Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating the performance of AIC in selecting phylogenetic models

Abstract The popular likelihood-based model selection criterion, Akaike’s Information Criterion (AIC), is a breakthrough mathematical result derived from information theory. AIC is an approximation to Kullback-Leibler (KL) divergence with the derivation relying on the assumption that the likelihood function has finite second derivatives. However, for phylogenetic estimation, given that tree space is discrete with respect to tree topology, the assumption of a continuous likelihood function with finite second derivatives is violated. In this paper, we investigate the relationship between the expected log likelihood of a candidate model, and the expected KL divergence in the context of phylogenetic tree estimation. We find that given the tree topology, AIC is an unbiased estimator of the expected KL divergence. However, when the tree topology is unknown, AIC tends to underestimate the expected KL divergence for phylogenetic models. Simulation results suggest that the degree of underestimation varies across phylogenetic models so that even for large sample sizes, the bias of AIC can result in selecting a wrong model. As the choice of phylogenetic models is essential for statistical phylogenetic inference, it is important to improve the accuracy of model selection criteria in the context of phylogenetics.
Ventricular Fibrillation and Polymorphic Ventricular Tachycardia with Critical Coronary Artery Stenosis:

ICD Therapy and CABG for Sudden Death. Introduction: Previous studies have suggested that coronary artery bypass surgery is sufficient to prevent recurrence of sudden death in patients with critical coronary artery stenosis presenting with ventricular fibrillation or polymorphic ventricular tachycardia. We present our experience in patients with one or more episodes of sudden death associated with documented ventricular fibrillation or polymorphic ventricular tachycardia and severe operable coronary artery disease who underwent defibrillator implant at the time of bypass surgery.
Toxicity and Characterization of Cotton Expressing Bacillus thuringiensis Cry1Ac and Cry2Ab2 Proteins for Control of Lepidopteran Pests

Abstract Cry1Ac protoxin (the active insecticidal toxin in both Bollgard and Bollgard II cotton [Gossypium hirsutum L.]), and Cry2Ab2 toxin (the second insecticidal toxin in Bollgard II cotton) were bioassayed against five of the primary lepidopteran pests of cotton by using diet incorporation. Cry1Ac was the most toxic to Heliothis virescens (F.) and Pectinophora gossypiella (Saunders), demonstrated good activity against Helicoverpa zea (Boddie), and had negligible toxicity against Spodoptera exigua (Hübner) and Spodoptera frugiperda (J. E. Smith). Cry2Ab2 was the most toxic to P. gossypiella and least toxic to S. frugiperda. Cry2Ab2 was more toxic to S. exigua and S. frugiperda than Cry1Ac. Of the three insect species most sensitive to both Bacillus thuringiensis (Bt) proteins (including H. zea), P. gossypiella was only three-fold less sensitive to Cry2Ab2 than Cry1Ac, whereas H. virescens was 40-fold less sensitive to Cry2Ab2 compared with Cry1Ac. Cotton plants expressing Cry1Ac only and both Cry1Ac and Cry2Ab2 proteins were characterized for toxicity against H. zea and S. frugiperda larvae in the laboratory and H. zea larvae in an environmental chamber. In no-choice assays on excised squares from plants of different ages, second instar H. zea larvae were controlled by Cry1Ac/Cry2Ab2 cotton with mortality levels of 90% and greater at 5 d compared with 30–80% mortality for Cry1Ac-only cotton, depending on plant age. Similarly, feeding on leaf discs from Cry1Ac/Cry2Ab2 cotton resulted in mortality of second instars of S. frugiperda ranging from 69 to 93%, whereas exposure to Cry1Ac-only cotton yielded 20–69% mortality, depending on plant age. When cotton blooms were infested in situ in an environmental chamber with neonate H. zea larvae previously fed on synthetic diet for 0, 24, or 48 h, 7-d flower abortion levels for Cry1Ac-only cotton were 15, 41, and 63%, respectively, whereas for Cry1Ac/Cry2Ab2 cotton, flower abortion levels were 0, 0, and 5%, respectively. Cry1Ac and Cry2Ab2 concentrations were measured within various cotton tissues of Cry1Ac-only and Cry1Ac/Cry2Ab2 plants, respectively, by using enzyme-linked immunosorbent assay. Terminal leaves significantly expressed the highest, and large leaves, calyx, and bracts expressed significantly the lowest concentrations of Cry1Ac, respectively. Ovules expressed significantly the highest, and terminal leaves, large leaves, bracts, and calyx expressed significantly (P < 0.05) the lowest concentrations of Cry2Ab2. These results help explain the observed differences between Bollgard and Bollgard II mortality against the primary lepidopteran cotton pests, and they may lead to improved scouting and resistance management practices, and to more effective control of these pests with Bt transgenic crops in the future.
Role of NF- (cid:1) B and PI 3-kinase/Akt in TNF- (cid:2) -induced cytotoxicity in microvascular endothelial cells

