Miracle-dz/UniFAR-FTUs huggingface dataset:
Urethral strictures after radiation therapy for prostate cancer

Urethral stricture after radiation therapy for localized prostate cancer is a delicate problem as the decreased availability of tissue healing and the close relation to the sphincter complicates any surgical approach. We here review the pathophysiology, dosimetry, and the disease specific aspects of urethral strictures after radiotherapy. Moreover we discuss different treatment option such as direct vision internal urethrotomy as well as techniques for open reconstruction with and without tissue transfer.
Learning dependent sources using mixtures of Dirichlet: Applications on hyperspectral unmixing

This paper is an elaboration of the DECA algorithm [1] to blindly unmix hyperspectral data. The underlying mixing model is linear, meaning that each pixel is a linear mixture of the endmembers signatures weighted by the correspondent abundance fractions. The proposed method, as DECA, is tailored to highly mixed mixtures in which the geometric based approaches fail to identify the simplex of minimum volume enclosing the observed spectral vectors. We resort then to a statitistical framework, where the abundance fractions are modeled as mixtures of Dirichlet densities, thus enforcing the constraints on abundance fractions imposed by the acquisition process, namely non-negativity and constant sum. With respect to DECA, we introduce two improvements: 1) the number of Dirichlet modes are inferred based on the minimum description length (MDL) principle; 2) The generalized expectation maximization (GEM) algorithm we adopt to infer the model parameters is improved by using alternating minimization and augmented Lagrangian methods to compute the mixing matrix. The effectiveness of the proposed algorithm is illustrated with simulated and read data.
Comparative Chewing Efficiency in Mammalian Herbivores

Although the relevance of particle size reduction in herbivore digestion is widely appreciated, few studies have investigated digesta particle size across species in relation to body mass or digestive strategy. We investigated faecal particle size, which reflects the size of ingesta particles after both mastication and specialized processes such as rumination. Particle size was measured by wet sieving samples from more than 700 captive individuals representing 193 mammalian species. Using phylogenetic generalized least squares, faecal particle size scaled to body mass with an exponent of 0.22 (95% confidence interval: 0.160.28). In comparisons among different digestive strategies, we found that (1) equids had smaller faecal particles than other hindgut fermenters, (2) non-ruminant foregut fermenters and hindgut fermenters had similar-sized faecal particles (not significantly different), and (3) ruminants had finer faecal particles than non-ruminants. These results confirm that the relationship between chewing efficiency and body mass is modified by morphological adaptations in dental design and physiological adaptations to chewing, such as rumination. This allometric relationship should be considered when investigating the effect of body size on digestive physiology, and digestion studies should include a measure of faecal particle size.
SAVA at MediaEval 2015: Search and Anchoring in Video Archives

The Search and Anchoring in Video Archives (SAVA) task at MediaEval 2015 consists of two sub-tasks: (i) search for multimedia content within a video archive using multimodal queries referring to information contained in the audio and visual streams/content, and (ii) automatic selection of video segments within a list of videos that can be used as anchors for further hyperlinking within the archive. The task used a collection of roughly 2700 hours of the BBC broadcast TV material for the former sub-task, and about 70 les taken from this collection for the latter sub-task. The search sub-task is based on an ad-hoc retrieval scenario, and is evaluated using a pooling procedure across participants submissions with crowdsourcing relevance assessment using Amazon Mechanical Turk (MTurk). The evaluation used metrics that are variations of MAP adjusted for this task. For the anchor selection sub-task overlapping regions of interest across participants submissions were assessed using MTurk workers, and mean reciprocal rank (MRR), precision and recall were calculated for evaluation.
Advanced Radiology Utilization in a Tertiary Care Emergency Department from 2001 to 2010

