Miracle-dz/UniFAR-FTUs huggingface dataset:
A20 deletion is associated with copy number gain at the TNFA/B/C locus and occurs preferentially in translocation‐negative MALT lymphoma of the ocular adnexa and salivary glands

The genetic basis of MALT lymphoma is largely unknown. Characteristic chromosomal translocations are frequently associated with gastric and pulmonary cases, but are rare at other sites. We compared the genetic profiles of 33 ocular adnexal and 25 pulmonary MALT lymphomas by 1 Mb array–comparative genomic hybridization (CGH) and revealed recurrent 6q23 losses and 6p21.2–6p22.1 gains exclusive to ocular cases. High‐resolution chromosome 6 tile‐path array–CGH identified NF‐κB inhibitor A20 as the target of 6q23.3 deletion and TNFA/B/C locus as a putative target of 6p21.2–22.1 gain. Interphase fluorescence in situ hybridization showed that A20 deletion occurred in MALT lymphoma of the ocular adnexa (8/42 = 19%), salivary gland (2/24 = 8%), thyroid (1/9 = 11%) and liver (1/2), but not in the lung (26), stomach (45) and skin (13). Homozygous deletion was observed in three cases. A20 deletion and TNFA/B/C gain were significantly associated (p < 0.001) and exclusively found in cases without characteristic translocation. In ocular cases, A20 deletion was associated with concurrent involvement of different adnexal tissues or extraocular sites at diagnosis (p = 0.007), a higher proportion of relapse (67% versus 37%) and a shorter relapse‐free survival (p = 0.033). A20 deletion and gain at TNFA/B/C locus may thus play an important role in the development of translocation‐negative MALT lymphoma. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Who Sees the School Counselor for College Information? A National Study.

Using the 2002 Educational Longitudinal Study database a national survey conducted by the National Center of Education Statistics the authors investigated the characteristics of students who seek out professional school counselors in order to receive college information. Results indicated that African Americans and female students were more likely to contact the school counselor for college information. In addition, students in high-poverty, large schools and schools with smaller numbers of counselors were less likely to seek school counselors for college information. School counselors' postsecondary aspirations for students also impacted students' contact with the school counselor. Implications for school counselors and future research are included.
Survival advantage for etoposide/cisplatin over paclitaxel/carboplatin concurrent chemoradiation in patients with inoperable stage III NSCLC: a subgroup analysis for ECOG 2 patients would be of great interest.

The phase III trial of Liang et al. on the optimal chemotherapy regimen for concurrent chemoradiation in patients with inoperable stage III NSCLC is of interest as it contradicts, in part, previously published data. Surprisingly, the study revealed a survival advantage for Etoposide/Cisplatin (EP) (administered every 4 weeks) over Paclitaxel/Carboplatin (PC) weekly concurrent chemoradiation and did not confirm results from the previous Veterans Affairs (VA) Central Cancer Registry (VACCR) analysis. Despite a relatively high rate of stage IIIB disease and low rate of complete remission, favorable 2and 3-year overall survival was achieved. To the best of our knowledge, the study was the first randomized phase III trial addressing the feasibility and efficacy of concurrent chemoradiation in Eastern Cooperative Oncology Group (ECOG) 2 patients with inoperable locally-advanced disease. Previous relevant publications on this topic have focused exclusively on patients with good performance status (ECOG 0-1) (see Table 1). In contrast, the proportion of ECOG 2 patients in the present study was relatively high (32.6 and 41.7%) in both arms, respectively i.e. this randomized trial provides the unique opportunity for detailed analysis of treatment toxicity in ECOG 2 patients treated with different concurrent chemoradiotherapy protocols.
Barriers to exclusive breast-feeding in Indonesian hospitals: a qualitative study of early infant feeding practices