Role of NF- (cid:1) B and PI 3-kinase/Akt in TNF- (cid:2) -induced cytotoxicity in microvascular endothelial cells. Am J Physiol Renal Physiol 295: F932–F941, 2008. July 16, 2008; doi:10.1152/ajprenal.00066. 2008. —The interaction of tumor necrosis factor (TNF)- (cid:2) with the endothelium is a pivotal factor during endotoxemia. Inﬂammatory conditions are characterized by the activation of the transcription factor NF- (cid:1) B and the expression of inﬂammatory mediators. Previous reports indicate that inhibition of NF- (cid:1) B activation during sepsis may be beneﬁcial to the microvascu-lature. In addition, the phosphatidylinositol-3-kinase/Akt signaling pathway (PI3-kinase/Akt) has been shown to be cytoprotective. In this study, we examined the effect of inhibition of NF- (cid:1) B and PI3-kinase/ Akt on cell viability, cytokine production, inducible nitric oxide synthase (iNOS) expression, and nitric oxide (NO) generation by TNF- (cid:2) -treated cultured microvascular endothelial cells. TNF- (cid:2) induced signiﬁcant cytotoxicity and was associated with increased inﬂammatory cytokines and NO and increased expression of iNOS. The NF- (cid:1) B inhibitor, pyrrolidine dithiocarbamate (PDTC), prevented these increases and signiﬁcantly attenuated the TNF- (cid:2) -induced cytotoxicity. TNF- (cid:2) also caused PI3-kinase/Akt activation, which was further increased by PDTC and prevented by the PI3-kinase inhibitor, LY294002. Inhibition of PI3-kinase/Akt also signiﬁcantly potentiated TNF- (cid:2) -mediated cytotoxicity. LY294002 treatment resulted in the appearance of increased apoptosis, compatible with the known anti-apoptotic properties of PI3-kinase/Akt. The present results therefore demonstrate a cytotoxic effect of TNF- (cid:2) in microvascular endothelial cells which can be attenuated by NF- (cid:1) B inhibition. In addition, PI3-kinase/Akt activation during TNF- (cid:2) exposure may represent a compensatory anti-necrotic and anti-apoptotic pathway. The cytoprotective effects of NF- (cid:1) B inhibition and PI3-kinase/Akt activation may have potential implications in the treatment of endotoxemia and septic shock.
Metabolic Syndrome and Cardiovascular Risk: The Nurse's Role

A B S T R A C T Metabolic Syndrome (MS) is characterized by dysglycemia, arterial hypertension, atherogenic dyslipidemia and central obesity. Its presence has been associated with increased risk for the development of diabetes mellitus and cardiovascular disease. The main treatment goal is to lower the incidence of both MS and its cardiovascular sequelae and includes diet, exercise, weight loss, control of blood glucose and pharmacological therapy of hypertension and dyslipidemia. Nursing care focuses in the development of a concise treatment plan based upon patient’s education, psychosocial support and close follow-up. Nurses should have a wide knowledge of MS pathophysiology which will facilitate their active participation in both diagnosis and treatment processes. The final goal is to assure the long-term compliance of patients with both the proposed lifestyle changes and the medical treatment in order to achieve a significant reduction in their cardiovascular morbidity and mortality.
Towards a More Complete Record of Magmatism and Exhumation in Continental Arcs , Using Detrital Fission-Track Thermochrometry

The NE Asian margin was the locus of an Andean-style subduction zone during most of the Mesozoic and Cenozoic. The Ukelayat flysch is a 10 to 15 km thick section of marine turbidites that were deposited in a 500 km long forearc basin along the outboard edge of this convergent margin. It was structurally overridden during the early Tertiary by an obducted island arc, the Olytorsky terrane. We present new fission-track (Ff) grain ages from unreset detrital zircons. These data provide precise information about depositional age of the Ukelayat and the temporal evolution of the Asian margin continental arc, which provided much of the sediment for the Ukalayat. Because all sandstones contain a large fraction of first-cycle volcanic zircons (euhedra\, colorless), we infer that the youngest component of the Ff grain age distribution, designated P l , closely approximates the time of deposition. Twenty-seven samples have yielded P l ages ranging from -44 to 88 Ma, which indicates continuous magmatic activity in the arc from the Late Cretaceous to Middle Eocene. A second component (P2) records progressive exhumation of the basement to the Okhotsk-Chukotka arc. The difference between P l and P2 ages indicates steady exhumation at -200-400 m/Myr from -90 to 44 Ma. This finding implies the removal of 9 to 18 km of rock in the most deeply exhumed parts of the source region. A change in exhumation rates at -70 Ma may coincide with an eastward shift in the locus of volcanism from the Okhotsk-Chukotka arc to the younger Western Kamchatka-Koryak arc. © 2000 Elsevier Science Ltd. All rights reserved.
Synaptonemal Complex Protein SYCP3 Exists in Two Isoforms Showing Different Conservation in Mammalian Evolution

