Miracle-dz/UniFAR-FTUs huggingface dataset:
A case study in comparing therapies involving informative drop‐out, non‐ignorable non‐compliance and repeated measurements

Virtually no comparisons of different psychotherapies with long follow‐up times have been carried out until now. The Helsinki Psychotherapy Study is a randomized clinical trial, where patients were monitored for 12 months after the onset of study treatments, of which each lasted approximately 6 months. The patients' psychiatric status was measured at five pre‐determined time points during the follow‐up period. In general, the analyses of trials are complicated in cases where compliance with the given treatment is incomplete or the drop‐out from the follow‐up is non‐ignorable. In the present study, the quality of the treatment deviated from the protocol for some patients and some patients took auxiliary treatments which had similar effects to the study treatment during the study treatment or follow‐up period. This might have resulted in standard intention‐to‐treat analyses providing excessively conservative or liberal conclusions. Non‐compliance may have been non‐ignorable in some cases, so subject‐specific latent factors may have influenced the outcome both directly and indirectly via compliance behaviour. The most and least healthy patients are the most likely to dropout from the follow‐up a priori, so the missing data process is informative. The missing data can partly be augmented with surrogate information collected during interviews with patients who dropped out. A Bayesian hierarchical as‐treated model, which uses random‐effects‐based selection models to account for non‐ignorable missing data and non‐compliance, was compared with different mixed effects models. Copyright © 2005 John Wiley & Sons, Ltd.
Stromal biology of pancreatic cancer

The genetic paradigm of cancer, focused largely on sequential molecular aberrations and associated biological impact in the neoplastic cell compartment of malignant tumors, has dominated our view of cancer pathogenesis. For the most part, this conceptualization has overlooked the dynamic and complex contributions of the surrounding microenvironment comprised of non‐tumor cells (stroma) that may resist, react to, and/or foster tumor development. Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease in which a prominent tumor stroma compartment is a defining characteristic. Indeed, the bulk of PDAC tumor volume consists of non‐neoplastic fibroblastic, vascular, and inflammatory cells surrounded by immense quantities of extracellular matrix, far exceeding that found in most other tumor types. Remarkably, little is known about the composition and physiology of the PDAC tumor microenvironment, in particular, the role of stroma in tumor initiation and progression. This review attempts to define key challenges, opportunities and state‐of‐knowledge relating to the PDAC microenvironment research with an emphasis on how inflammatory processes and key cancer pathways may shape the ontogeny of the tumor stroma. Such knowledge may be used to understand the evolution and biology of this lethal cancer and may convert these insights into new points of therapeutic intervention. J. Cell. Biochem. 101: 887–907, 2007. © 2007 Wiley‐Liss, Inc.
Modeling of Temporomandibular Joint Function Using MRI and Jaw-Tracking Technologies – Mechanics

The study of mechanics of the temporomandibular joint (TMJ) is important because its dysfunction and breakdown could be, at least partially, of mechanical origin. The incongruity of the articular surfaces of the TMJ is compensated by a fibrocartilaginous articular disc. Its dislocation and failure seem to be closely related to the development of osteoarthritis of the TMJ. The analysis of mandibular kinematics permits the detection and assessment of irregularities of TMJ function due to internal obstacles such as a displaced articular disc. Furthermore, the measurement of the dynamic relationship between the articular surfaces of the TMJ is useful to determine the strains undergone by the disc that if too high might compromise its integrity. The development of our research in TMJ mechanics has evolved from the acquisition of the traces of single mandibular points to an accurate and compact description of mandibular motion, in which the mechanical advantage of jaw muscles, and forces and torques acting on the jaw are considered as well. The combination of three-dimensional software models of TMJ anatomies obtained from MRI and jaw tracking with six degrees of freedom permits a subject-specific dynamic analysis of the intra-articular space, providing insight into individual disc deformation during function and TMJ loading. Studies performed with this system indicate that both TMJs are loaded during chewing, the balancing more so than the working joint. In fact, during chewing, the intra-articular distance is smaller for hard than for soft food, on closing than on opening, on the balancing than on the working side. This last finding is confirmed by static biting experiments, in which the condyle-fossa distance decreases more on the side contralateral to the bite force, depending on its magnitude. Also studies on the dynamics of compression areas indicate that plowing can occur through the disc during function, especially mediolaterally, due to stress field translation. This effect might contribute to cartilage wear and fatigue also because the disc is weaker mediolaterally. Further data indicate that the lateral area of the disc is mostly exposed to a higher mechanical energy density. This will be more intensively investigated using finite element method.
Induction of fas ligand expression by an acutely lethal simian immunodeficiency virus, SIVsmmPBj14.