Objective To evaluate the utilization trends of advanced radiology, i.e. computed tomography (CT) and magnetic resonance imaging (MRI), examination in an emergency department (ED) of an academic medical center from 2001 to 2010. Patients and Methods We assessed the overall CT and MRI utilization, and the ED patient encounters. Each examination was evaluated according to the patient’s age and anatomically relevant regions. Results During the study period, 737,760 patient visited the ED, and 156,287 CT and 35,018 MRI examinations were performed. The number of annual ED patients increased from 63,770 in 2001 to 94,609 in 2010 (P = 0.018). The rate of CT utilization increased from 105.5 per 1000 patient visits in 2001 to 289.2 in 2010 (P<0.001), and the rate of MRI utilization increased from 8.1 per 1000 patient visits in 2001 to 74.6 in 2010 (P<0.001). In all of the patient age groups, the overall CT and MRI utilization increased. The greater the patient age, the more likely the use of advanced radiology [CT: 87.1 per 1000 patients in age <20 vs. 293.9 per 1000 in age>60 (P<0.001); MRI: 5.1 per 1000 patients in age <20 vs. 108.7 per 1000 in age>60 (P<0.001)]. Abdomen-pelvis (40.2%) and the head (35.7%) comprised the majority of CT scans, while the head (86.4%) comprised the majority of MRI examinations. The rates of advanced radiology use increased across all anatomical regions, with the highest increase being in chest CT (5.9 per 1000 to 49.2) and head MRI (7.2 per 1000 to 61.9). Conclusion We report a three-fold and nine-fold increase in the use of CT and MRI, respectively, during the study period. Additional studies will be required to understand the causes of this change and to determine the effect of advanced radiology utilization on the patient outcome.
Early placentation and local immune regulation

It was once thought that processes of conceptus implantation and placentation vary among mammalian species. However, physiological and biochemical processes including gene expression show more similarities than differences. In fact, recent progress has identified that in addition to the hormones, cytokines, proteases and cell adhesion molecules classically characterized, epithelial-mesenchymal transition (EMT), epigenetic regulation and the expression of endogenous retroviruses (ERV) are all required for the progression of conceptus implantation to placentation. Thus, continued research into EMT, epigenetic regulation, the expression of ERVs and immunoregulatory systems will aid in enhancing understanding of their impact on reproductive physiology in humans and domestic animals. findings suggest that changes in the degree of DNA methylation in the upstream sequences of the IFNT gene could be one of the major mechanisms
Reinforcement selection acting on the European house mouse hybrid zone

Behavioural isolation may lead to complete speciation when partial postzygotic isolation acts in the presence of divergent‐specific mate‐recognition systems. These conditions exist where Mus musculus musculus and M. m. domesticus come into contact and hybridize. We studied two mate‐recognition signal systems, based on urinary and salivary proteins, across a Central European portion of the mouse hybrid zone. Introgression of the genomic regions responsible for these signals: the major urinary proteins (MUPs) and androgen binding proteins (ABPs), respectively, was compared to introgression at loci assumed to be nearly neutral and those under selection against hybridization. The preference of individuals taken from across the zone regarding these signals was measured in Y mazes, and we develop a model for the analysis of the transition of such traits under reinforcement selection. The strongest assortative preferences were found in males for urine and females for ABP. Clinal analyses confirm nearly neutral introgression of an Abp locus and two loci closely linked to the Abp gene cluster, whereas two markers flanking the Mup gene region reveal unexpected introgression. Geographic change in the preference traits matches our reinforcement selection model significantly better than standard cline models. Our study confirms that behavioural barriers are important components of reproductive isolation between the house mouse subspecies.
DEFINING SUPPLY CHAIN MANAGEMENT