Abstract Objective Although initiating breast-feeding is common in Indonesia, rates of exclusive breast-feeding are low. Our objective was to identify early barriers to exclusive breast-feeding in Indonesian hospitals. Design Qualitative. Semi-structured interviews were conducted in April–June 2015. The data were analysed using thematic analysis. Setting Indonesian provinces of Jakarta, Banten and West Java. Subjects Fifty-four participants including public health officials, hospital administrators, health-care professionals and parents. Results Five themes were identified as contributing to low rates of early exclusive breast-feeding in Indonesian hospitals: (i) quality and quantity of breast-feeding education; (ii) marketing and influence of infant formula manufacturers; (iii) hospital infrastructure; (iv) policy, legislation and protocols; and (v) perceived need for infant formula supplementation. Participants noted that providers and mothers receive inadequate or incorrect education regarding breast-feeding; manufacturers promote infant formula use both inside and outside hospitals; constraints in physical space and hospital design interfere with early breast-feeding; legislation and protocols designed to promote breast-feeding are inconsistently enforced and implemented; and providers and mothers often believe infant formula is necessary to promote infant health. All participants identified numerous barriers to early exclusive breast-feeding that related to more than one identified theme. Conclusions Our study identified important barriers to early exclusive breast-feeding in Indonesian hospitals, finding that participants consistently reported multifaceted barriers to early exclusive breast-feeding. Future research should examine whether system-level interventions such the Baby-Friendly Hospital Initiative might improve rates of exclusive breast-feeding by improving breast-feeding education, reducing manufacturer influence, modifying existing infrastructure and providing tools needed for protocols and counselling.
Prevalence thresholds for wasting, overweight and stunting in children under 5 years

Abstract Objective Prevalence ranges to classify levels of wasting and stunting have been used since the 1990s for global monitoring of malnutrition. Recent developments prompted a re-examination of existing ranges and development of new ones for childhood overweight. The present paper reports from the WHO–UNICEF Technical Expert Advisory Group on Nutrition Monitoring. Design Thresholds were developed in relation to sd of the normative WHO Child Growth Standards. The international definition of ‘normal’ (2 sd below/above the WHO standards median) defines the first threshold, which includes 2·3 % of the area under the normalized distribution. Multipliers of this ‘very low’ level (rounded to 2·5 %) set the basis to establish subsequent thresholds. Country groupings using the thresholds were produced using the most recent set of national surveys. Setting One hundred and thirty-four countries. Subjects Children under 5 years. Results For wasting and overweight, thresholds are: ‘very low’ (<2·5 %), ‘low’ (≈1–2 times 2·5 %), ‘medium’ (≈2–4 times 2·5 %), ‘high’ (≈4–6 times 2·5 %) and ‘very high’ (>≈6 times 2·5 %). For stunting, thresholds are: ‘very low’ (<2·5 %), ‘low’ (≈1–4 times 2·5 %), ‘medium’ (≈4–8 times 2·5 %), ‘high’ (≈8–12 times 2·5 %) and ‘very high’ (>≈12 times 2·5 %). Conclusions The proposed thresholds minimize changes and keep coherence across anthropometric indicators. They can be used for descriptive purposes to map countries according to severity levels; by donors and global actors to identify priority countries for action; and by governments to trigger action and target programmes aimed at achieving ‘low’ or ‘very low’ levels. Harmonized terminology will help avoid confusion and promote appropriate interventions.
Use of Monte Carlo Modeling to Aid Interpretation and Quantification of the Low Energy-Loss Electron Yield at Low Primary Energies

Abstract Experimental low-loss electron (LLE) yields were measured as a function of loss energy for a range of elemental standards using a high-vacuum scanning electron microscope operating at 5 keV primary beam energy with losses from 0 to 1 keV. The resulting LLE yield curves were compared with Monte Carlo simulations of the LLE yield in the particular beam/sample/detector geometry employed in the experiment to investigate the possibility of modeling the LLE yield for a series of elements. Monte Carlo simulations were performed using both the Joy and Luo [Joy, D.C. & Luo, S. , Scanning11(4), 176–180 (1989)] expression for the electron stopping power and recent tabulated values of Tanuma et al. [Tanuma, S. et al., Surf Interf Anal37(11), 978–988 (2005)] to assess the influence of the more recent stopping power data on the simulation results. Further simulations have been conducted to explore the influence of sample/detector geometry on the LLE signal in the case of layered samples consisting of a thin C overlayer on an elemental substrate. Experimental LLE data were collected from a range of elemental samples coated with a thin C overlayer, and comparisons with Monte Carlo simulations were used to establish the overlayer thickness.
Injury‐induced sequential transformation of notochordal nucleus pulposus to chondrogenic and fibrocartilaginous phenotype in the mouse

