Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of routine follow‐up after treatment for laryngeal cancer on life expectancy and mortality

Routine follow‐up is offered to all patients with laryngeal cancer who are treated with curative intent. Although time and resources are devoted to surveillance, the effect of asymptomatic recurrence detection is not well understood. For this study, the authors evaluated the effect that routine follow‐up may have on life expectancy and disease‐specific mortality rate for patients with laryngeal cancer.
Measurements of desmosine and isodesmosine by mass spectrometry in COPD.

OBJECTIVES Application of mass spectrometry (MS) for direct measurements of desmosine (D) and isodesmosine (I) in urine, plasma, and sputum as markers of elastin degradation in patients with alpha(1)-antitrypsin deficiency (AATD) and non-AATD-related COPD. BACKGROUND In COPD patients, the lungs undergo elastin injury, which can be monitored by measurements of D and I in body fluids as specific markers of elastin degradation using the specificity and sensitivity of MS. METHODS Acid hydrolysis of blood plasma, 24-h urine and sputum measurements, followed by chromatographic separation for mass spectrometric analysis. RESULTS Each patient group had levels of plasma D and I that were statistically significantly higher than those of control subjects. AATD patients had higher levels than COPD patients with normal alpha(1)-antitrypsin (AAT) levels. Twenty-four-hour urine measurements demonstrated no significant difference in total levels of D and I among control subjects and patients but showed a free (unbound) concentration of D and I in urine, which was statistically significantly higher in patients with COPD with and without AAT. The D and I levels in the sputum of patients with AATD exceeded the levels in COPD patients with normal AAT levels. CONCLUSIONS MS allows a sensitive and specific analysis of D and I in body fluids. The quantification of D and I in sputum, along with increases of D and I in plasma and an elevated free component of D and I in urine provide indexes that characterize patients with COPD and can be followed in relation to the course of the disease and/or therapy.
Adult bone marrow is a rich source of human mesenchymal ‘stem’ cells but umbilical cord and mobilized adult blood are not

Summary. In postnatal life, mesenchymal stem cells (MSC) self‐replicate, proliferate and differentiate into mesenchymal tissues, including bone, fat, tendon, muscle and bone marrow (BM) stroma. Possible clinical applications for MSC in stem cell transplantation have been proposed. We have evaluated the frequency, phenotype and differentiation potential of MSC in adult BM, cord blood (CB) and peripheral blood stem cell collections (PBSC). During culture, BM MSC proliferated to confluence in 10–14 d, maintaining a stable non‐haemopoietic phenotype, HLA class‐1+, CD29+, CD44+, CD90+, CD45–, CD34– and CD14 through subsequent passages. Using the colony forming unit fibroblasts assay, the estimated frequency of MSC in the BM nucleated cell population was 1 in 3·4 × 104 cells. Both adipogenic and osteogenic differentiation of BM MSC was demonstrated. In contrast, CB and PBSC mononuclear cells cultured in MSC conditions for two passages produced a population of adherent, non‐confluent fibroblast‐like cells with a haemopoietic phenotype, CD45+, CD14+, CD34–, CD44–, CD90– and CD29–. In paired experiments, cultured BM MSC and mature BM stroma were seeded with CB cells enriched for CD34+. Similar numbers of colony‐forming units of granulocytes–macrophages were produced by MSC‐based and standard stroma cultures over 10 weeks. We conclude that adult BM is a reliable source of functional cultured MSC, but CB and PBSC are not.
Normal variation in the length of the follicular phase of the menstrual cycle: effect of chronological age

Normal probability plots were used to analyse the distribution of follicular phase length in a population of 293 apparently ovulatory menstrual cycles from women aged between 18 and 39 years. The length of the follicular phase was defined as the interval (in days) from the onset of menstruation up to, but not including, the day of the LH peak. Follicular phase length appeared to be log‐normally distributed and graphical inspection of the probability plot suggested that the geometric mean (and 95% confidence limits) of follicular phase length in this study group was 12–9 (10–3 to 16–3) days. There was a significant decrease (P<0.001) in follicular phase length with chronological age, from 14–2 days in women aged 18–24 years to 10.4 days in women aged 40–44 years.
Functional Network Community Detection Can Disaggregate and Filter Multiple Underlying Pathways in Enrichment Analyses

