Miracle-dz/UniFAR-FTUs huggingface dataset:
Domestication and the distribution of genetic variation in wild and cultivated populations of the Mesoamerican fruit tree Spondias purpurea L. (Anacardiaceae)

Domestication occurs as humans select and cultivate wild plants in agricultural habitats. The amount and structure of variation in contemporary cultivated populations has been shaped, in part, by how genetic material was transferred from one cultivated generation to the next. In some cultivated tree species, domestication involved a shift from sexually reproducing wild populations to vegetatively propagated cultivated populations; however, little is known about how domestication has impacted variation in these species. We employed AFLP data to explore the amount, structure, and distribution of variation in clonally propagated domesticated populations and sexually reproducing wild populations of the Neotropical fruit tree, Spondias purpurea (Anacardiaceae). Cultivated populations from three different agricultural habitats were included: living fences, backyards, and orchards. AFLP data were analysed using measures of genetic diversity (% polymorphic loci, Shannon's diversity index, Nei's gene diversity, panmictic heterozygosity), population structure (FST analogues), and principal components analyses. Levels of genetic variation in cultivated S. purpurea populations are significantly less than variation found in wild populations, although the amount of diversity varies in different agricultural habitats. Cultivated populations have a greater proportion of their genetic variability distributed among populations than wild populations. The genetic structure of backyard populations resembles that of wild populations, but living fence and orchard populations have 1/3 more variability distributed among populations, most likely a reflection of relative levels of vegetative reproduction. Finally, these results suggest that S. purpurea was domesticated in two distinct regions within Mesoamerica.
[Complications after femoral lengthening with ring fixators in congenital femoral deficiency].

PURPOSE OF THE STUDY Congenital femoral deficiency (CFD) is a rare and complex deformity. The results and complications of surgical correction of this deformity using ring fixators (Ilizarov/Taylor Spatial Frame) have been evaluated. MATERIAL AND METHODS We retrospectively reviewed a consecutive series of 30 patients with CFD, between the ages of 3.3 and 17 years (mean, 9.3 years), with 35 lengthening procedures. Ten cases were treated with an Ilizarov frame, 25 cases with a Taylor Spatial Frame (TSF). RESULTS The average lengthening at femoral osteotomy was 44.3 mm. Nine patients underwent an additional tibial lengthening by an average of 24.2 mm. The total lengthening was 50.5 mm (28-85 mm). A fracture after removal of the fixator occurred in 25.7% of the cases, and a pin-site infection with the subsequent need of operative revision was found in 8.5%. A subluxation of the knee joint was observed in 11.4% and a persistent limitation of the knee joint range of motion in 22.8%. CONCLUSIONS Despite several complications, the use of ring fixators, especially the TSF, is an effective method for treatment of this complex deformity. The complication rate was similar with the use of either ring fixator. Some complications can be decreased with experience. The risk of knee dislocation can be reduced by joint bridging and fractures after frame removal can be avoided by prophylactic rodding.
Biliary Lipid Composition in Patients with Cystic Fibrosis

Lipid composition of gallbladder bile was determined in 20 patients with cystic fibrosis (CF) (9 females and 11 males, ranging in age from 3 to 18 years). The results were compared with 47 normal subjects matched for age, sex, and pubertal stage. In patients with CF, bile was undersaturated with cholesterol before puberty in both sexes and no differences with normal controls could be observed. After puberty, a similar increase in cholesterol saturation was noted in females with CF (85 ± 15% vs. 130 ± 38%, p < 0.01) and normal controls (82 ± 11% vs. 138 ± 31%, p < 0.01). No change in cholesterol saturation could be observed in male patients and controls after puberty. Molar percentage of chenodeoxy-cholic acid (CDCA) was lower (p < 0.05) in postpubertal females (31 ± 9%) and males (36 ± 7%) with CF compared to controls (42 ± 8% and 40 ± 5%, respectively), while cholic acid (CA) was higher in all patients with CF. In females with CF, lithocholic acid (LCA) increased after puberty (2.2 ± 0.8% vs. 5.3 ± 2.6%, p < 0.05) and was higher compared to controls (2.2 ± 0.8%, p < 0.001). An increase was also noted for deoxycholic acid (DCA) in postpubertal females with CF (1.7 ± 2.6% vs. 10.8 ± 7%, p < 0.05), but it was lower in both sexes after puberty than in respective controls. The present results suggest that cholesterol saturation of bile in patients with CF is not different from respective controls. Thus, the higher incidence of gallstone disease in patients with CF reported in the literature might be related to other hepato-biliary disorders known in this disease.
Phosphatase of Regenerating Liver-1 Promotes Cell Migration and Invasion and Regulates Filamentous Actin Dynamics