Simian immunodeficiency virus strain PBj14, SIVsmmPBj14, is unique among primate lentiviruses in its ability to trigger the proliferation of resting simian lymphocytes and to cause the rapid death of experimentally inoculated pigtailed macaques. Severe enteropathy, immune activation, and extensive apoptosis, particularly within gut-associated lymphoid tissue, characterize the acute disease syndrome associated with SIVsmmPBj14 infection. In the present study, we examined whether the ability of this virus to cause widespread apoptosis might be linked to the up-regulation of Fas ligand (CD95L) expression in virally infected cells. In vitro studies revealed that expression of the viral Nef protein, in the absence of any other viral gene product, was sufficient to up-regulate the transcriptional activity of the CD95L promoter and to cause cell surface expression of Fas ligand. This up-regulation was NFAT dependent (inhibited by cyclosporin A) and did not occur in cells that expressed a mutated derivative of the viral Nef protein, lacking a previously defined immunoreceptor tyrosine-based activation motif. These findings were corroborated by analysis of tissue sections from virally infected macaques. Immunohistochemical staining revealed that Fas ligand expression was efficiently up-regulated in the GALT of animals that had been experimentally infected with wild-type SIVsmmPBj14 but not in animals that were infected with a nonacutely pathogenic viral mutant lacking the Nef ITAM. Taken together, these results suggest that the ability of SIVsmmPBj14 to cause acutely lethal disease and to up-regulate FasL expression may be linked. Additional studies will be required to determine whether the induction of FasL expression is in itself important for acute disease pathogenesis.
Prediction equations for pulmonary function values in healthy young Iranians aged 8–18 years

Objective: Pulmonary function test (PFT) variables are dependent on height, age and gender. In addition, there is evidence of PFT variation in different ethnic groups. Prediction equations for PFT from a healthy, non‐smoking, urban young population in the city of Mashhad (north‐east Iran) have been derived.
Observationally constrained estimates of carbonaceous aerosol radiative forcing

Carbonaceous aerosols (CA) emitted by fossil and biomass fuels consist of black carbon (BC), a strong absorber of solar radiation, and organic matter (OM). OM scatters as well as absorbs solar radiation. The absorbing component of OM, which is ignored in most climate models, is referred to as brown carbon (BrC). Model estimates of the global CA radiative forcing range from 0 to 0.7 Wm-2, to be compared with the Intergovernmental Panel on Climate Change’s estimate for the pre-Industrial to the present net radiative forcing of about 1.6 Wm-2. This study provides a model-independent, observationally based estimate of the CA direct radiative forcing. Ground-based aerosol network data is integrated with field data and satellite-based aerosol observations to provide a decadal (2001 through 2009) global view of the CA optical properties and direct radiative forcing. The estimated global CA direct radiative effect is about 0.75 Wm-2 (0.5 to 1.0). This study identifies the global importance of BrC, which is shown to contribute about 20% to 550-nm CA solar absorption globally. Because of the inclusion of BrC, the net effect of OM is close to zero and the CA forcing is nearly equal to that of BC. The CA direct radiative forcing is estimated to be about 0.65 (0.5 to about 0.8) Wm-2, thus comparable to or exceeding that by methane. Caused in part by BrC absorption, CAs have a net warming effect even over open biomass-burning regions in Africa and the Amazon.
Improving the filtering performance of the BDND algorithm in impulse noise removal

