observed at 35 WG (90·109/L), which was treated with intravenous immunoglobulin (IvIg); no maternal anti-platelet autoantibody was detected. A total of 12 h after delivery, the newborn’s platelet count was 24·109/L, and he was admitted into the intensive care unit even though no bleeding had been observed. He was given two platelet transfusions and IvIg. The baby’s platelet count slowly rose, and he was finally discharged in good health 16 days after delivery (Fig. 1a). In the absence of any evidence of a non-immune aetiology, tests were carried out to investigate this case of neonatal thrombocytopenia. HPA genotyping of the parents and baby by PCR-SSP (HPA Ready Gene Plus kit, Inno-Train) showed HPA-5b feto-maternal incompatibility. Using the MAIPA method, antibodies against HPA-5b were detected in the mother’s blood, confirming the diagnosis of FNAIT. Surprisingly, the newborn’s genotype was found to be HPA-3bb, whereas the mother was HPA-3aa and the father HPA-3ab (PCR-SSP). In order to investigate this, exon 26 of the integrin αIIb gene (GPIIb) was sequenced (Fig. 1b). The HPA-3 typing of the parents was confirmed, but the newborn was HPA-3ab not HPA-3bb; the ‘a’ allele was not amplified by
Tarih Öğretiminde Tarih Dizilerinin Kullanımına İlişkin Öğrenci Görüşleri-Nitel Bir Analiz-

Bu calismanin amaci tarih derslerinde tarih dizilerinin kullanimina iliskin ogrenci goruslerini belirlemektir. Calismada nitel arastirma desenlerinden olgu bilim deseni kullanilmistir. Arastirmanin verileri Afyonkarahisar ilinde ogrenim goren lise ogrencileriyle bes acik uclu sorudan olusan odak gorusme formu yoluyla toplanmistir. Arastirmanin calisma grubunu Afyon Endustri Meslek Lisesinde ve Afyon Milli Piyango Anadolu Lisesinde ogrenim goren on dort ogrenci olusturmaktadir. Verilerin analizinde icerik analizi yontemi kullanilmistir. Arastirma bulgularina gore: On dort ogrenciden dokuzu tarih dizilerinin tarihi gercekleri yansitmadigini ifade etmistir. Alti ogrenciye gore tarih dizileri ogrencileri arastirmaya ve sorgulamaya sevk etmektedir. Sekiz ogrenci dizilerdeki karakter ve nesnelerin tarihi gercekleri yansitmadigini ifade etmistir. On bir ogrenci dizilerin ogrencileri olumsuz yonde etkiledigini ifade etmistir. Sekiz ogrenci dizilerin bu sekliyle ogretim materyali olarak kullanilamayacagini belirtmistir. Sonuc olarak tarih dizilerinin tarih ogretiminde oldukca onemli olduguna fakat dizilerin bu sekliyle tarih derslerinde kullaniminin mumkun olamayacagi sonucuna varilmistir.
The ability of general practitioners to detect mental disorders among primary care patients in a stressful environment: Gaza Strip.

BACKGROUND The aim of the present study was to investigate the detection rate by general practitioners (GPs) of mental disorders in a primary health care setting and relating the findings to selected GP characteristics and the patient sociodemographic characteristics. METHODS The patients were assessed with respect to mental disorders by Hopkins Symptom Checklist 25 (HSCL-25), and the GPs were independently asked to fill in the Goldberg checklist II to assess the patient after consultation. The sample consisted of 10 primary health care clinics in the Gaza Strip, which were randomly selected from the five regions that form the Gaza Strip (Northern, Southern region, Gaza City, Middle region, Khan-Younis and Rafah). Thirty-two GPs and 661 patients participated in the study. RESULTS The study showed that the GPs detected only 11.6 per cent of patients with mental disorders at HSCL-25 score >1.75, and that the GP's assessment was not significantly associated with the HSCL-25 scores. GPs with postgraduate psychiatric training performed better in detecting mental disorders, likewise female GPs and those who were more than 40 years old. The results also revealed that the GPs were more able to detect mental disorders among patients older than 25 years, and in female patients. CONCLUSIONS The GPs' poor detection rate of mental disorders indicates the importance of mental health training for GPs working in primary health care clinics.