The phosphatases of regenerating liver (PRLs) are a unique family of plasma membrane-associated protein tyrosine phosphatases that have been hypothesized to be involved in metastatic cancer. How PRLs control cancer cell migration, invasion, and proliferation remains largely unknown. In the current study, we demonstrate a role for PRL-1 in the regulation of filamentous actin dynamics, which could promote cell metastatic processes. Human A549 non–small-cell lung cancer cells stably expressing wild-type PRL-1 exhibited a 60% increase in migration and a 3-fold increase in invasion. Cells expressing catalytic mutants of PRL-1 (C104S and D72A) lacked increased cell migration and invasion, indicating that these phenotypic changes required PRL-1 phosphatase activity. In contrast, PRL-1 small interfering RNA decreased in vitro lung cancer cell migration and invasion. The cadherin-catenin complex and dynamic filamentous actin are believed to control cellular invasiveness. Expression of wild-type PRL-1, but not phosphatase-inactive PRL-1 (C104S or D72A), decreased E-cadherin, vinculin, and paxillin expression. Ectopic expression of wild-type PRL-1 increased RhoA levels, which have an important role in actin filament assembly and stabilization of focal adhesion, and decreased activated Cdc42 and Rac. The Rho-associated protein kinase inhibitor, (R)-(+)-trans-4-(1-aminoethyl)-N-(4-pyridyl) cyclohexanecarboxamide dihydrochloride (Y-27632), decreased RhoA activity, actin filament levels, and cellular migration and invasion in PRL-1-expressing cells. These results suggest that PRL-1 could be a productive cancer therapeutic target and support further efforts to identify its substrates.
The product of the EMS1 gene, amplified and overexpressed in human carcinomas, is homologous to a v-src substrate and is located in cell-substratum contact sites

We have previously identified two genes (EMS1 and PRAD1/cyclin D1) in the chromosome 11q13 region that are frequently coamplified and overexpressed in human breast cancer and in squamous cell carcinomas of the head and neck (E. Schuuring, E. Verhoeven, W.J. Mooi, and R.J.A.M. Michalides, Oncogene 7:355-361, 1992). We now report on the characterization of the 80/85-kDa protein that is encoded by the EMS1 gene. Amino acid sequence comparison shows a high homology (85%) to a chicken protein that was recently identified as a substrate for the src oncogene (H. Wu, A.B. Reynolds, S.B. Kanner, R.R. Vines, and J.T. Parsons, Mol. Cell. Biol. 11:5113-5124, 1991). Immunocytochemistry reveals that in epithelial cells, the human EMS1 protein is localized mainly in the cytoplasm and, to a very low extent, in protruding leading lamellae of the cell. However, in carcinoma cells that constitutively overexpress the protein as a result of amplification of the EMS1 gene, the protein, except in cytoplasm, accumulates in the podosome-like adherens junctions associated with the cell-substratum contact sites. The protein was not found in intercellular adherens junctions. Our findings, and the previously reported observations in src-transformed chicken embryo fibroblasts, suggest that the EMS1 protein is involved in regulating the interactions between components of adherens-type junctions. Since amplification of the 11q13 region has been associated with an enhanced invasive potential of these tumors, overexpression and concomitant accumulation of the EMS1 protein in the cell-substratum contact sites might, therefore, contribute to the invasive potential of these tumor cells.
Letter: effects of hepatitis C infection on the post‐lung transplant mortality

