Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling

Reliable detection of peptides in LC‐MS data is a key algorithmic step in the analysis of quantitative proteomics experiments. While highly abundant peptides can be detected reliably by most modern software tools, there is much less agreement on medium and low‐intensity peptides in a sample. The choice of software tools can have a big impact on the quantification of proteins, especially for proteins that appear in lower concentrations. However, in many experiments, it is precisely this region of less abundant but substantially regulated proteins that holds the biggest potential for discoveries. This is particularly true for discovery proteomics in the pharmacological sector with a specific interest in key regulatory proteins. In this viewpoint article, we discuss how the development of novel software algorithms allows us to study this region of the proteome with increased confidence. Reliable results are one of many aspects to be considered when deciding on a bioinformatics software platform. Deployment into existing IT infrastructures, compatibility with other software packages, scalability, automation, flexibility, and support need to be considered and are briefly addressed in this viewpoint article.
Microstructure and Martensitic Transformation Behavior in Thermal Cycled Equiatomic CuZr Shape Memory Alloy

Equiatomic CuZr alloy undergoes a martensitic transformation from the B2 parent phase to martensitic phases (P21/m and Cm) below 150 °C. We clarified the effect of the thermal cycling on the morphology and crystallography of martensite in equiatomic CuZr alloy using a transmission electron microscopy. The 10th cycled specimens consisted of different multiple structures at the maximum temperature of differential scanning calorimetry (DSC) measurement −400 °C and 500 °C, respectively. At the maximum temperature 400 °C of DSC measurement, it is composed of the fine plate-like variants, and a lamellar eutectoid structure consisting of Cu10Zr7 and CuZr2 phases on the martensitic variant. Concerning the maximum temperature of 500 °C of DSC measurement, it is observed the martensitic structure and the lamellar structure in which the martensitic phase was completely eutectoid transformed. The formation of this lamellar eutectoid structure, due to thermal cycling leads to the shift of forward and reverse transformation peaks to low and high temperature side. In addition, new forward and reverse transformation peaks indicating a new transformation appeared by thermal cycling, and the peaks remained around −20 °C. This new martensitic transformation behavior is also discussed.
Pediatric tracheal and endobronchial tumors: an institutional experience.

OBJECTIVES To report the pathologic findings in cases involving endotracheal and endobronchial tumors in the pediatric population and to describe the presenting symptoms and treatment modalities for endotracheal and endobronchial tumors. DESIGN Retrospective chart review. SETTING Tertiary care children's hospital. PATIENTS The study included 14 patients with endotracheal and endobronchial tumors. MAIN OUTCOME MEASURES Patients were selected if bronchoscopy was performed to obtain biopsy specimens from the trachea or bronchus. RESULTS There were 14 cases that met the inclusion criteria between 1993 and 2009. The patients ranged in age from 4 to 18 years. The most common presenting symptom was recurrent pneumonia (n = 6), followed by wheezing or asthma that was unresponsive to treatment (n = 4). Nine lesions (64%) were malignant and 5 (36%) were benign. Of the malignant tumors, 5 (55%) were carcinoid, 3 (33%) were mucoepidermoid carcinoma, and 1 was adenoid cystic carcinoma. There were 1 or 2 cases of each of the following benign to intermediate malignant potential lesions: histoplasmosis nodules, chondroid hamartoma, pulmonary chondroma, and inflammatory myofibroblastic tumor. In 12 cases, definitive treatment included surgical resection. Three of these cases required postoperative chemotherapy and radiotherapy. CONCLUSIONS The results of this series suggest that in the pediatric population tracheal and endobronchial tumors are most likely to be carcinoid tumors or mucoepidermoid carcinomas, both malignant processes. For patients with recurrent pneumonias or chronic wheezing, an occult tumor is a diagnostic consideration that may require additional studies.
Leading learning for Māori students : the challenges of leadership for teaching principals in small rural primary schools