Switching median filters are very popular in the removal of impulse noise in digital images. The boundary discriminative noise detection (BDND) is shown to supersede existing algorithms especially under high noise densities. However, careful investigation of the filtering step in this algorithm reveals some problems that may affect the sharpness of the output image. In this paper, we propose two simple, yet effective modifications, to the filtering step in the BDND algorithm. The modifications loosen the condition on expanding the filtering window and incorporate the spatial information of pixels in the filtering operations. Experimental evaluation proved the effectiveness of the proposed modifications in producing sharper images than the BDND algorithm.
Family Structure, Human Capital Investment, and Aggregate College Attainment

We provide new facts about the increase in US college attainment from 1995-2015. College attendance grew more among children from low resource families than among those from high resource families (7pp vs 1pp). However, college completion grew less among low resource children than high resource children (4pp vs 13pp). We propose a theory to explain the increase in aggregate college completion since 1995 that is consistent with these trends. The theory has two key components: (i) High resource families increased pre-college investment relative to low-resource families in response to a growing college wage premium. (ii) Pre-college investment is an important determinant of college completion conditional on attendance. Consistent with this theory, we provide empirical evidence of growing gaps in pre-college investment and college preparedness between children from high and low resource families. Finally, we construct a model of intergenerational human capital investment and college attainment to quantitatively test our theory.
Total Factor Productivity Analysis in Food Sector

In this study we to try to analyze the total factor productivity of 22 firms listed in Borsa Istanbul (BIST) in terms of economics perspective with the 2011-2015 years data. Equity, raw material cost and personnel cost were used as input variables; total sales and total export values also as output variables in accordance with the data acquired from BIST. Malmquist Total Factor Productivity Index was applied to data with input oriented models. According to research findings; all firms seems to have decreasing values only in technical efficiency; but on the contrary increasing values in technological efficiency, pure efficiency, scale efficiency and total factor productivity. The most improvements was observed to be approximately 4.5% in total factor productivity. A.V. O.D, Tarim and Dardanel were seen to be firms improving their values in all efficiency forms for five years; whereas Kent, Oylum and Pinar Et were observed to have decreasing values in all efficiency forms for five years. Keywords: Borsa Istanbul, Food Industry, Efficiency, Malmquist Total Factor, Productivity.
Twelve-year course and outcome predictors of anorexia nervosa.

OBJECTIVE The current study presents the long-term course of anorexia nervosa (AN) over 12 years in a large sample of 103 patients diagnosed according to criteria in the 4th ed. of the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV). METHOD Assessments were made at the beginning of therapy, at the end of therapy, at the 2-year follow-up, at the 6-year follow-up, and at the 12-year follow-up. Self-rating and an expert-rating interview data were obtained. RESULTS The participation rate at the 12-year follow-up was 88% of those alive. There was substantial improvement during therapy, a moderate (in many instances nonsignificant) decline during the first 2 years posttreatment, and further improvement from 3 to 12 years posttreatment. Based on a global 12-year outcome score, 27.5% had a good outcome, 25.3% an intermediate outcome, 39.6% had a poor outcome, and 7 (7.7%) were deceased. At the 12-year follow-up 19.0% had AN, 9.5% had bulimia nervosa-purging type (BN-P), 19.0% were classified as eating disorder not otherwise specified (EDNOS). A total of 52.4% showed no major DSM-IV eating disorder and 0% had binge eating disorder (BED). Systematic-strictly empirically based-model building resulted in a parsimonious model including four predictors of unfavorable 12-year outcome explaining 45% of the variance, that is, sexual problems, impulsivity, long duration of inpatient treatment, and long duration of an eating disorder. CONCLUSION Mortality was high and symptomatic recovery protracted. Impulsivity, symptom severity, and chronicity were the important factors for predicting the 12-year outcome.
Research on a new and generalized method of discontinuous PWM strategies to minimize the switching loss