SIRS, We read with great interest the retrospective study by Koenig et al. The study included 319 HCV-positive lung transplant recipients and 17 443 HCV-negative patients with age, gender, race/ethnicity and pre-transplant history, and found that chronic HCV infection was linked to a higher mortality in lung transplant patients with long-term follow-up data (adjusted hazard ratio = 1.24, 95% CI: 1.04–1.46, P = 0.014). This is the largest cohort and longest follow-up to study the effect of recipient hepatitis C infection on lung transplantation in the USA. However, we think there are several points that were required further discussion. First, the authors only compared HCV-positive with HCV-negative on the living donor case numbers and donor’ age. Recently, Englum et al. investigated the impact of donor hepatitis C infection in lung transplant and indicated that HCV-negative patients got worse outcomes if they received HCV-positive lungs. Is it any possibility that HCV-negative patients were likely to receive HCV-negative lungs in current article. Second, several evidences suggested certain co-morbidities were associated with progression chronic hepatitis C, such as HIV infection, vitamin D deficiency, HCV genotype and renal dysfunction. 4 And there is a growing number of patients who are co-infected with HIV and HCV. In this article, the authors had not shown the related results. Third, studies had suggested that survival rates of HCV-positive and HCV-negative patients undergoing lung transplantation were similar since 2000, 6 which may be explained by the advent of stable HCV RNA testing. In this article, the authors included lung transplant patients between 1995 and 2011. What will be the results if the patients were selected since 2000? Furthermore, it is contradictory to findings of a recent study that HCV did not impact lung transplantation, which was published by Doucette et al. Further information is needed to confirm the results.
Familial vulnerability factors to post‐traumatic stress disorder in male military veterans

The question has been frequently raised about whether there are emotional disorders that predispose to post‐traumatic stress disorder (PTSD). We do know that those with PTSD do have many comorbid disorders, but due to the difficulty in performing prospective studies it is hard to tell what is cause and what is effect. This study bypassed the problem caused by comorbidity by examining family history of four proband groups: PTSD, mixed anxiety disorders, coexisting anxiety and depressive disorders, and screened normal controls. Two questions were examined. First, whether family history predicted who experienced combat situations and second, whether the proband groups could be distinguished by family history. Logistic regression identified two variables that predicted the experience of combat: major depression (odds ratio 2.17) and the DSM‐III dramatic personality disorder cluster (odds ratio 1.36). Although there was considerable overlap, family history variables distinguished PTSD from other proband groups. Overall, the pattern of psychopathology in the families of the PTSD probands most closely resembled that in the families of the coexisting anxiety and depressive disorders probands. We conclude that family history methods may be an addition to possible variables that predict who will be exposed to combat and also that family history variables may be able to distinguish a PTSD population from some other types of emotional disorders.
Microscopic mass formulas.

By assuming the existence of a pseudopotential smooth enough to do Hartree-Fock variations and good enough to describe nuclear structure, we construct mass formulas that rely on general scaling arguments and on a schematic reading of shell model calculations. Fits to 1751 known binding energies for {ital N},{ital Z}{ge}8 lead to rms errors of 375 keV with 28 parameters. Tests of the extrapolation properties are passed successfully. The Bethe-Weizsaecker formula is shown to be the asymptotic limit of the present one(s). The surface energy of nuclear matter turns out to be probably smaller than currently accepted.
A new Late Miocene great ape from Kenya and its implications for the origins of African great apes and humans

Extant African great apes and humans are thought to have diverged from each other in the Late Miocene. However, few hominoid fossils are known from Africa during this period. Here we describe a new genus of great ape (Nakalipithecus nakayamai gen. et sp. nov.) recently discovered from the early Late Miocene of Nakali, Kenya. The new genus resembles Ouranopithecus macedoniensis (9.6–8.7 Ma, Greece) in size and some features but retains less specialized characters, such as less inflated cusps and better-developed cingula on cheek teeth, and it was recovered from a slightly older age (9.9–9.8 Ma). Although the affinity of Ouranopithecus to the extant African apes and humans has often been inferred, the former is known only from southeastern Europe. The discovery of N. nakayamai in East Africa, therefore, provides new evidence on the origins of African great apes and humans. N. nakayamai could be close to the last common ancestor of the extant African apes and humans. In addition, the associated primate fauna from Nakali shows that hominoids and other non-cercopithecoid catarrhines retained higher diversity into the early Late Miocene in East Africa than previously recognized.
[Causes and risk factors of pleural empyema and complicated parapneumonic pleural effusion].