Intervertebral disc degeneration has been widely studied in different animal models. To test the hypothesis that needle puncture could induce progressive biochemical and molecular changes in murine discs, we established a mouse tail model to investigate the pathogenesis and molecular mechanism of puncture‐induced disc degeneration. Caudal discs in mouse tails were punctured using a 31G gauge needle at controlled depth under microscopic guidance. The progress of the disc degeneration was evaluated by radiographic analysis of disc height, histological grading and glycosaminoglycan (GAG) quantification pre‐operation and 1, 2, 6 and 12 weeks post‐puncture. Gene and protein expression of the extracellular matrix (ECM) was analysed by RT–PCR, in situ hybridization and immunohistochemistry. Histological study and disc height analysis revealed progressive degenerative changes in the punctured discs. Compared with the pre‐operation control group, total GAG content decreased 40% (p < 0.05) and aggrecan (Acan), decorin (Dcn) and versican (Vcan; Cspg2) expression was down‐regulated at 12 weeks post‐puncture. A transient increase of Col2a1‐expressing cells and elevation of collagen II protein in the nucleus pulposus (NP) was detected. Fibronectin (Fn1) expression was up‐regulated 50% and deposition of collagen I in NP was observed at 12 weeks post‐puncture. This study is the first to use an injury‐induced model to study disc degeneration in mouse. The disc degeneration involves a transient transformation of NP from notochordal to chondrogenic and eventually into fibrocartilaginous phenotype. The degenerative changes have some similarity to human disc degeneration, suggesting that this model may potentially be used in future to study the molecular mechanism and dissect the pathways of disc degeneration. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Changes in the use of end points in clinical trials for elderly cancer patients over time

Background Physicians need well-addressed clinical trials assessing benefits and harm of treatments to avoid under-treatment or over-treatment of elderly patients. The main objectives of this report were to present an overview of end points used in clinical trials dedicated to elderly patients; and to assess the evolution in chosen end points before and after the creation of the International Society of Geriatric Oncology in the early 2000s. Patients and methods All phases I, II and III trials dedicated to the treatment of cancer among elderly patients published between 2001 and 2004 and between 2011 and 2014 were reviewed. All phase III clinical trials assessing cancer treatments among adults in the same periods were also reviewed to identify subgroup analyses of elderly patients among these trials. Results Among phase III trials dedicated to elderly patients, overall survival was a common primary end point. Interestingly, tumor centered end points were very common in the first time period and very uncommon in the second time period, whereas composite end points were very uncommon in the first time period but very common in the second time period. Concerningly, disease-specific survival was very infrequently reported in dedicated clinical trials of elderly patients despite their importance in evaluating competing risk of death from non-oncology causes. The use of patient-reported outcomes (PROs) as a primary end point remained very uncommon but the reporting of PROs as a secondary end point tended to increase in the second time period, from 19% to 33% (P = 0.10). Functional status was infrequently reported. Conclusion During the past decade, the use of clinically meaningful end points such as PROs and functional status in elderly patients remained moderate. Yet, the use of PROs as a secondary end point tended to increase between the two time periods.
Prediction of the phase diagram of rigid C60 molecules.

An integral-equation approach combined with molecular dynamics simulations based on the Girifalco spherical intermolecular potential has been used to predict the phase diagram for rigid C 60 molecules. The boundary of the liquid-vapor coexistence region and the location of freezing and melting lines have been sketched out. The liquid phase is only observed in a very narrow temperature range compared with atomic systems (e.g., the rare gases). Unfortunately, the dense fluid is predicted to exist above ∼1800 K, which is sufficiently high that the C 60 molecule may be unstable
Do we see what we think we see? The complexities of morphological assessment