A novel generalized method of discontinuous pulse width modulation (DPWM) strategies such as DPWM0, DPWM1, DPWM2 ,DPWM3, DPWMMAX and DPWMMIN usually called as DPWMx is proposed in this paper to minimize the switching loss for three-phase voltage source inverters. Six sectors are re-carved up into twelve ones. Analyzing and summarizing all kinds of conventional DPWMx strategies, come to a conclusion that the reference voltage of each III-type DPWMx strategy can be obtained by I-type DPWMx strategy by means of linear transformation. Substantial relations between I-type and III-type DPWMx strategies are debated. The feasibility of analyzing and implementing of the presented generalized DPWMx strategies is proved by theoretical analysis and simulation results.
Massive Infection of Seabird Ticks with Bacterial Species Related to Coxiella burnetii

ABSTRACT Seabird ticks are known reservoirs of bacterial pathogens of medical importance; however, ticks parasitizing tropical seabirds have received less attention than their counterparts from temperate and subpolar regions. Recently, Rickettsia africae was described to infect seabird ticks of the western Indian Ocean and New Caledonia, constituting the only available data on bacterial pathogens associated with tropical seabird tick species. Here, we combined a pyrosequencing-based approach with a classical molecular analysis targeting bacteria of potential medical importance in order to describe the bacterial community in two tropical seabird ticks, Amblyomma loculosum and Carios (Ornithodoros) capensis. We also investigated the patterns of prevalence and host specificity within the biogeographical context of the western Indian Ocean islands. The bacterial community of the two tick species was characterized by a strong dominance of Coxiella and Rickettsia. Our data support a strict Coxiella-host tick specificity, a pattern resembling the one found for Rickettsia spp. in the same two seabird tick species. Both the high prevalence and stringent host tick specificity suggest that these bacteria may be tick symbionts with probable vertical transmission. Detailed studies of the pathogenicity of these bacteria will now be required to determine whether horizontal transmission can occur and to clarify their status as potential human pathogens. More generally, our results show that the combination of next generation sequencing with targeted detection/genotyping approaches proves to be efficient in poorly investigated fields where research can be considered to be starting from scratch.
Prenatal diagnosis of Ullrich congenital muscular dystrophy using haplotype analysis and collagen VI immunocytochemistry

Ullrich congenital muscular dystrophy (UCMD) is a recessively inherited condition characterised by proximal joint contractures, marked distal joint hyperextensibility, rigidity of the spine and early respiratory failure. Recently, mutations in the genes encoding the subunits of collagen VI have been identified in this disease. We undertook two prenatal diagnoses for UCMD in a consanguineous family where the disease was consistent with linkage to the COL6A3 locus and immunolabelling of collagen VI in the proband's skeletal muscle was severely reduced.
Interaction between beta 2- and alpha 2-adrenoceptor responses in the vascular system: effect of clenbuterol.

Subchronic treatment with the beta 2-adrenoceptor agonist, clenbuterol (0.3 mg X kg-1, twice daily for 14 days), significantly increased the median blood pressure in anaesthetized normotensive rats. The treatment produced a marked reduction in the vasodilator effect of isoproterenol. Acute clenbuterol administration (0.01 mg X kg-1 i.v.) reduced the contractile response induced by the alpha 2-adrenoceptor agonists, guanabenz or B-HT 920, and the alpha 1- and alpha 2-adrenoceptor agonist, clonidine, whereas it did not affect the vasoconstriction by the alpha 1-adrenoceptor agonist, methoxamine, in the pithed rat. Subchronic treatment with clenbuterol attenuated the effect of the beta 2-adrenoceptor agonist on the vascular alpha 2-adrenoceptor responses and enhanced the alpha 1-adrenoceptor response to phenylephrine in pithed rats. The effect of the beta 2-adrenoceptor agonist was reduced by 1- but not d-propranolol. These results suggest that subchronic treatment with clenbuterol produces a subsensitivity of the beta 2-adrenoceptors and reduced the interaction between beta 2- and alpha 2-adrenoceptors at the vascular wall.
Skeletal pathology and variable anatomy in elephant feet assessed using computed tomography