A management construct cannot be used effectively by practitioners and researchers if a common agreement on its definition is lacking. Such is the case with the term “supply chain management”—so many definitions are used that there is little consensus on what it means. Thus, the purpose of this paper is to examine the existing research in an effort to understand the concept of “supply chain management. ” Various definitions of SCM and “supply chain” are reviewed, categorized, and synthesized. Definitions of supporting constructs of SCM and a framework are then offered to establish a consistent means to conceptualize SCM. Antecedents and consequences of SCM are identified, and the boundaries of SCM in terms of business functions and organizations are proposed. A conceptual model and unified definition of SCM are then presented that indicate the nature, antecedents, and consequences of the phenomena.
Analyzing Lateral Root Development: How to Move Forward

Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Therefore, understanding the development and architecture of roots holds potential for the manipulation of root traits to improve the productivity and sustainability of agricultural systems and to better understand and manage natural ecosystems. While lateral root development is a traceable process along the primary root and different stages can be found along this longitudinal axis of time and development, root system architecture is complex and difficult to quantify. Here, we comment on assays to describe lateral root phenotypes and propose ways to move forward regarding the description of root system architecture, also considering crops and the environment.
Increased elastin-degrading activity and neointimal formation in porcine aortic organ culture. Reduction of both features with a serine proteinase inhibitor.

We investigated the association between tissue elastolytic activity and the development of neointimal formation using a previously described porcine aortic organ culture. Neointimal formation is associated with the presence of intact endothelium (nondenuded cultures) but is markedly reduced if endothelial cells are removed (denuded cultures). In nondenuded organ cultures, elastolytic activity assessed by using [3H]elastin increased sixfold at day 3 after initiation of the culture (P < .01), a time earlier than the previously published increase in intimal smooth muscle cells (ISMCs). Elastolytic activity did not increase from day 3 to day 7 despite doubling of ISMCs but did double by day 14 (P < .01) and remained elevated to day 28, correlating with increases in ISMCs. In denuded organ cultures, elastolytic activity was much lower than in nondenuded organ cultures at day 3 (P < .05) but increased fivefold in the presence of nondenuded organ culture conditioned medium (P < .01). Addition of alpha 1-proteinase inhibitor for 14 days caused a 60% decrease in elastolytic activity in nondenuded organ cultures and a 27% reduction in ISMCs compared with untreated controls (P < .05 for both). The elastolytic activity, resolved as lytic bands on an elastin substrate gel, reflected candidate enzymes, one at 76 kD and perhaps a doublet at 43 and 50 kD. Our study suggests that endothelial cells release a soluble agent that enhances elastin-degrading activity in the aorta and may at least partially account for the initiation of neointimal formation.
Male psychological adaptation to unsuccessful medically assisted reproduction treatments: a systematic review.

BACKGROUND Similarly to women, men suffer from engaging in fertility treatments, both physically and psychologically. Although there is a vast body of evidence on the emotional adjustment of women to infertility, there are no systematic reviews focusing on men's psychological adaptation to infertility and related treatments. OBJECTIVE AND RATIONALE The main research questions addressed in this review were 'Does male psychological adaptation to unsuccessful medically assisted reproduction (MAR) treatment vary over time? ' and 'Which psychosocial variables act as protective or risk factors for psychological maladaptation? ' SEARCH METHODS A literature search was conducted from inception to September 2015 on five databases using combinations of MeSH terms and keywords. Eligible studies had to present quantitative prospective designs and samples including men who did not achieve pregnancy or parenthood at follow-up. A narrative synthesis approach was used to conduct the review. OUTCOMES Twelve studies from three continents were eligible from 2534 records identified in the search. The results revealed that psychological symptoms of maladjustment significantly increased in men 1 year after the first fertility evaluation. No significant differences were found two or more years after the initial consultation. Evidence was found for anxiety, depression, active-avoidance coping, catastrophizing, difficulties in partner communication and the use of avoidance or religious coping from the wife as risk factors for psychological maladjustment. Protective factors were related to the use of coping strategies that involve seeking information and attribution of a positive meaning to infertility, having the support of others and of one's spouse, and engaging in open communication about the infertility problem. WIDER IMPLICATIONS Our findings recommend an active involvement of men during the treatment process by health care professionals, and the inclusion of coping skills training and couple communication enhancement interventions in counselling. Further prospective large studies with high-quality design and power are warranted.
Hyper-parameter Learning for Sparse Structured Probabilistic Models