This study focused on examining teaching principals’ perceptions of educational leadership practices that were perceived to transform Māori achievement in small rural primary schools. A kaupapa Māori framework was applied to this research. This involved meeting and interviewing eight teaching principals, in their schools throughout the greater Wairoa, Gisborne and Eastern Bay of Plenty education regions. A sizeable proportion of Māori students are located in isolated, small rural primary schools that are led by teaching principals. The literature suggests a myriad of leadership challenges exist for teaching principals in small rural primary schools. An assumption is made that these challenges have stemmed from the implementation of the self-managing model, Tomorrows Schools (Brooking, Collins, Court, & O'Neil, 2003; Springford, 2006). Findings were analysed qualitatively, generating themes grounded from within each participant’s story. Mentoring and lifestyle choices were considered determinants that influenced people into taking up positions in small rural primary schools. The findings also indicated that there is an alarmingly increasing number of challenges that some teaching principals face alone and without appropriate support. Although twenty five years have gone by since the implementation of the self-managing model of Tomorrow’s Schools teaching principals are continuing to spend a considerable amount of their time supporting and managing responsibilities that should be carried out by Boards of Trustees. A new finding of this research highlights the positive value of having iwi and external providers collaboratively working together with teaching principals to strengthen strategic management, particularly the shaping of the vision of education for the identified iwi primary schools. In these iwi primary schools, teaching principals have committed to implementing and fostering te reo Māori (language), school wide, as part of strengthening and adopting Māori culture, karakia and values through ruma rumaki and mainstream classes.
Back to Anatomy: Improving Landmarking Accuracy of Clinical Procedures Using a Novel Approach to Procedural Teaching

Objectives Many believe that knowledge of anatomy is essential for performing clinical procedures; however, unlike their surgical counterparts, internal medicine (IM) programs rarely incorporate anatomy review into procedural teaching. This study tested the hypothesis that an educational intervention focused on teaching relevant surface and underlying anatomy would result in improved bone marrow procedure landmarking accuracy. Methods This was a preintervention–postintervention prospective study on landmarking accuracy of consenting IM residents attending their mandatory academic half-day. The intervention included an interactive video and visualization exercise; the video was developed specifically to teach the relevant underlying anatomy and includes views of live volunteers, cadavers, and skeletons. Results Thirty-one IM residents participated. At pretest, 48% (15/31) of residents landmarked accurately. Inaccuracy of pretest landmarking varied widely (n = 16, mean 20.06 mm; standard deviation 30.03 mm). At posttest, 74% (23/31) of residents accurately performed the procedure. McNemar test revealed a nonsignificant trend toward increased performance at posttest (P = 0.076; unadjusted odds for discordant pairs 3; 95% confidence interval 0.97–9.3). The Wilcoxon signed rank test demonstrated a significant difference between pre- and posttest accuracy in the 16 residents who were inaccurate at pretest (P = 0.004). No association was detected between participant baseline characteristics and pretest accuracy. Conclusions This study demonstrates that residents who were initially inaccurate were able to significantly improve their landmarking skills by interacting with an educational tool emphasizing the relation between the surface and underlying anatomy. Our results support the use of basic anatomy in teaching bone marrow procedures. Results also support the proper use of video as an effective means for incorporating anatomy teaching around procedural skills.
A cross-region analysis of the output elasticity of transport investment in China

This paper aims to investigate the linkage between transport investment and economic development. To achieve it, the contribution of transport investment stock to economic growth was measured using provincial panel data from 1990 to 2010 in China. Empirical result showed the contribution was indeed various across regions. The greatest contribution was found in the central region, followed by the western region and then the eastern region. The cross-region comparison indicated economic returns of extra transport investment were generally positive but their degrees were quite different in different development stages. More specifically, a large contribution was found in pre-policy and deepening stages for the eastern and western regions while it was found in pre-policy and primary stages for the central region. A moderate contribution was seen in deepening stage for the central region while it was seen in primary and expansion stages for the western region. Accordingly, China needs to allocate more transport investments in the central region due to its higher economic returns and important connection position. Additionally, as an extension, the positive impact of transport investment on regional economic growth in China can be taken as an experiment to be replicated by other developing or less-developed nations.
Correlations among enthesitis, clinical, radiographic and quality of life parameters in patients with ankylosing spondylitis