Foot problems are a major cause of morbidity and mortality in elephants, but are underreported due to difficulties in diagnosis, particularly of conditions affecting the bones and internal structures. Here we evaluate post-mortem computer tomographic (CT) scans of 52 feet from 21 elephants (seven African Loxodonta africana and 14 Asian Elephas maximus), describing both pathology and variant anatomy (including the appearance of phalangeal and sesamoid bones) that could be mistaken for disease. We found all the elephants in our study to have pathology of some type in at least one foot. The most common pathological changes observed were bone remodelling, enthesopathy, osseous cyst-like lesions, and osteoarthritis, with soft tissue mineralisation, osteitis, infectious osteoarthriti, subluxation, fracture and enostoses observed less frequently. Most feet had multiple categories of pathological change (81% with two or more diagnoses, versus 10% with a single diagnosis, and 9% without significant pathology). Much of the pathological change was focused over the middle/lateral digits, which bear most weight and experience high peak pressures during walking. We found remodelling and osteoarthritis to be correlated with increasing age, more enthesopathy in Asian elephants, and more cyst-like lesions in females. We also observed multipartite, missing and misshapen phalanges as common and apparently incidental findings. The proximal (paired) sesamoids can appear fused or absent, and the predigits (radial/tibial sesamoids) can be variably ossified, though are significantly more ossified in Asian elephants. Our study reinforces the need for regular examination and radiography of elephant feet to monitor for pathology and as a tool for improving welfare.
Helping family physicians improve their cardiac auscultation skills with an interactive CD‐ROM

Introduction: There have been few studies of the cardiac auscultation skills of residents and family physicians. This study assessed a group of family physicians' cardiac auscultation skills and use of a computerized self‐instructional program to improve these skills. Methods: Forty‐two volunteer family physicians participated in an initial assessment of cardiac auscultation skills using test recordings of 12 common heart sounds. They were provided with a CD‐ROM instructional program and were asked to devote 15 hours of self‐study to the program and to return in 9 months for reassessment. Results: The 42 family physicians in the initial assessment identified 39% of the heart sounds. Twenty‐one returned for reassessment and showed significant improvement. Their initial mean score was 4.3 of 12 (35%), and their final mean score was 8.0 of 12 (67%). They found the CD‐ROM program to be a valuable resource. The feature most liked was the unlimited opportunity to review sounds, cases, and tutorials. Most frequent problems related to computer access or skills. Eleven respondents reported using the program to resolve patient problems in their clinical practices. Discussion: The cardiac auscultation skills of group of volunteer family physicians showed low initial scores that improved significantly after self‐study with a CD‐ROM instructional program. The program was a valuable self‐instructional aid, and physicians used it as a resource in clinical practice. However, only 50% of the initial group completed the self‐study and returned for final assessment. Providing more support and assistance in the initial phase, especially computer uses, may enable completion of similar computerized self‐study programs.
Effective therapeutic anticancer vaccines based on precision guiding of cytolytic T lymphocytes

Summary: In natural immune responses CD4+ T helper (Th) cells, reactive with peptide antigens presented by major histocompatibility complex (MHC) class II molecules on dendritic cells (DC), can drive the maturation of DC that is required for induction of CD8+ cytolytic T‐lymphocyte (CTL) immunity. Proper induction, expansion and maintenance of CTL responses are achieved through delicate interactions between CD4+ T cells, DC and CD8+ T cells involving several ligand–receptor pairs. Th cells to a large extent operate through up‐regulation of CD40L, which then interacts with CD40 on DC to cause DC maturation. Subsequent CTL induction by activated DC requires CD80/CD86 on the DC to interact with the CD28 costimulatory receptor on CD8+ T cells. For maintenance and full expansion of CTL, interaction of the DC‐expressed 4–1BB ligand with its receptor 4–1BB on CTL is also important. Alternative molecular triggers of DC activation that can support induction of powerful CTL responses include agonistic anti‐CD40 antibody or ligands of Toll‐like receptors (TLR) such as LPS (TLR4 ligand) or oligodeoxynucleotides containing CpG‐motifs (TLR9 ligand). The combination of CpG adjuvant with a 35 amino acid long synthetic peptide comprising both tumor‐specific CTL and Th epitopes proved to be a highly effective vaccine formulation capable of inducing therapeutic immunity against human papillomavirus‐induced mouse tumors. The recently acquired insights into antigen presentation and costimulatory signals have made possible the development of a new generation of therapeutic anticancer vaccines.