Reliable pathological interpretation is vital to so many aspects of tissue‐based research as well as being central to patient care. Understanding the complex processes involved in decision‐making is the starting point to improve both diagnostic reproducibility and the definition of diagnostic groups that underpin our experiments. Unfortunately, there is a paucity of research in this field and it is encouraging to see The Journal of Pathology publishing work in this area. This review attempts to highlight the opportunities that exist in this field and the technologies that are now available to support this type of research. Key amongst these are the use of decision analysis tools such as inference networks, and virtual microscopy that allows us to simulate diagnostic decision‐making. These tools have roles, not only in studying the subtleties of diagnostic decision‐making, but also in delivering new methods of training and proficiency testing. Research which helps us to better understand what we see, why we see it, and standardizing interpretative reasoning in pathological classification is essential for improving the wide range of activities that pathologists support, including clinical diagnosis, teaching, training, and experimental research. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Revisiting the definition of estrogen receptor positivity in HER2-negative primary breast cancer

Background Although 1% has been used as cut-off for estrogen receptor (ER) positivity, several studies have reported that tumors with ER < 1% have characteristics similar to those with 1% ≤ ER < 10%. We hypothesized that in patients with human epidermal growth factor 2 (HER2)-negative breast cancer, a cut-off of 10% is more useful than one of 1% in discriminating for both a better pathological complete response (pCR) rate to neoadjuvant chemotherapy and a better long-term outcome with adjuvant hormonal therapy. Our objectives were to identify a percentage of ER expression below which pCR was likely and to determine whether this cut-off value can identify patients who would benefit from adjuvant hormonal therapy. Patients and methods Patients with stage II or III HER2-negative primary breast cancer who received neoadjuvant chemotherapy followed by definitive surgery between June 1982 and June 2013 were included. Logistic regression models were used to assess the association between each variable and pCR. Cox models were used to analyze time to recurrence and overall survival. The recursive partitioning and regression trees method was used to calculate the cut-off value of ER expression. Results A total of 3055 patients were analyzed. Low percentage of ER was significantly associated with high pCR rate (OR = 0.99, 95% CI = 0.986-0.994, P < 0.001). The recommended cut-off of ER expression below which pCR was likely was 9.5%. Among patients with ER ≥ 10% tumors, but not those with 1%≤ER < 10% tumors, adjuvant hormonal therapy was significantly associated with long time to recurrence (HR = 0.24, 95% CI = 0.16-0.36, P < 0.001) and overall survival (HR = 0.32, 95% CI = 0.2-0.5, P < 0.001). Conclusion Stage II or III HER2-negative primary breast cancer with ER < 10% behaves clinically like triple-negative breast cancer in terms of pCR and survival outcomes and patients with such tumors may have a limited benefit from adjuvant hormonal therapy. It may be more clinically relevant to define triple-negative breast cancer as HER2-negative breast cancer with <10%, rather than <1%, of ER and/or progesterone receptor expression.
Management of Patients With Upper Gastrointestinal Bleeding

Upper gastrointestinal bleeding (UGIB) is a serious clinical problem, which is fatal in 6-10% of the cases (1, 2, 3). The incidence of acute massive UGIB is estimated at 40-150 episodes per 100 000 per year (1, 2, 3). The mortality rate increases with age and the number of co-morbidities, especially renal and liver failure, heart disease and neoplasms (1, 2, 3). Mortality seems to be lower in specialist centres, which is a consequence of following the adopted management standards rather than the possession of advanced equipment. Gastric or duodenal peptic ulcer is the most common cause of UGIB, accounting for 35-50% of the cases. Other causes of bleeding include gastric or duodenal erosion (8-15%), oesophagitis (5-15%), oesophageal varices (5-10%), MalloryWeiss syndrome (15%), vascular malformations (5%), neoplasms (1%). Other rare causes account for 5% of the cases. Risk groups and resuscitation
Dual actions of substance P on nociception: possible role of endogenous opioids