OBJECTIVE To analyze the causes and risk factors of pleural empyema and complicated parapneumonic pleural effusion and to evaluate age, sex, concomitant pathology of the patients studied, time of consulting a doctor, and antibacterial treatment before the diagnosis. MATERIAL AND METHODS A total of 120 patients with pleural empyema (n=67) and complicated parapneumonic pleural effusion (n=53) were studied. When pus in the pleural space was present, pleural empyema was considered. Complicated parapneumonic pleural effusion was diagnosed when multiloculated fluid in the pleural cavity by ultrasound examination, more than 50% neutrophils of all leukocytes in the pleural fluid, and pleural fluid pH <7.0 were found. RESULTS Most patients with pleural empyema and complicated parapneumonic pleural effusion were middle aged (53+/-17 years); men were twice as likely as women to have these conditions. Less than half (46%) of patients had at least one risk factor such as neoplasia (37%), treatment with immunosuppressive medicine (15%), alcohol abuse (15%). Persons consulted a doctor after 12 days, on the average, following the onset of the symptoms of the illness. The risk factors were found more often for the patients with pleural empyema than with complicated parapneumonic pleural effusion (50.75% versus 39.62%). Patients with pleural empyema consulted a doctor later than patients with complicated parapneumonic pleural effusion (21+/-28.6 days versus 9.5+/-9.8 days, P=0.0052). Three-fourths (75%) of the patients were treated with antibiotics, and monotherapy was applied most frequently (86% of cases). Penicillins (28%), cephalosporins (26%), aminoglycosides (20%), and macrolides (10%) were prescribed most commonly. One-quarter (25%) of patients were not treated with antibiotics mostly because of misdiagnosed intercostal neuralgia. CONCLUSIONS Causes of pleural empyema and complicated parapneumonic pleural effusion are multifactorial. Patients consult a doctor too late after the onset of the symptoms, nearly half of the studied patients were found to have conditions that might cause immunosuppression, and a part of patients did not receive antibiotics or antibacterial treatment was administered improperly.
Convergence of the Wang-Landau algorithm

We analyze the convergence properties of the Wang-Landau algorithm. This sampling method belongs to the general class of adaptive importance sampling strategies which use the free energy along a chosen reaction coordinate as a bias. Such algorithms are very helpful to enhance the sampling properties of Markov Chain Monte Carlo algorithms, when the dynamics is metastable. We prove the convergence of the Wang-Landau algorithm and an associated central limit theorem.
Infection and transfusion therapy in acute leukaemia.

Granulocytopenia is the single most important risk factor for infection in patients with acute leukaemia. There are limitations to the effective prophylaxis of infection in granulocytopenic patients, but practical measures include the management of the patient in a private hospital room, the requirement of all medical personnel and visitors to wash their hands carefully and to wear masks, restricting the patient to a low-bacteria diet devoid of fresh fruit, vegetables and salads, and the administration of oral antimicrobial agents for gastrointestinal decontamination. When fever develops, empirical therapy with a combination of an aminoglycoside plus an antipseudomonal beta-lactam should be started promptly. A double beta-lactam combination of cefoperazone or ceftazidime plus piperacillin can be substituted if nephrotoxicity is a concern. The addition of empirical intravenous amphotericin may be useful in patients who remain febrile and granulocytopenic on broad-spectrum antibiotics, especially if surveillance cultures indicate fungal colonization. Amphotericin is also the most reliable agent for the treatment of established fungal infections. Acyclovir is not recommended for prophylaxis in acute leukaemia patients but should be reserved for the treatment of well-documented and clinically significant herpes simplex viral infections. During periods of remission, most patients with AML remain free of infection except when they become granulocytopenic again during intensification or consolidation chemotherapy. On the other hand, children with ALL in remission may experience frequent infections unrelated to granulocytopenia as a consequence of their maintenance chemotherapy. Pneumocystis carinii, varicella zoster, and other viruses are common pathogens. Trimethoprim-sulphamethoxazole is effective prophylaxis against Pneumocystis carinii pneumonia in patients with ALL, while intravenous acyclovir is the drug of choice for treatment of varicella zoster infection. Transfusion therapy in the acute leukaemia patient is guided by the patient's peripheral blood counts and degree of sensitization to blood products. Generally, packed red blood cells are given in order to maintain the haematocrit at greater than 30%, while random-donor platelets are administered to keep the platelet count at greater than 20 X 10(9)/l. If refractoriness to platelet transfusions develops, HLA-matched platelets from family members or selected unrelated donors can be used. Similarly, washed or filtered red blood cells may be given to patients with previous and recurrent non-haemolytic febrile reactions to red blood cell transfusions. (ABSTRACT TRUNCATED AT 400 WORDS)
Comparative effectiveness of pegfilgrastim, filgrastim, and sargramostim prophylaxis for neutropenia-related hospitalization: two US retrospective claims analyses