In this paper, we consider the estimation of hyperparameters for regularization terms commonly used for obtaining structured sparse parameters in signal estimation problems, such as signal denoising. By considering the convex regularization terms as negative log-densities, we propose approximate maximum likelihood estimation for estimating parameters for continuous log-supermodular distributions, which is a key property that many sparse priors have. We then show how "perturb-and-MAP" ideas based on the Gumbel distribution and efficient discretization can be used to approximate the log-partition function for these models, which is a crucial step for approximate maximum likelihood estimation. We illustrate our estimation procedure on a set of experiments with flow-based priors and signal denoising.
Hybrid Facial Model Fitting using Active Appearance Models and Contour-Based Facial Feature Location

Model-based coding techniques require a very accurate initial fit of a facial model to an image sequence in order to achieve realistic results, particularly around the eyes and mouth. This paper presents a facial model-fitting technique which uses a combination of texture analysis using an active appearance model and feature position location to give accurate initial fits. Results, based on the XM2VTS database, show this hybrid technique superior to using active appearance models alone especially in the ability to locate the eyes and mouth.
Nonperturbative Kinetic Description of Electron-Hole Excitations in Graphene in a Time Dependent Electric Field of Arbitrary Polarization

On the basis of the well-known kinetic description of e − e + vacuum pair creation in strong electromagnetic fields in D = 3 + 1 QED we construct a nonperturbative kinetic approach to electron-hole excitations in graphene under the action of strong, time-dependent electric fields. We start from the simplest model of low-energy excitations around the Dirac points in the Brillouin zone. The corresponding kinetic equations are analyzed by nonperturbative analytical and numerical methods that allow to avoid difficulties characteristic for the perturbation theory. We consider different models for external fields acting in both, one and two dimensions. In the latter case we discuss the nonlinear interaction of the orthogonal currents in graphene which plays the role of an active nonlinear medium. In particular, this allows to govern the current in one direction by means of the electric field acting in the orthogonal direction. Investigating the polarization current we detected the existence of high frequency damped oscillations in a constant external electric field. When the electric field is abruptly turned off residual inertial oscillations of the polarization current are obtained. Further nonlinear effects are discussed.
Improved Metrical Alignment of Midi Performance Based on a Repetition-aware Online-adapted Grammar

This paper presents an improvement on an existing grammar-based method for metrical structure detection and alignment, a task which involves aligning a repeated tree structure with an input stream of musical notes. The previous method achieves state-of-the-art results, but performs poorly when it lacks training data. Data annotated as it requires is not widely available, making this drawback of the method significant. We present a novel online learning technique to improve the grammar’s performance on unseen rhythmic patterns using a dynamically learned piece-specific grammar. The piece-specific grammar can measure the musical well-formedness of the underlying alignment without requiring any training data. It instead relies on musical repetition and self-similarity, enabling the model to recognize repeated rhythmic patterns, even when a similar pattern was never seen in the training data. Using it, we see improved performance on a corpus containing only Bach compositions, as well as a second corpus containing works from a variety of composers, indicating that the online-learned grammar helps the model generalize to unseen rhythms and styles.
Functional Impact and Health Utility of Anxiety Disorders in Primary Care Outpatients

