Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and clinical correlates of irritability in major depressive disorder: a preliminary report from the Sequenced Treatment Alternatives to Relieve Depression study.

BACKGROUND Irritability is a common feature of major depressive disorder (MDD), though it is not included in the DSM-IV diagnostic criteria for adult MDD and is not assessed in most standard depression rating scales. Irritability with or without depression has been associated with risk for suicide, violence, and cardiovascular disease. METHOD The prevalence of significant levels of irritability was examined among the first 1456 outpatients with nonpsychotic MDD entering the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Sociodemographic and clinical features were compared for participants who did and did not report irritability at least 50% of the time during the week preceding study entry. RESULTS Of 1456 evaluable subjects, 582 (40%) reported irritability more than half the time. These individuals were more likely than nonirritable subjects to be female, to be younger, to be unemployed, and to report a history of at least 1 suicide attempt. Functional status and quality of life were also poorer in this group. Irritability was correlated with overall depressive severity, which accounted for nearly all of the clinical differences noted, with the exception of vascular disease, for which the association persisted after controlling for age, sex, and depressive severity. CONCLUSION Irritability is prevalent among depressed outpatients and associated with a greater likelihood of suicide attempts, poorer functional status, and greater prevalence of vascular disease. It is correlated with overall depression severity and thus may not represent a distinct depressive subtype per se. The impact of irritability on course and treatment outcome merits further study.
Electrostatic stabilization of a thermophilic cold shock protein.

The cold shock protein Bc-Csp from the thermophile Bacillus caldolyticus differs from its mesophilic homolog Bs-CspB from Bacillus subtilis by 15.8 kJ mol(-1) in the Gibbs free energy of denaturation (DeltaG(D)). The two proteins vary in sequence at 12 positions but only two of them, Arg3 and Leu66 of Bc-Csp, which replace Glu3 and Glu66 of Bs-CspB, are responsible for the additional stability of Bc-Csp. These two positions are near the ends of the protein chain, but close to each other in the three-dimensional structure. The Glu3Arg exchange alone changed the stability by more than 11 kJ mol(-1). Here, we elucidated the molecular origins of the stability difference between the two proteins by a mutational analysis. Electrostatic contributions to stability were characterized by measuring the thermodynamic stabilities of many variants as a function of salt concentration. Double and triple mutant analyses indicate that the stabilization by the Glu3Arg exchange originates from three sources. Improved hydrophobic interactions of the aliphatic moiety of Arg3 contribute about 4 kJ mol(-1). Another 4 kJ mol(-1) is gained from the relief of a pairwise electrostatic repulsion between Glu3 and Glu66, as in the mesophilic protein, and 3 kJ mol(-1) originate from a general electrostatic stabilization by the positive charge of Arg3, which is not caused by a pairwise interaction. Mutations of all potential partners for an ion pair within a radius of 10 A around Arg3 had only marginal effects on stability. The Glu3-->Arg3 charge reversal thus optimizes ionic interactions at the protein surface by both local and global effects. However, it cannot convert the coulombic repulsion with another Glu residue into a corresponding attraction. Avoidance of unfavorable coulombic repulsions is probably a much simpler route to thermostability than the creation of stabilizing surface ion pairs, which can form only at the expense of conformational entropy.
Genome-wide codon usage profiling of ocular infective Chlamydia trachomatis serovars and drug target identification

Chlamydia trachomatis (C.t) is a Gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B and C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering potential drug targets and genomic influence on pathogenesis. Hence, in this study we performed deep statistical profiling of codon usage in these serovars. The overall base composition analysis reveals that these serovars are over biased to AU than GC. Similarly, relative synonymous codon usage also showed preference towards A/U ending codons. Parity Rule 2 analysis inferred unequal distribution of AT and GC, indicative of other unknown factors acting along with mutational pressure to influence codon usage bias (CUB). Moreover, absolute quantification of CUB also revealed lower bias across these serovars. The effect of natural selection on CUB was also confirmed by neutrality plot, reinforcing natural selection under mutational pressure turned to be a pivotal role in shaping the CUB in the strains studied. Correspondence analysis (COA) clarified that, C.t C/TW-3 to show a unique trend in codon usage variation. Host influence analysis on shaping the codon usage pattern also inferred some speculative relativity. In a nutshell, our finding suggests that mutational pressure is the dominating factor in shaping CUB in the strains studied, followed by natural selection. We also propose potential drug targets based on cumulative analysis of strand bias, CUB and human non-homologue screening.
Research methodology education in computing: Arrangements and results from two courses