Differential expression experiments or other analyses often end in a list of genes. Pathway enrichment analysis is one method to discern important biological signals and patterns from noisy expression data. However, pathway enrichment analysis may perform suboptimally in situations where there are multiple implicated pathways – such as in the case of genes that define subtypes of complex diseases. Our simulation study shows that in this setting, standard overrepresentation analysis identifies many false positive pathways along with the true positives. These false positives hamper investigators’ attempts to glean biological insights from enrichment analysis. We develop and evaluate an approach that combines community detection over functional networks with pathway enrichment to reduce false positives. Our simulation study demonstrates that a large reduction in false positives can be obtained with a small decrease in power. Though we hypothesized that multiple communities might underlie previously described subtypes of high-grade serous ovarian cancer and applied this approach, our results do not support this hypothesis. In summary, applying community detection before enrichment analysis may ease interpretation for complex gene sets that represent multiple distinct pathways.
KlSEC53 is an essential Kluyveromyces lactis gene and is homologous with the SEC53 gene of Saccharomyces cerevisiae

Phosphomannomutase (PMM) is a key enzyme, which catalyses one of the first steps in the glycosylation pathway, the conversion of D‐mannose‐6‐phosphate to D‐mannose‐1‐phosphate. The latter is the substrate for the synthesis of GDP‐mannose, which serves as the mannosyl donor for the glycosylation reactions in eukaryotic cells. In the yeast Saccharomyces cerevisiae PMM is encoded by the gene SEC53 (ScSEC53) and the deficiency of PMM activity leads to severe defects in both protein glycosylation and secretion. We report here on the isolation of the Kluyveromyces lactis SEC53 (KlSEC53) gene from a genomic library by virtue of its ability to complement a Saccharomyces cerevisiae sec53 mutation. The sequenced DNA fragment contained an open reading frame of 765 bp, coding for a predicted polypeptide, KlSec53p, of 254 amino acids. The KlSec53p displays a high degree of homology with phosphomannomutases from other yeast species, protozoans, plants and humans. Our results have demonstrated that KlSEC53 is the functional homologue of the ScSEC53 gene. Like ScSEC53, the KlSEC53 gene is essential for K. lactis cell viability. Phenotypic analysis of a K. lactis strain overexpressing the KlSEC53 gene revealed defects expected for impaired cell wall integrity. The sequence of the KlSEC53 has been deposited in the EMBL database under Accession No. AJ428418. Copyright © 2003 John Wiley & Sons, Ltd.
Outcomes from Peptic Ulcer Surgery Have Not Benefited from Advances in Medical Therapy

Given the advancements in medical treatment of peptic ulcer disease such as Helicobacter pylori eradication and proton-pump inhibitors, we sought to assess their impact on the need for surgical intervention. Patients who underwent peptic ulcer surgery between 1981 and 1998 were evaluated in a retrospective chart review from a tertiary-care hospital (n = 222). The number of operations performed for peptic ulcers decreased annually (24 vs 11.3). Seventy-seven per cent of all cases were done urgently; most were performed for acute perforated ulcers. The overall 30-day mortality rate was 13 per cent, which remained unchanged over the past two decades. The highest mortality rate (82%) was in the transplanted population (n = 11). Our institutional experience demonstrates that despite the lower volume of patients requiring operative management a greater percentage of these patients are presenting with urgent need for surgery. Also despite the aggressive endoscopic management of acutely bleeding ulcers there was no change in the percentage of patients taken to the operating room for uncontrollable hemorrhage. Improvements in medical management of peptic ulcer disease have decreased the surgical volume; nevertheless we show a rising proportion of urgent operations performed annually, and mortality remains high.
Assessment of scapholunate instability and review of evidence for management in the absence of arthritis