Objective:The objective of this study was to examine the relative impact of anxiety disorders and major depression on functional status and health-related quality of life of primary care outpatients. Method:Four hundred eighty adult outpatients at an index visit to their primary care provider were classified by structured diagnostic interview as having anxiety disorders (panic disorder with or without agoraphobia, social phobia, and posttraumatic stress disorder; generalized anxiety disorder was also assessed in a subset) with or without major depression. Functional status, sick days from work, and health-related quality of life (including a preference-based measure) were assessed using standardized measures adjusting for the impact of comorbid medical illnesses. Relative impact of the various anxiety disorders and major depression on these indices was evaluated. Results:In multivariate regression analyses simultaneously adjusting for age, sex, number of chronic medical conditions, education, and/or poverty status, each of major depression, panic disorder, posttraumatic stress disorder, and social phobia contributed independently and relatively equally to the prediction of disability and functional outcomes. Generalized anxiety disorder had relatively little impact on these indices when the effects of comorbid major depression were considered. Overall, anxiety disorders were associated with substantial decrements in preference-based health states. Conclusions:These observations demonstrate that the presence of each of 3 common anxiety disorders (ie, panic disorder, posttraumatic stress disorder, and social phobia)—over and above the impact of chronic physical illness, major depression, and other socioeconomic factors—contributes in an approximately additive fashion to the prediction of poor functioning, reduced health-related quality of life, and more sick days from work. Greater awareness of the deleterious impact of anxiety disorders in primary care is warranted.
Applicability of the ACOSOG Z 0011 Criteria in Women with High-Risk Node-Positive Breast Cancer Undergoing Breast Conserving Surgery

Background. The relevance of the American College of Surgeons Oncology Group (ACOSOG) Z0011 trial in patients with high-risk breast cancer has been questioned. We hypothesize that Z0011 applies to women with HER2positive disease (HER2? ), triple-negative breast cancer (TNBC), and/or age \50 years at diagnosis (YA). Methods. Women with node-positive HER2? , TNBC, or YA were identified from a prospectively maintained database. Patients were grouped based on Z0011 trial eligibility criteria into those meeting criteria (eligible) and those who did not (ineligible). Patient and tumor characteristics were compared; survival of those meeting Z0011 criteria was determined. Results. We identified 186 node-positive women undergoing lumpectomy/radiation for high-risk breast cancer: 57 of 186 (31 %) HER2? , 55 of 186 (30 %) TNBC, 74 of 186 (40 %) YA. Overall, 125 of 186 (67 %) met Z0011 criteria. HER2-positivity was associated with the lowest rate of ineligibility compared with TNBC and YA (16 vs. 53 and 31 %, respectively, p \ 0.01). Larger tumor size, high grade, extranodal extension, and high Ki67 were associated with Z0011 ineligibility. Among those who were eligible, 105 of 125 (84 %) had ALND and 48 of 125 (38 %) had involvement of nonsentinel nodes (NSLN); median number of NSLNs involved was one (range 1–3). With median follow-up of 5.5 years, there was no difference in survival between those who had ALND and those who did not. After patients with clinically palpable nodes were excluded, 125 of 149 (84 %) met criteria. Conclusions. The Z0011 trial eligibility requirements apply to a significant proportion of patients with HER2? , TNBC, and YA. ALND can be avoided in 67 % nodepositive cases and in 84 % of those with clinically negative nodes. The American College of Surgeons Oncology Group (ACOSOG) Z0011 trial demonstrated that sentinel lymph node biopsy (SNB) without completion axillary lymph node dissection (ALND) in patients with clinical T1-2N0 breast cancer resulted in excellent local control without compromising survival. Although the results of the trial triggered changes in the standard paradigm in the surgical management of axillary lymph nodes in breast cancer, there remain concerns that the large majority of the Z0011 study population included older patients with estrogenreceptor positive (ER? ), less aggressive tumors and that the higher risk populations were underrepresented in the trial. Therefore, there is controversy whether ALND should be performed in these populations even if the eligibility criteria for the Z0011 trial have been met. The purpose of this study was to determine how often the ACOSOG Z0011 eligibility requirements apply in patients with higher risk tumors, such as triple-negative (TNBC) and HER2-positive (HER2? ) breast cancer, and/or young age at diagnosis (YA) and to examine the reasons for inapplicability of the trial in these subgroups of patients.