Research methodology education is one of the less studied and discussed areas of computing education. Underplaying methodological education starts from computing curricula, which discuss methodology to different degrees, depending on the branch of computing. In computer science education research, programming courses have been analyzed through and through, but methodology courses in computing are largely devoid of course descriptions, analytic studies, and experimental studies. This paper presents the learning objectives, contents, and arrangements for a fully online graduate level course on research methodology and research design in computing. The course was run twice in a relatively large school of computing (6915 students) and it included students from a neighboring institution of the same size. Students' (N=136) learning was analyzed from multiple viewpoints. Their final work was analyzed qualitatively by course facilitators as well as scored on a 90-point scale. Their coursework was qualitatively reviewed and graded by their peers and facilitators. The effect of students' learning approaches to course results was analyzed using Biggs' R-SPQ-2F questionnaire. Student feedback was collected using a slightly modified course feedback questionnaire of the university. This paper presents the course arrangements, course results, and analysis of students' learning.
Quality of Indian mackerel as affected by pomegranate peel and tea leaf extracts during ice storage

The effect of dip treatments of Indian mackerel ( Rastriliger kanagurta ) in 0.5 % & 1 % pomegranate peel extracts (Punica granatum) (PPE) and 3 % & 5 % green tea (Camelia sinensis) (GTE) extracts; on the ice storage characteristics was evaluated. Total phenolic content of PPE and GTE were found to be 212±20.55 and 159.3±7.72 mg g -1 tannic equivalent. Fish treated with PPE and GTE were evaluated for bio-chemical, microbiological and sensory attributes during the period of storage in ice. Indicator organisms like Escherichia coli , and Staphylococcus aureus were not detected in any sample, whereas biochemical attributes increased significantly (p < 0.05) during the storage period. The fishes were acceptable up to 17th and 16th days in ice in case of PPE & GTE treatments, respectively. On the other hand the untreated fish was acceptable only up to 8 days. From this study it is concluded that; the natural extracts of PPE & GTE can be used to preserve the fatty fish and extend the shelf life during ice storage for a considerable period. SAARC J. Agri. , 13(1): 109-122 (2015)
Early Life Body Fatness and Risk of Colorectal Cancer in U.S. Women and Men—Results from Two Large Cohort Studies

Background: The association between body fatness before adulthood and later risk of colorectal cancer remains unclear. We hypothesized that, independent of adult body fatness, early life body fatness would be associated with a higher risk of developing colorectal cancer. Methods: We assessed body fatness during childhood and adolescence using a validated 9-level somatotype and inquired body weight in young adulthood in the Nurses' Health Study and Health Professionals Follow-up Study. We used the Cox proportional hazard regression modeling to estimate relative risks [RR, 95% confidence intervals (CI)] adjusting for adult body mass index (BMI) and other known colorectal cancer risk factors. Results: We identified 2,100 incident colorectal cancer cases (1,292 in women and 808 in men) during 22 years of follow-up. Among women, the RR (95% CI) for childhood body fatness of level 5 or higher versus level 1 was 1.28 (1.04–1.58; Ptrend = 0.08) and for adolescent body fatness, it was 1.27 (1.01–1.60; Ptrend = 0.23). The corresponding RRs for men were 1.04 (0.82–1.31; Ptrend = 0.48) and 0.98 (0.75–1.27; Ptrend = 0.20), respectively. Results were generally similar across anatomic subsites within the colorectum. In addition, the RRs comparing BMI categories ≥27.5 to <19 kg/m2 were 1.44 (1.06–1.95, at age 18; Ptrend = 0.009) for women and 1.18 (0.84–1.65, at age 21; Ptrend = 0.57) for men. Conclusion: Increased body fatness in early life, independent of adult obesity, might be a risk factor for colorectal cancer in women, but we observed a weaker association in men. Impact: Our findings support the growing evidence that early life body fatness affects the risk of colorectal cancer many decades later. Cancer Epidemiol Biomarkers Prev; 24(4); 690–7. ©2015 AACR.
Isolated Pancreatic Islets in Three-Dimensional Matrices are Responsive to Stimulators and Inhibitors of Angiogenesis