Scapholunate ligament tear is a common wrist injury and may lead to degenerative arthritis of the wrist in the long term. We review the assessment and classification of scapholunate instability and discuss the findings from our search for evidence for the management of scapholunate instability in the absence of arthritis. Strong evidence (level 1 or 2) for management is lacking and published recommendations are largely experience-based. The choice of procedure in the absence of arthritis depends on the extent of the tear, quality of the ligament remnants, and reducibility of the joint. Prospective, randomized studies with validated outcome measures are needed to establish the efficacy of intervention on symptoms and function and its effect on the risk of future arthritis.
Sub‐Saharan African coding sequence variation and haplotype diversity at the NAT2 gene

A total of 530 chromosomes from 12 sub‐Saharan African populations were sequenced at the human arylamine N‐acetyltransferase NAT2 gene. We identified seven novel non‐synonymous mutations observed at low frequencies (<11%) in our African multi‐ethnic panel. By using algorithms based on evolutionary conservation, two mutations (c.70T>A [p.L24I] and c.578C>T [p.T193M]) for which the activity of their encoded protein has never been determined, were predicted to entail a potentially damaging effect on protein activity. In addition, approximately 5% of the overall NAT2 African haplotypes presented an unknown functional effect. More interestingly, NAT2 haplotype frequencies and acetylation status inference revealed that the hunter‐gatherer Western Pygmies and ! Kung San were mainly composed of fast and intermediate acetylators, in clear contrast with most agriculturalist populations. These observations highlight the need of a detailed genetic characterization of African populations at this locus to adapt medical treatment, such as the antitubercular isoniazid, to individual/population make‐up in the most effective manner. © 2006 Wiley‐Liss, Inc.
Low-molecular-weight heparins and heparinoids in acute ischemic stroke : a meta-analysis of randomized controlled trials.

BACKGROUND AND PURPOSE Low-molecular-weight heparins and heparinoids (LMWHs) are superior to unfractionated heparin in the prevention and treatment of venous thromboembolism and acute coronary syndromes. We performed a systematic review of randomized controlled trials (RCTs) to examine the safety and efficacy of LMWH in acute ischemic stroke. METHODS Randomized, controlled, and nonconfounded trials of LMWH in acute ischemic stroke were identified from the Cochrane Library (version 2, 1999), previous systematic reviews, and a review of publication quality relating to acute stroke trials. The authors each independently extracted data by treatment group and assessed trial quality using Cochrane Collaboration criteria. RESULTS Eleven completed RCTs involving 3048 patients were identified; data were available from 10 of these. Four trials explicitly excluded patients with presumed cardioembolic stroke. Treatment with LMWH was associated with significant reductions in prospectively identified deep vein thrombosis (OR 0.27, 95% CI 0.08 to 0.96) and symptomatic pulmonary embolism (OR 0.34, 95% CI 0.17 to 0.69) and with increased major extracranial hemorrhage (OR 2.17, 95% 1.10 to 4.28). Nonsignificant increases in end-of-treatment (OR 1.20, 95% CI 0.86 to 1.69) and end-of-trial (OR 1.05, 95% CI 0.83 to 1.32) case fatality and symptomatic intracranial hemorrhage (OR 1.77, 95% CI 0. 95 to 3.31) were observed. End-of-trial death and disability was nonsignificantly reduced (OR 0.87, 95% CI 0.72 to 1.06). CONCLUSIONS ++LMWHs reduce venous thromboembolic events in patients with acute ischemic stroke and increase the risk of extracranial bleeding. A nonsignificant reduction in combined death and disability and nonsignificant increases in case fatality and symptomatic intracranial hemorrhage were also observed. On the basis of the current evidence, LMWH should not be used in the routine management of patients with ischemic stroke.
Retrospective study of the safety of caspofungin in immunocompromised pediatric patients

Caspofungin is an antifungal medication proved efficacious and well-tolerated in adults. Twenty-five pediatric patients at St. Jude Children's Research Hospital who had received at least one dose of caspofungin were identified, and their records were reviewed retrospectively. Caspofungin was well-tolerated; only three patients experienced any adverse event judged possibly related to drug. Caspofungin appears to be safe in immunocompromised pediatric patients.
Diabetic infections: clinical and bacteriological study at Tikur Anbessa Specialized University Hospital, Addis Ababa, Ethiopia.