Meiosis-specific protein SYCP3 is a major structural component of synaptonemal complex (SC) lateral elements. SYCP3 is rather well conserved in vertebrates. However, some differences in SYCP3 expression have been shown among mammals. To clarifiy these differences, we have investigated SYCP3 expression with the aid of bioinformatic, biochemical and cell biological methods. Here we show that, in contrast to other vertebrates, rat and mouse SYCP3 exist in 2 isoforms. The short isoform is conserved among vertebrates. However, the longer isoform, which represents an N-terminal extension of the shorter one, most likely appeared about 15 million years ago in a common ancestor of rat and mouse and after separation from the hamster branch.
Phytochemical High Performance Thin Layer Chromatography basedEstimation of Lawsone in Lawsonia inermis (Henna) obtained from TwoNatural Habitats and Dye Products Collected from Local Market

The present study elucidates the preliminary phytochemical analysis and High Performance Thin Layer Chromatography (HPTLC) fingerprint analysis of lawsone extract of the leaves of Lawsonia inermis (henna) and evaluates their regions and products based quantitative estimations. The lawsone content has been evaluated quantitatively in two plants samples collected from Rewa and Bhopal and one commercial henna powder procured from open market of Bhopal city. Here we aimed to optimize high performance thin layer chromatography for the determination of lawsone. The chromatography development was carried out on the TLC silica gel 60 F254 aluminum plate and good resolution was achieved with toluene: ethyl acetate: formic acid (22:16:2) as mobile phase. Lawsone detected was carried out densitometrically at 254 nm by absorption mode and a linear regression coefficient was obtained with Y=133.527+13.470 × R=0.99092 ± 6.43%. The methods were applied are validated with respect to specificity, linearity, accuracy precision and robustness, and also find out the linear calibration come with respect to the concentration and regression coefficient. The developed method was validated as percentage relative standard deviation of peak areas was found to be which indicates the suitability of system for the further validation parameters. There was the presence of the peak at Rf 0.4 in the placebo, indicates the method is specific as none of the recipients interfered with the analytes of interest. The peak purity of Lawsone was achieved from 560-1865 Au.
Integrating Massage into Rural Caregiving at End-of-Life

mands of providing end-of-life care negatively affect all aspects-e-physical, social, emotional, and financial-of a family caregiver's quality of life (1). On average, family caregivers provide 10.8 hours of direct care per day, often have to make adjustments to their homes or living arrangements, and average more than $500 in outof-pocket care-related expenses during the last month of their loved ones' lives (2). Compared to noncaregivers, caregivers are at increased risk for anxiety, depression, and health problems, and for less satisfaction with life (8,9). However, those risks are diminished if they are able to find meaning and subjective benefits from providing care (10). While providing care, caregivers find their roles more physically than socially, emotionally, or financially draining (1). Those more physically involved with direct patient care report more burden and are less satisfied with social support received from others (2,3,11). Six months following their loved ones' deaths, however, caregivers report that "standing by" or observing their spouses' illness was the most difficult aspect of providing care (2,3). The cost of caregiving is not only realized during the time care is given, but is also borne later. Three months after their family members' death caregivers continue to display more depressive symptoms than the general public (2).
Sucralfate versus antacids or H2‐antagonists for stress ulcer prophylaxis: A meta‐analysis on efficacy and pneumonia rate