The formation of a new microvasculature is essential for the long-term survival and function of the islet graft. In this study we examined endothelium of isolated pancreatic islets by stimulation with growth factors, different culture conditions, and genetic modification. We also inspected the effect of immunosuppressives used in human transplantation on angiogenesis. Isolated islets were embedded in a three-dimensional fibrin or Matrigel matrix. The effect of hyperglycemia, hypoxia, and the addition of VEGF and bFGF was investigated. We exposed islets from transgenic mice expressing the VEGF gene (RIP1VEGF-A) to high glucose (16.7 mmol/L) medium and tested the immunosuppressive agents rapamycin (100 ng/ml) and FK506 (100 ng/ml). To quantify angiogenesis the percentage of sprouting islets was determined. New endothelial capillary-like structures protruded from isolated pancreatic islets. Addition of VEGF to the islets and transgenic RIP-VEGF islets showed a two- to threefold increase of sprouting islets compared to control. Hypoxic culture conditions stimulated angiogenesis, resulting in a twofold increase of capillary sprouting. Rapamycin and FK506 proved to be potent inhibitors of angiogenesis in this system, because a decrease of sprouting islets of more than 20% by both agents was observed. Isolated pancreatic islets are capable of forming new capillary structures and are susceptible to pro- and antiangiogenic stimuli.
Effects of magnesium chloride on smooth muscle actomyosin adenosine-5'-triphosphatase activity, myosin conformation, and tension development in glycerinated smooth muscle fibers.

The contractile system of smooth muscle exhibits distinctive responses to varying Mg2+ concentrations in that maximum adenosine-5'-triphosphatase (ATPase) activity of actomyosin requires relatively high concentrations of Mg2+ and also that tension in skinned smooth muscle fibers can be induced in the absence of Ca2+ by high Mg2+ concentrations. We have examined the effects of MgCl2 on actomyosin ATPase activity and on tension development in skinned gizzard fibers and suggest that the MgCl2-induced changes may be correlated to shifts in myosin conformation. At low concentrations of free Mg2+ (less than or equal to 1 mM) the actin-activated ATPase activity of phosphorylated turkey gizzard myosin is reduced and is increased as the Mg2+ concentration is raised. The increase in Mg2+ (over a range of 1-10 mM added MgCl2) induces the conversion of 10S phosphorylated myosin to the 6S form, and it was found that the proportion of myosin as 10S is inversely related to the level of actin-activated ATPase activity. Activation of the actin-activated ATPase activity also occurs with dephosphorylated myosin but at higher MgCl2 concentrations, between 10 and 40 mM added MgCl2. Viscosity and fluorescence measurements indicate that increasing Mg2+ levels over this concentration range favor the formation of the 6S conformation of dephosphorylated myosin, and it is proposed that the 10S to 6S transition is a prerequisite for the observed activation of ATPase activity. With glycerinated chicken gizzard fibers high MgCl2 concentrations (6-20 mM) promote tension in the absence of Ca2+. (ABSTRACT TRUNCATED AT 250 WORDS)
Quantitative gray‐scale analysis in skeletal muscle ultrasound: A comparison study of two ultrasound devices

Muscle ultrasound is a useful technique to detect neuromuscular disorders. Quantification of muscle echo intensity (EI) using gray‐scale analysis is more reliable and more sensitive compared with visual evaluation of the images. We devised a method to reliably use EI normal values established with one ultrasound device for use with another device. Based on measurements in a dedicated phantom and in 7 healthy subjects, a conversion equation was calculated to convert the mean EI. The reliability of this equation was next evaluated in a follow‐up study of 22 healthy children. Mean muscle EI could be reliably converted from one ultrasound device to another. This allows for normal values obtained with one device to be used with other devices, which is an important step forward toward the use of quantitative muscle ultrasound in daily clinical care. Muscle Nerve, 2009
Citation classics in radiology journals: the 100 top-cited articles, 1945-2012.