INTRODUCTION Infection is the most serious complication of diabetes and recognized as causing significant morbidity and mortality. OBJECTIVES To assess the prevalence and pattern of infection, determine the causative organisms. METHODS A cross sectional study involved 179 diabetic patients admitted to the Department of Internal Medicine of Tikur Anbessa Specialized University Hospital performed between Nov. 2000 - Nov 2002, clinical data were documented, a total of 114 clinical specimens (40 pus, 23 blood and 51 urine) were submitted to bacteriology laboratory for bacterial isolation and identification. RESULTS The mean +/- SD fasting blood sugar was 246.0 +/- 153.3 mg/dl. Fifty eight (32.4%) of patients were admitted in state of diabetic ketoacidosis. The prevalence of infection in diabetic patients was 44%. Diabetic foot infection (35%) was the commonest, followed by pulmonary tuberculosis 22%, urinary tract infection (14%), pneumonia (12.8%), skin and subcutaneous infection (12.8%). About 30% of bacterial isolates were Staphylococcus aureus followed by Klebsiella pnumeniae (23.4%), Escherichia coli (19%) and Pseduomonas spp (15%). The rest of the isolates were less frequent and ranged between 2 to 6.4%. More than one bacterial species were also isolated from 10% of the positive cultures. Main causes of deaths in hospitalized diabetic patients were cardiovascular diseases (6/15), end stage renal disease (3/15) and sepsis (2/15). CONCLUSION Infections were the leading cause of morbidity while cardiovascular diseases were the leading cause of mortality. Diabetic foot ulcers were the major cause of infection followed by tuberculosis, skin and subcutaneous infections and pneumonia. The prevalence of tuberculosis in diabetic patient is increasing; S. aureus from wound infection and E. colifrom urinary tract infection were the common pathogens.
Teacher Beliefs, Teacher Concerns, and School Leadership Support as Influences on School Readiness for Implementing a Research-Based Reform Model.

TEACHER BELIEFS, TEACHER CONCERNS, AND SCHOOL LEADERSHIP SUPPORT AS INFLUENCES ON SCHOOL READINESS FOR IMPLEMENTING A RESEARCH-BASED REFORM MODEL Elizabeth Hoag Carhart Old Dominion University, 2013 Director: Linda Bol Federal policy makers and school leaders increasingly recognize middle school math as a turning point in students’ academic success. An i3 scale-up grant allowed grant partners to conduct a large-scale implementation of PowerTeaching (PT), a researchbased reform to increase student math achievement. In a mixed-methods study during the pilot phase of the project, eight schools’ readiness for reform was explored. Teacher questionnaires; interviews with project managers, school leaders, and teachers; classroom observations; and school evaluation forms were used to describe school characteristics that affected variability in initial implementation of the PT model. A cluster analysis demonstrated the relative importance of multiple factors in defining clusters of schools with varying levels of implementation. Classroom observations of teachers’ instructional practices and classroom structure as well as teacher beliefs about team learning were found to be statistically significant. Fundamental to a reform’s successful implementation are a stable network of strong players, and an ability by the school leader to point the organization in one direction.
Modeling of image variability for recognition

This thesis presents the application of different models of image variability to visual recognition problems using the paradigm of appearance-based recognition. We first discuss linear models of variability and relate them to the use of Gaussian distributions. This allows us to use well-understood estimation methods to determine the vectors representing the variability. We also relate the discriminative maximum entropy approach to the Gaussian case and use the relationship to derive the novel maximum entropy linear discriminant analysis. Secondly, we investigate discrete deformation models — that map pixels onto pixels — of order zero, one, and two, where the order is determined by the constraints imposed on the two-dimensional image distortion. We prove for the first time that the determination of the best match for the second order model belongs to the class of NP-hard problems. We show that it is important to include a suitable context for each pixel to achieve low error rates, which is then possible using the less complex models of lower order. We furthermore discuss the use of local patches for visual object categorization as a model allowing high image variability and show how the use of discriminative training leads to very competitive results. Finally, we describe a model for holistic scene analysis that allows us to determine a visual representation of objects present in a set of images. The methods are primarily applied to the tasks of handwritten character recognition and medical image categorization, yielding excellent results in both cases. In particular, we achieve an error rate of 0.52% on the well-known MNIST benchmark and 12.6% on the IRMA-10,000 database, the lowest within the 2005 ImageCLEF evaluation. We show that the models of image variability also improve the recognition performance of appearancebased sign language and gesture recognition systems. This emphasizes the models’ broad applicability.
Addressing the Millennium Development Goals from a surgical perspective: essential surgery and anesthesia in 8 low- and middle-income countries.