Abstract Objectives. To investigate the relationship between enthesitis and disease activity, functional status, fatigue, joint mobility, radiological damage, laboratory parameter and quality of life in patients with ankylosing spondylitis (AS). Methods. A total of 421 patients with AS (323 male and 98 female) who were included in the Turkish League Against Rheumatism Registry were enrolled in the study. The Bath AS Disease Activity Index (BASDAI), fatigue, the Bath AS Functional Index (BASFI), the Bath AS Metrology Index (BASMI), the Maastricht AS Enthesitis Score (MASES), AS quality of life (ASQoL), the Bath AS Radiology Index (BASRI) and erythrocyte sedimentation rate (ESR) were evaluated. Results. Enthesitis was detected in 27.3% of patients. There were positive correlations between MASES and BASDAI, BASFI and fatigue (p < 0.05). MASES was not correlated with BASRI, BASMI, ASQoL and ESR. The mean MASES score was 1.1 ± 2.4. The most frequent regions of enthesopathies were right iliac crest, spinous process of L5 and proximal to the insertion of left achilles tendon, respectively. Conclusions. Enthesitis was found to be associated with higher disease activity, higher fatigue, worse functional status and lower disease duration. As enthesitis was correlated with BASDAI, we conclude that enthesitis can reflect the disease activity in patients with AS.
Carbon Monoxide Protects Against Ischemia-Reperfusion Injury in an Experimental Model of Controlled Nonheartbeating Donor Kidney

Background. CO-releasing molecule-3 (CORM-3) is a transitional metal carbonyl that liberates carbon monoxide under appropriate conditions. Carbon monoxide exerts effects on intracellular apoptotic and inflammatory pathways, which suggest a role in reducing the effects of renal ischemia/reperfusion (I/R) injury. This study investigated the effects of CORM-3 administered at the time of reperfusion in a model of controlled nonheartbeating donor kidneys. Methods. Porcine kidneys (n=4) were subjected to 10 min warm ischemia and 18 hr cold storage (CS) and then treated as follows: CORM-3 (50, 100, 200, and 400 &mgr;M doses), iCORM-3 (inactive carbon monoxide-releasing molecule, 50 &mgr;M), and control (no further intervention). Renal hemodynamics and function were then measured during 3-hr reperfusion with autologous blood using an isolated organ-perfusion system. Results. CORM-3 at a concentration of 50 &mgr;M improved renal blood flow (RBF) compared with the iCORM and control groups (area under the curve 774±19 vs. 448±88 vs. 325±70, respectively, P=0.002). CO-releasing molecule-3 at a concentration of 50 &mgr;M also improved renal function during reperfusion with a greater area under the curve for creatinine clearance (CORM-3: 14±6 vs. iCORM: 3.3±0.1 vs. control: 2.2±2 mL/min, P=0.006) and higher urine output (CORM-3: 793±212 vs. iCORM: 368±72 vs. control: 302±211 mL, P=0.01). CO-releasing molecule-3 at a concentration of 100 &mgr;M exerted similar effects. Treatment with CORM-3 at higher doses (200 and 400 &mgr;M) led to poor renal hemodynamics and function after reperfusion. Conclusion. Low-dose CORM-3 significantly ameliorates the effects of ischemia/reperfusion in a porcine model of controlled nonheartbeating donor kidney transplantation.
Evaluating the Prevalence of Candida Species in the Oral Cavity of Immunocompromised Patients