Objectives and MethodsHistamine2 (H2)-receptor antagonists and antacids have been the basic drugs for the prevention of stress bleeding in ICU patients during the past decade. Recently, drugs without major influence on gastric pH have been investigated in stress bleeding prophylaxis. Therefore, a meta-analysis (Mantel-Haenszel test) was undertaken to determine the efficacy of sucralfate in the prevention of macroscopically visible stress bleeding, as well as the influence of sucralfate on the frequency of pulmonary infections. ResultsThe efficacy of sucralfate was compared with H2-antagonists in nine studies and with antacids in eight studies. Sucralfate was significantly more effective than H2-antagonists (typical odds ratio 0.532, 95% confidence interval 0.303 to 0.933) and equally as effective as antacids (typical odds ratio 0.868, 95% confidence interval 0.452 to 1.667). The pneumonia rates of those patients who were administered sucralfate were compared with the rates of those patients who were given H2-antagonists in five studies and with those patients who were given antacids in four studies. Pneumonia was a significantly more frequent occurrence under prophylaxis with H2-antagonists (typical odds ratio 0.498, 95% confidence interval 0.316 to 0.783) as well as with antacids (typical odds ratio 0.402, 95% confidence interval 0.235 to 0.687). ConclusionSucralfate is an effective drug for the prevention of stress bleeding that minimizes the risk of nosocomial pneumonia in long-term ventilated ICU patients. (Crit Care Med 1991; 19:942)
Algorithms for sorting by reversals or transpositions, with application to genome rearrangement : Algoritmos para problemas de ordenação por reversões ou transposições, com aplicações em rearranjo de genomas

Ao longo da evolucao, eventos de rearranjo podem alterar a ordem e a orientacao dos genes de um genoma. O problema de calcular a menor sequencia de rearranjos que transforma um genoma em outro e um problema bastante estudado que encontra aplicacoes em genomica comparativa. Representando genomas como permutacoes, nas quais os genes aparecem como elementos, esse problema pode ser reduzido ao problema combinatorio de ordenar uma permutacao utilizando o menor numero de rearranjos. Tal problema combinatorio, referido como problema da ordenacao por rearranjo, varia de acordo com os tipos de rearranjo considerados. Nesta tese, focamos nosso estudo em dois tipos de rearranjo: reversoes e transposicoes. Muitas variacoes do problema da ordenacao por rearranjo que envolvem esses rearranjos tem sido atacadas na literatura e, para a maior parte delas, os melhores algoritmos conhecidos sao aproximacoes ou heuristicas. Em razao disso, apresentamos uma ferramenta, chamada GRAAu, que auxilia a avaliacao dos resultados produzidos por esses algoritmos. Alem disso, apresentamos uma heuristica generica que pode ser usada para melhorar as solucoes produzidas por qualquer algoritmo nao exato. Alem de apresentar o GRAAu e a heuristica de melhoria, os quais possuem um apelo mais geral, apresentamos contribuicoes relacionadas a variacoes especificas do problema da ordenacao por rearranjo. Primeiro, consideramos o problema da ordenacao por transposicoes e apresentamos resultados teoricos e praticos relacionados a tres algoritmos aproximados baseados em uma abordagem alternativa ao grafo de ciclos, que e uma ferramenta padrao para atacar o problema da ordenacao por rearranjo. Depois, voltamos nossa atencao a variacoes que envolvem rearranjos curtos. Mais precisamente, estudamos cinco variacoes: (i) o problema de ordenar uma permutacao linear com sinal por reversoes super curtas, (ii) o problema de ordenar uma permutacao circular com sinal por reversoes super curtas, (iii) o problema de ordenar uma permutacao linear com sinal por reversoes curtas, (iv) o problema de ordenar uma permutacao linear com sinal por rearranjos super curtos e (v) o problema de ordenar uma permutacao linear com sinal por rearranjos curtos. Apresentamos algoritmos polinomiais para os problemas (i), (ii) and (iv), um algoritmo 5-aproximado para o problema (iii) e um algoritmo 3-aproximado para o problema (v). Usamos o algoritmo desenvolvido para o problema (ii) para reconstruir a filogenia de genomas de bacterias do genero Yersinia e comparamos os resultados com as filogenias apresentadas em trabalhos anteriores. Abstract
Continuous glucose monitoring after islet transplantation in type 1 diabetes: an excellent graft function (β-score greater than 7) Is required to abrogate hyperglycemia, whereas a minimal function is necessary to suppress severe hypoglycemia (β-score greater than 3).