HYPOTHESIS Surgical and anesthetic care is increasingly recognized as a neglected but cost-effective component of primary health care in low- and middle-income countries (LMICs). Strengthening delivery can help achieve Millennium Development Goals 4, 5, and 6. Large gaps in access to essential surgical care in LMICs result in considerable morbidity and mortality. The goal of this study was to provide a baseline overview of essential surgical and anesthetic capacity at district-level health facilities in multiple LMICs. DESIGN Survey. SETTING District-level health facilities in multiple LMICs MAIN OUTCOME MEASURES A standardized World Health Organization tool was used at selected district-level hospitals to assess infrastructure, supplies, and procedures relating to essential surgical and anesthetic capacity. The analysis included facilities from countries that assessed more than 5 health facilities. All data were aggregated and blinded to avoid intercountry comparisons. RESULTS Data from 132 facilities were analyzed from 8 countries: Democratic Socialist Republic of Sri Lanka (n = 32), Mongolia (n = 31), United Republic of Tanzania (n = 25), Islamic State of Afghanistan (n = 13), Republic of Sierra Leone (n = 11), Republic of Liberia (n = 9), Republic of The Gambia (n = 6), and Democratic Republic of São Tomé and Príncipe (n = 5). Universally, facilities demonstrated shortfalls in basic infrastructure (water, electricity, oxygen) and functioning anesthesia machines. Although 73% of facilities reported performing incision and drainage of abscesses, only 48% were capable of undertaking an appendectomy. In line with Millennium Development Goals 4, 5, and 6, only 32% of facilities performed congenital hernia repairs, 44% of facilities performed cesarean sections, and few facilities always had goggles and aprons to protect surgical health care workers from human immunodeficiency virus. CONCLUSION Enormous shortfalls in infrastructure, supplies, and procedures undertaken are common at district-level health facilities in LMICs.
Tetraploidization increases sensitivity to Aurora B kinase inhibition

Aurora kinases are overexpressed in many cancers and are targets for anticancer drugs. The yeast homolog of Aurora B kinase, IPL1, was found to be a ploidy-specific lethality gene. Given that polyploidization is a common feature of many cancers, we hypothesized polyploidization also sensitizes mammalian cells to inhibition of Aurora kinases. Using two models of apparent diploid vs. tetraploid cell lines (one based on the hepatocellular carcinoma cell line Hep3B and another on untransformed mouse fibroblasts), we found that tetraploid cells were more sensitive to Aurora B inhibition than their diploid counterparts. Apoptosis could be induced in tetraploid cells by two different Aurora B inhibitors. Furthermore, tetraploid cells were sensitive to Aurora B inhibition but were not affected by Aurora A inhibition. Interestingly, the underlying mechanism was due to mitotic slippage and the subsequent excessive genome reduplication. In support of this, abolition of cytokinesis with dihydrocytochalasin B resulted in similar effects on tetraploid cells as Aurora B inhibition. These results indicate that inhibition of Aurora B or cytokinesis can promote apoptosis effectively in polyploid cancer cells.
Observations on the Factor Structure of the WAIS-R

Confirmatory factor analyses (CFAs) revealed 2 important characteristics of the standardization data of the Wechsler Adult Intelligence Scale-Revised. One finding was that Digit Symbol fit better on an attentional factor in younger groups, but fit was better when Digit Symbol loaded on a visual-perceptual factor in older groups. A second observation was that specifying correlated errors or a fourth factor to explain covariance between Block Design and Object Assembly improved model fit in all age groups except 70to 74-year-olds. The results illustrate the value of CFA and have implications for investigating other samples and other Wechsler tests.