Abstract Objective: Few studies have compared the effectiveness of filgrastim (FIL), pegfilgrastim (PEG), and sargramostim (SAR) to reduce the risk of febrile neutropenia (FN) associated with myelosuppressive chemotherapy (M-CT). Two large commercial database analyses were separately conducted to examine the incidence of neutropenia-related and all-cause hospitalizations associated with FIL, PEG, and SAR prophylaxis for patients receiving M-CT for non-Hodgkin lymphoma (NHL), Hodgkin lymphoma, or solid tumors. Methods: Separate retrospective US claims database analyses utilized patient data from January 1, 2004 to April 30, 2010 using the HealthCore Integrated Research Database (HIRDSM) and January 1, 2001 to August 31, 2009 using OptumInsight’s (formerly Ingenix) database. Patients were ≥18 years old and treated with M-CT for NHL, Hodgkin lymphoma, and solid tumors. All identified M-CT cycles with prophylactic (first 5 days of cycle) FIL, PEG, or SAR were included in the analysis. Patterns of administration and incidence rates of all-cause and neutropenia-related hospitalization were examined on a per-cycle basis. Results: In total, 9330 and 8762 patients with cancer, representing 30,264 and 24,215 chemotherapy cycles (28,189 and 22,649 (PEG), 1669 and 1351 (FIL), 406 and 215 (SAR)) from the HIRDSM and OptumInsight databases, respectively, were included in the separate database analyses. Both the HIRDSM and OptumInsight analysis showed that SAR and FIL prophylaxis had a higher risk of neutropenia-related hospitalization (SAR: OR = 3.48 [95%CI = 2.11, 5.74] and 2.81 [1.62, 4.87]; FIL: 1.78 [1.28, 2.48] and 2.36 [1.82, 3.06], respectively) and all-cause hospitalization (SAR: 2.18 [1.41, 3.36] and 2.41 [1.58, 3.68]; FIL:1.57 [1.25, 1.97] and 1.95 [1.60, 2.38], respectively) vs PEG. Limitations: Medical claims do not contain information about chemotherapy dose, and hospitalizations were not validated against the patient’s chart. Conclusion: In this comparative effectiveness study, use of PEG was associated with a lower risk of neutropenia-related and all-cause hospitalizations compared to use of FIL or SAR prophylaxis.
EMERGENCY MEDICAL SERVICES PROVIDERS

Objective. The investigation seeks to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) on the stethoscopes of emergency medical services (EMS) providers. While stethoscopes are known fomites for MRSA, the prevalence of MRSA in the prehospital setting is not well documented in the literature. Methods. This was a prospective, observational cohort study of 50 stethoscopes provided by consecutive, consenting EMS providers at our academic emergency department (ED). Stethoscopes were swabbed with saline culture applicators and samples were cultured on a commercial MRSA test kit containing mannitol salt agar with oxacillin. After 72 hours of incubation at 37◦C, two emergency physicians and one microbiologist analyzed the plates independently. MRSA colonization was recorded as positive if all three reviewers agreed that colonization had occurred. Results. Of 50 stethoscopes, 16 had MRSA colonization, and 16 (32%) EMS professionals had no recollection of when their stethoscopes had been cleaned last. Reported length of time since last cleaning was grouped into six categories: one to seven days, eight to 14 days, 15 to 30 days, 31 to 180 days, 181 days to 365 days, and unknown. The median time frame reported since the last cleaning was one to seven days. In the model, an increase from one time category to the next increased the odds of MRSA colonization by 1.86 (odds ratio = Presented at the 2008 National Association of EMS Physician Confer-