Candida species are normal commensal of the oral microbial flora and get established there during or soon after birth. Lesions of thrush are seen in children and adults of all ages whenever the number of candida in the oral cavity increases significantly . During the past two decades, there has been a significant increase in the prevalence of fungal infections caused by Candida species. The yeast candida being the main cause of candidiasis is commonly isolated pathogen from immunocompromised patients. The trend in the resistance acquired by some species of candida leads to the importance of identification to the species level in immunocompromised patients. In present study we have selected 50 subjects (male and female) who are HIV positive(10),diabetes mellitus(10),vitamin deficiencies(10),radiotherapy patients(10) and the patients on broad spectrum antibiotics(10). Oral samples were collected with the help of sterile cotton swabs, and inoculated on sabouraud`s dextrose agar (SDA) for isolation. After appearance of the colonies on SDA, individual colony is tested for identification of different species of candida on the basis of biochemical and assimilation test. The prevalence of oral candidosis and frequency of isolation of Candida species and its distribution were determine statistically by using x test ,it is found that difference is not statistical significant between Candida albicans and Candida non albicans among the sex, it can be present in target population.
Temporal and Spatial Expression of Integrins and Their Extracellular Matrix Ligands at the Maternal-Fetal Interface in the Rhesus Monkey During Pregnancy1

Abstract The integrin and extracellular matrix protein (ECM)-mediated adhesion and invasion of the receptive maternal uterine endometrium by trophoblasts is a critical event in the complex physiological process of pregnancy. Although the process has been largely characterized in mice, the relevant mechanism in primates remains unclear. We investigated the expression patterns and dynamic alterations of integrin subunits (α1, α5, α6, β1, and β4) and their ECM ligands, such as laminin (LN), type IV collagen (Col IV), and fibronectin (FN), at the maternal-fetal interface during Gestational Days 15, 25, 50, and 100 and at full term in 20 pregnant rhesus monkeys. Immunohistochemistry and in situ hybridization revealed that a relatively high expression of integrins occurred in trophoblast cells at Gestational Day 15, with the peak level occurring at Day 25. The expression level decreased from Day 50 to term. Along the invasive pathway, expression levels of integrin α1, α5, and β1 subunits were gradually elevated from the proximal to distal column, reaching peak level in the trophoblast shell, but were reduced in those invasive extravillous cytotrophoblast (EVCT) cells in contact with the decidua. Integrin α1, α5, β1, and β4 subunits were also highly expressed in decidual stromal cells and moderately expressed in the maternal epithelium and endothelium. Immunoreactive FN, LN, and Col IV were distributed in EVCT and decidual stromal cells and part of the uterine epithelial and endothelial cells. These data suggest that the correlated expression of integrins and their ECM ligands at the maternal-fetal interface might be involved in regulation of cell proliferation and differentiation and the counterbalanced invasion-accelerating and invasion-restraining processes in trophoblast cells during the early stage of pregnancy.
R&D profitability: the role of risk and Knightian uncertainty

This paper provides the first empirical attempt of linking firms’ profits and investment in R&D revisiting Knight’s (Risk, uncertainty and profit, Hart, Schaffner & Marx, Boston, 1921) distinction between uncertainty and risk. Along with the risky profit-maximising scenario, identifying a second, off-setting, unpredictable bias that leads to heterogeneous returns to R&D investments is crucial to fully understand the drivers of corporate profits. Consistently with the Knightian theory that relates risk to profitability, we model the impact of risk and uncertainty on profits and provide a first empirical attempt to model the effect of ambiguity, a particular type of uncertainty, on R&D returns.
Accelerometry to distinguish psychogenic from essential or parkinsonian tremor

The authors measured postural wrist tremor with accelerometry in patients with psychogenic (n = 6), essential (n = 11), and parkinsonian (n = 12) tremor. Tremor was measured in one hand, while the other hand either rested or tapped to an auditory stimulus at 3 and 4 or 5 Hz. Psychogenic tremors showed larger tremor frequency changes and higher intraindividual variability while tapping. Accelerometry may differentiate psychogenic from essential and parkinsonian tremor.
Why Firms Favour the AIM When They Can List on Main Market?