CONTEXT For the last 10 yr, continuous glucose monitoring (CGM) has brought up new insights into the accuracy of blood glucose analysis. OBJECTIVE Our objective was to determine how islet graft function was able to influence the various components of dysglycemia after islet transplantation (IT). DESIGN AND SETTING We conducted a single-arm open-labeled study with a 3-yr follow-up in a referral center (ClinicalTrial.gov identifiers NCT00446264 and NCT01123187). PATIENTS Twenty-three consecutive patients with type 1 diabetes (14 islet alone, nine islet after kidney) received IT within 3 months using the Edmonton protocol. INTERVENTION INTERVENTION included 72-h CGM before and 3, 6, 9, 12, 24, and 36 months after transplantation. MAIN OUTCOME MEASURE Graft function was estimated via β-score, a previously validated index (range 0-8) based on treatment requirements, C-peptide, blood glucose, and glycated hemoglobin. RESULTS At the 3-yr visit, graft function persisted in 19 patients (82%), and 10 (43%) remained insulin independent. Glycated hemoglobin decreased in the whole cohort from 8.3% (7.3-9.0%) at baseline to 6.7% (5.9-7.7%) at 3 yr [median (interquartile range), P < 0.01]. Mean glucose, glucose sd, and time spent with glycemia above 10 mmol/liter (hyperglycemia) and below 3 mmol/liter (hypoglycemia) were significantly lower after IT (P < 0.05 vs. baseline). The four CGM outcomes were related to β-score (P < 0.001). However, partial function (β-score >3) was sufficient to abrogate hypoglycemia; suboptimal function (β-score >5) was necessary to significantly improve mean glucose, glucose sd, and hyperglycemia; and optimal function (β score >7) was necessary to normalize them. CONCLUSION The four components of dysglycemia were not equally affected by the degree of islet graft function, which could have important implications for future development of β-cell replacement. A β-score above 3 dramatically reduced the occurrence of hypoglycemia.
Long‐term experience with low‐dose interferon‐α and PUVA in the management of early mycosis fungoides

Abstract: Objectives: Combined high‐dose Interferon‐α and psoralen plus ultraviolet A irradiation (PUVA) have been reported to be effective in the treatment of early mycosis fungoides (MF); however, our study is the first controlled prospective study in the literature exploring the activity and tolerability of the combination with low dosages and evaluating further clinical outcome of early‐MF patients. Methods: We carried out a multicentric prospective Phase II clinical study on 89 patients with early‐stage IA to IIA MF treated for 14 months with low‐dose IFN‐α2b (6–18 MU/wk) and PUVA. Treatment success was analysed in terms of freedom from treatment failure. Results and conclusions: Complete remission (CR) was achieved in 84% and an overall response rate in 98% of cases: six‐month CR was associated with a non‐confluent skin infiltrate at histology (P = 0.044) and 14‐month CR with high epidermal CD1a+ dendritic‐cell density (P = 0.030). The combination protocol was successfully tolerated and the most common reason of ‘failure’ was related to relapse and not to toxicity. Sustained remissions were achieved in 20% of patients. High CD8+ lymphoid T‐cell density was associated with a lower relapse rate (P = 0.002). We think that our combination therapy can be considered an alternative approach compared with other modalities. Good immunological host surveillance in the skin lesions seems to be an optimal basis for the therapeutic success.
ÖĞRETMEN ADAYLARININ OKUDUĞUNU ANLAMA VE OKUMA STRATEJİLERİNİ KULLANMA DÜZEYLERİ

Bu arastirmada ogretmen adaylarinin okudugunu anlama duzeyleri ve okuma stratejilerini kullanma duzeyleri arastirilmistir. Calismada okudugunu anlama duzeyi ve okuma stratejilerini kullanma duzeyinin; ana bilim dali, ogretim turu, cinsiyet ve akademik basari puanina gore anlamli bir farklilik gosterip gostermedigi incelenmistir.Balikesir Universitesi Necatibey Egitim Fakultesi Turkce EgitimiBolumu Turkce Egitimi Ana Bilim Dali, Ilkogretim Bolumu Fen BilgisiEgitimi, Sinif Ogretmenligi Egitimi, Sosyal Bilgiler Ogretmenligi Egitimi, Matematik Ogretmenligi Egitimi Ana Bilim Dallarinda 2008–2009egitim-ogretim yilinda 4. sinifta okuyan toplam 569 ogrenci calisma grubu olarak belirlenmistir.Arastirmanin sonucunda ogretmen adaylarinin okudugunu anlamaduzeyleri yetersiz bulunmustur. Basari duzeyi en yuksek grup Turkce, endusuk grup ise sosyal bilgiler ogretmenligi ogrencileridir.Okudugunu anlama bakimindan ogretim turune gore anlamli birfarklilik bulunmamis fakat kiz ogrencilerin erkek ogrencilere gore, akademik basari puani yuksek ogrencilerin de akademik basari puani dusukogrencilere gore daha basarili olduklari gorulmustur.Okuma stratejilerini kullanma bakimindan katilimcilar orta duzeyde bulunmustur. Okuma stratejileri acisindan en ust duzeyde olan grupTurkce, en dusuk duzeyde olan grup ise sosyal bilgiler ogretmenligi ogrencileridir. Okuma stratejilerini kullanma bakimindan ogretim turune gore anlamli bir farklilik bulunmamistir