OBJECTIVE The number of citations an article receives after its publication reflects its impact in the scientific community. The aim of this study was to identify and characterize the 100 top-cited articles published in radiology journals. MATERIALS AND METHODS The top-cited articles published in 12 radiology journals were identified using the database of Science Citation Index Expanded (1945-2012). The 100 top-cited articles were selected and analyzed with regard to the number of citations, year of publication, publishing journal, authorship, institution and country of origin, type of article, radiologic subspecialty, main topic, and radiologic technique. RESULTS The 100 top-cited articles were published in eight radiology journals, led by Radiology (n=67) and followed by the American Journal of Roentgenology (n=11). These articles were published between 1939 and 2006 with a mean of 664.3 citations per article (range, 371-6931). Seventy-eight articles were published after 1979, 57 originated from the United States, and 69 were original articles. The most common subspecialties of study were interventional radiology (n=19), neuroradiology (n=15), and breast imaging (n=11). The main topics of articles were radiofrequency ablation of hepatic tumors (n=9), followed by receiver operating characteristic curves (n=6). CONCLUSION Our study presents a detailed list and analysis of the 100 top-cited articles published in radiology journals, which provides insight into historical developments in the field of radiology.
Antibodies against Phosphorylcholine among New Guineans Compared to Swedes: An Aspect of the Hygiene/Missing Old Friends Hypothesis

ABSTRACT Background: We here study antibodies against phosphorylcholine (anti-PC) which we reported to be inversely associated with atherosclerosis, cardiovascular disease (CVD), and autoimmune conditions. In previous studies, we determined that this inverse association is more pronounced at low levels with high risk and at high levels, with decreased risk. We compare individuals from Kitava, New Guinea (with low risk of these conditions), with Swedish controls. Methods: We studied a group of 178 individuals from Kitava (age 20–86), and compared those above age 40 (n = 108) with a group of age- and sex-matched individuals from a population based cohort in Sweden (n = 108). Traditional risk factors for CVD and fatty acids were determined. IgM, IgG, and IgA anti-PC were tested by enzyme-linked immunosorbent assay (ELISA). Results: All anti-PC measures were significantly lower among Swedish controls as compared to Kitavans (p < 0.001), independent of traditional risk factors. Having low levels of anti-PC, defined as below 25th percentile of values among Swedish controls, was associated with this cohort after adjustment for other risk factors (OR 5.7, 95% CI 2.2–14.7 for IgM; OR 31.7, 95% CI 3.9–252 for IgA; and OR 11.1, 95% CI 2.4–51 for IgG). Conclusions: PC is highly exposed on microorganisms and helminths (common on Kitava) exposing much PC which humans and hominids may have been exposed to for millions of years. We propose that low anti-PC levels in the developed world could be a new aspect of the hygiene hypothesis, generating a pro-inflammatory and pro-atherosclerotic state.
Identification and characterization of bovine oviductal glycoproteins synthesized at estrus.

Published reports indicate that in several mammalian species the oviduct synthesizes and secretes specific glycoproteins which are components of the luminal fluids at the time of ovulation and fertilization. The present study characterized the secretory glycoproteins synthesized by the bovine oviduct at estrus. Oviducts obtained from four crossbred cows in estrus were flushed with saline, and segments of the ampullary and isthmic regions were fixed for immunocytochemical analyses. The remainder of the tissue was subjected to explant culture for 24 h in medium containing either 3H-leucine or 3H-glucosamine. Analysis of culture media by one- and two-dimensional SDS-PAGE followed by fluorography indicated that both the ampullary and isthmic regions synthesized a major class of Mr 97,000 glycoproteins with isoelectric points ranging from 5.5 to 8.1. A polyclonal antibody was generated to the glycoproteins after their isolation by gel filtration followed by electrophoretic separation. Western blot analysis of oviductal culture media indicated that the antisera cross-reacted with a doublet at Mr 97,000 and to a lesser extent with two additional bands at Mr greater than 200,000. Immunoreactive antigens were not identified in serum or in culture media of ovary, uterus, and nonreproductive tract tissues. The Mr 97,000 glycoproteins were present in oviductal flushings obtained from cows in estrus. They were also detected to a lesser degree in oviductal flushings obtained from cows at Days 5, 10, 15, and 18 of the estrous cycle, with the least amount of immunoreactivity being observed in Day 10 samples. (ABSTRACT TRUNCATED AT 250 WORDS)
Detection of numerical chromosome 17 abnormalities in fine‐needle aspirates of breast cancer using a novel in situ hybridization signal amplification method