Substance P produces analgesia when administered to mice in very small doses by the intraventricular route (1.25 to 5 nanograms per mouse). The analgesic effect can be blocked by naloxone. At higher doses (greater than 50 nanograms per mouse), this activity is lost. At these higher doses, however, substance P produced hyperalgesia when combined with naloxone and analgesia when combined with baclofen [beta-(4-chlorophenyl)-gamma-aminobutyric acid]. Substance P may have dual actions in brain, releasing endorphins at very low doses and directly exciting neuronal activity in nociceptive pathways at higher doses.
PHYSICAL ENDURANCE, SOMATIC INDICES AND SWIMMING TECHNIQUE PARAMETERS AS DETERMINANTS OF FRONT CRAWL SWIMMING SPEED AT SHORT DISTANCES IN YOUNG SWIMMERS

Introduction: Appropriate swimming techniques and anaerobic capacity have a strong influence on factors related to performance in young swimmers. This study evaluated the factors attributed to performance in sprint front crawl swimmers. Aim of the study: To investigate the level of aerobic and anaerobic component of physical endurance, swimming technique and somatic indices, as well as to determine their influence on young swimmers’ all-out sprint front crawl swimming. Methods: The group of 26 swimmers (age: 16.1±1.09 years) was subject to anthropometric measurements including lean body mass (LBM), total body length (TBL) and arm span (AS). Each individual was subject to five laboratory tests and 2 swimming tests: alactic anaerobic test (vertical jump test – CMJ), incremental tests for assessment of arms (¦O 2 max AR) and legs aerobic capacity (¦O 2 max LG) in two different tests, one-minute anaerobic endurance tests for arms (60sAR) and legs (60sLG). Swimming include all-out tests at the distance of 25 and 100 meters. Results: The biometric (TBL, AS) and body structure (LBM) indices level was in general determining swimming speed at high and average level. The maximal power obtained in anaerobic endurance test with legs (PmxLG) and total work in the CMJ (counter movement jump) test had the strongest influence on 25 and 100 meters swimming speeds. At both distances speed statistically significantly correlated also with the swimming technique parameters: stroke rate (SR), index of coordination (IdC) and propulsion phases (PL+PS). Conclusions: Research on young swimmers confirmed essential influence of energy obtaining mechanisms from alactic, glycolitic and aerobic sources on swimming speed at short distances. Body size and swimming technique parameters had also significant influence on swimming results.
Evaluation of acute head injury by computed tomography scan in College of Medical Sciences-Teaching Hospital, Chitwan

This study was conducted to evaluate the computed tomography findings in patient with acute head injury and to emphasize the importance of computed tomography scan in head injury. One hundred consecutive patients presenting to the emergency department with head injury were evaluated by computed tomography scan of the head. Seventy five patients (75%) were male and twenty five (25%) were females. The age of the patients ranged from three to seventy years and the most affected age group was between thirty and forty (40%). The common causes of head injury were motor vehicle accident (70%), fall injury (25% ) and physical assault (5%). The most common computed tomographic findings were: cerebral contusions (52%), skull fractures (41%), intracerebral hematomas (24%), diffuse cerebral edema (23%), midline shift (18%), subdural hematomas (15%), subarachnoid hemorrhage (13%), diffuse axonal injury (8%), intraventricular hemorrhage (6%), extradural hemotomas (4%), pnemocephalus (2%) and normal scans were found in (5%). In conclusion, computed tomography is the mainstay in the imaging of head injury and helps in the patient management. DOI: http://dx.doi. org/10.3126/jcmsn.v7i1. 5971 JCMSN 2011; 7(1): 36-39
Unravelling the genetic basis of renal diseases; from single gene to multifactorial disorders

Chronic kidney disease is common with up to 5% of the adult population reported to have an estimated glomerular filtration rate of < 60 ml/min/1.73 m2. A large number of pathogenic mutations have been identified that are responsible for ‘single gene’ renal disorders, such as autosomal dominant polycystic kidney disease and X‐linked Alport syndrome. These single gene disorders account for < 15% of the burden of end‐stage renal disease that requires dialysis or kidney transplantation. It has proved more difficult to identify the genetic susceptibility underlying common, complex, multifactorial kidney conditions, such as diabetic nephropathy and hypertensive nephrosclerosis. This review describes success to date and explores strategies currently employed in defining the genetic basis for a number of renal disorders. The complementary use of linkage studies, candidate gene and genome‐wide association analyses are described and a collation of renal genetic resources highlighted. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.