It is often argued that the popularity of Alternative Investment Market (AIM) in terms of higher number of listings relative to the Main Market (MM) is mainly due to the strict listing requirements in the MM. During the 1995 to 2014 period, 577 out of 1143 AIM listed firms did not qualify for MM listing, but the rest (566) that raised equity in AIM could have joined the MM. This raises the question why firms that meet the heavier regulatory environment of the MM choose the AIM, a lighter regulatory environment. This paper subjects this question to a comprehensive investigation and finds that the market choice is a self-selection decision. The two markets attract companies with different characteristics, and dissimilar post-listing investment and financing priorities. The evidence also shows that smaller and younger companies choose to be listed on the AIM due to lower listing and on-going costs. Heckman Selection models addressing the important question of what would have been the operating performance if AIM companies joined MM indicate that AIM companies would not perform better had they selected to go public in the MM.
Trends in treatment and outcomes of rheumatoid arthritis in Germany 1997–2007: results from the National Database of the German Collaborative Arthritis Centres

Background New strategies and options for the treatment of rheumatoid arthritis (RA) have evolved during the past decade. A study was undertaken to investigate to what extent this influenced daily rheumatological care and how this translates into clinical and patient-reported outcomes. Methods Data from a total of 38 723 outpatients with RA enrolled in the National Database of the German Collaborative Arthritis Centres in the years 1997–2007 were analysed. The cross-sectional annual data were compared to detect time trends. Results Between 1997 and 2007 the prescription of combinations of traditional disease-modifying antirheumatic drugs (DMARDs) increased from 8% of all patients to 23%; biological agents were prescribed to 16% of patients with RA in 2007. The mean disease activity (DAS28) fell from 4.5 to 3.4 (median 4.5–3.2). The percentage of patients with low disease activity (DAS28 <3.2) increased significantly from 23% to 49%. The proportion of patients with ≥6 swollen joints fell from 43.1% in 1997 to 8.1% in 2007 and, in those with ≥6 tender joints, from 46.3% to 15.8%. There was a large decrease in the total annual number of days of sick leave due to the rheumatic condition from 27.2 to 8.8 days per gainfully employed person. This reduction is far beyond the decline in the general population. There was also a tendency to higher participation in the work force, specifically in older patients, reflecting the trend seen in the general population. Conclusions The intensity of drug treatment in patients with RA has increased during the past 7 years. This has been accompanied by not only a decrease in disease activity but also a considerable reduction of economic losses due to sick leave and permanent work disability.
Survey of Susceptibilities of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis Isolates to 26 Antimicrobial Agents: a Prospective U.S. Study

ABSTRACT An antimicrobial susceptibility surveillance study ofStreptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis isolates was performed during the winter of 1996–1997 in order to determine their susceptibilities to 5 fluoroquinolones and 21 other antimicrobial agents. Broth microdilution MICs were determined for 2,752 isolates from 51 U.S. medical centers. Of the 1,276 S. pneumoniaeisolates, 64% were susceptible, 17% were intermediate, and 19% were highly resistant to penicillin. On the basis of the MICs at which 90% of isolates are inhibited and modal MICs, the hierarchy of the five fluoroquinolones from most to least active was grepafloxacin > sparfloxacin > levofloxacin = ciprofloxacin > ofloxacin. For S. pneumoniae isolates for which penicillin MICs were elevated, the MICs of the cephalosporins, macrolides, clindamycin, tetracycline, and trimethoprim-sulfamethoxazole were also elevated, but the MICs of the fluoroquinolones, vancomycin, and rifampin were not. The prevalence of penicillin-susceptible pneumococci varied by U.S. Bureau of the Census region (range, 44% in the East South Central region to 75% in the Pacific region). In addition,S. pneumoniae isolates from blood were significantly more susceptible to penicillin than those from respiratory, ear, or eye specimens, and pneumococci from patients ≤2 years old were significantly more resistant to penicillin than those from older patients (by chi-square analysis, P < 0.05). β-Lactamase was produced by 35% of H. influenzaeisolates and 93% of M. catarrhalis isolates, resulting in increased MICs of amoxicillin and certain cephalosporins. We noted that the antimicrobial resistance patterns of S. pneumoniaeisolates, which correlate with the penicillin susceptibility phenotype, vary by site of infection, age group of the patient, and geographic source of the isolate.