We describe a method of in situ hybridization (ISH) to assess numerical chromosome abnormalities on alcohol‐fixed smears obtained by fine‐needle aspiration from breast cancer patients, using a commercially available amplification kit to demonstrate numerical chromosome alterations of chromosome 17. In this staining procedure after detection of the biotin‐labeled α‐satellite probe for chromosome 17 with avidin‐biotin‐peroxidase, we incorporated a signal amplification based on the peroxidase‐catalyzed deposition of a biotinylated phenolic compound followed by a secondary reaction with peroxidase. The reactions are revealed by deposition of diaminobenzidine and can be analyzed in an optical microscope, with total preservation of the morphology, allowing a direct morphologic‐cytogenetic correlation. A series of 25 cases of aspirates from breast cancer were analyzed with this methodology. Aneusomy was found in 14 cases (56%), whereas 11 (44%) had a normal number of chromosome 17 copies. Polysomy occurred in all aneusome cases except one. We did not find concordance between numerical chromosome abnormalities of chromosome 17 and nuclear grading as well as with the immunoexpression of p53 and c‐erbB2 studied in the smears. We conclude that the application of the ISH signal amplification method on alcohol‐fixed smears will eliminate the need for fresh material and will provide several advantages, such as improvement of morphological concomitant analysis without the need for a fluorescence microscope; utilization, whenever malignancy is found, without necessity to reaspirate the patient; and adequacy of archival material. Diagn. Cytopathol. 1998;19:141–146. © 1998 Wiley‐Liss, Inc.
Calretinin is essential for mesothelioma cell growth/survival in vitro: A potential new target for malignant mesothelioma therapy?

Malignant mesothelioma (MM) are highly aggressive asbestos‐related neoplasms, which show strong chemotherapy resistance, and there is no effective cure for MM so far. Calretinin (CR) is widely used as a diagnostic marker for epithelioid and mixed (biphasic) mesothelioma; however, little is known about CR's putative functions in tumorigenesis. CR protects against asbestos‐induced acute cytotoxicity mediated by the AKT/PI3K pathway, and furthermore, SV40 early region genes are able to upregulate CR in mesothelial cells. However, the precise role of CR in mesothelioma is still unknown. Downregulation of CR via lentiviral‐mediated short‐hairpin RNA significantly decreased the viability and proliferation of mesothelioma cells in vitro. The effect was strong in epithelioid‐dominated cell lines (ZL55 and MSTO‐211H). A weaker and delayed effect was observed in mesothelioma cells with prevalent sarcomatoid morphology (SPC111, SPC212 and ZL34). The specificity of the effect was confirmed by stable enhanced green fluorescent protein‐CR expression in mesothelioma cell lines and subsequent downregulation. Depletion of CR led these cancer cell lines to enter apoptosis within 72 hr postinfection via strong activation of the intrinsic caspase 9‐dependent pathway. Downregulation of CR in immortalized mesothelial cells LP9/TERT‐1 strongly blocked proliferation and caused a G1 block without decreasing viability or activating apoptosis pathways. These results demonstrate that downregulation of CR had a strong effect on the viability of MM cells and that CR is essential for cells derived from MM. The authors anticipate these findings to reveal CR as a highly interesting new putative therapeutic target for mesothelioma treatment of especially the epithelioid, as well as of the mixed and sarcomatoid type.