Miracle-dz/UniFAR-FTUs huggingface dataset:
OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data

A recent paper identified an artifact in multiple single-cell RNA-seq (scRNA-seq) data sets generated by the Fluidigm C1 platform. Specifically, Leng* et al. showed significantly increased gene expression in cells captured from sites with small or large plate output IDs. We refer to this artifact as an ordering effect (OE). Including OE genes in downstream analyses could lead to biased results. To address this problem, we developed a statistical method and software called OEFinder to identify a sorted list of OE genes. OEFinder is available as an R package along with user-friendly graphical interface implementations that allows users to check for potential artifacts in scRNA-seq data generated by the Fluidigm C1 platform. Availability and Implementation OEFinder is freely available at https://github.com/lengning/OEFinder Contact rstewart@morgridge.org
A Comprehensive Framework for Spectrum Sensing in Non-Linear and Generalized Fading Conditions

We derive a comprehensive analytical framework for the ED over generalized, extreme, and non-linear fading conditions which addresses the topic completely. This is carried out for both conventional and diversity receptions and it is based on the area under the ROC curve (AUC), which is an efficient performance measure that is widely used in physical sciences and engineering. This differentiates the considered methodology from the aforementioned routine approaches and additionally provides generic results on the arbitrary derivatives of the MGF of useful generalized processes. The asymptotic behavior of the derived expressions is also analyzed providing direct and concrete insights on the role and effect of the involved parameters on the ED performance. The offered analytic results are subsequently employed in quantifying the performance of ED over various types of fading conditions, which exhibits that ED performance is significantly degraded by even slight variations of the severity of fading. To this end, it is shown that the detrimental effects of fading can be effectively mitigated with the aid of square-law combining and switch-and-stay combining methods, as a low number of diversity branches can ensure sufficient and holistic performance improvement even in severe fading conditions.
Progress in the understanding and management of pulmonary arterial hypertension

In 1981 the “Patient Registry for the Characterization of Primary Pulmonary Hypertension” was set up, supported by the National Heart, Lung and Blood Institute, and recruited 194 patients across 32 clinical centres over 4 years in the United States1,2. The estimated median survival of these incident cases of primary pulmonary hypertension (which approximates to what we would now term idiopathic pulmonary arterial hypertension, IPAH) was 2.8 years, with a 68% survival rate at 1 year, 48% at 3 years and 35% at 5 years1. Since 2000 a number of national registries have been set-up across the world to study the developing epidemiology of pulmonary arterial hypertension (PAH)3. The largest of these is the REVEAL (Registry to Evaluate Early and Long-term Pulmonary Arterial Hypertension Disease Management) Registry in the United States4. Between 2006 and 2009, 2635 prevalent and incident cases were included in survival analysis across 55 centres. For IPAH, there was a 91% survival rate at 1 year, 74% at 3 years and 65% at 5 years4. The Spanish registry also recruited 866 prevalent and incident cases of IPAH between 2007 and 2008 and calculated 1-, 3- and 5-year survival rates of 87%, 75% and 65% respectively5. In the French registry, which also analysed prevalent and incident cases, for a sub-population of 190 patients with IPAH, hereditary PAH (HPAH) and anorexigen-associated PAH cases (which all have similar baseline characteristics and outcomes) between 2002 and 2003, a 1-year survival rate of 83% and 3-year of 58% was calculated6,7. In the UK there was a focus on incident cases, and 482 patients with IPAH, HPAH, and anorexigen-associated PAH were included between 2001 and 2009 and had 1-, 3- and 5-year survival rates of 93%, 73% and 61% respectively8. Although there is debate about the inclusion of both prevalent and incident cases in these registries (owing to survivor bias), there is broad agreement over current survival rates across these registries. Measurable progress has been made in the management of pulmonary arterial hypertension over the last 33 years – now, at 5 years, a larger proportion of people are living with the disease, rather than dying from it. In this review article we take a historical approach to reflect on the journey that has brought us to where we are today, focussing on the key milestones in the management of pulmonary arterial hypertension, signposted by the World Health Organisation (WHO) “World Symposia in Pulmonary Hypertension”. It will become apparent that this mirrors the developments and movements in medicine over the last 150 years: from pathology to physiology, from physiology to pharmacology, from pharmacology to cell biology, from cell biology to genetics9.
Scarfy: Augmenting Human Fashion Behaviour with Self-Actuated Clothes

Our clothes are objects we interact with constantly. They represent our attitude and the circumstances we live in. In the following we will present an example of how this information can be used. Scarfy is a system based on a scarf which augments the natural interaction between a person and her clothes. Scarfy is able to detect the way it is tied and it can deliver information by shape-change and vibration. In this paper we explore the technical and fabrication approaches of technologically extended clothes and their input and output generation and discuss future applications.
Traffic grooming in mesh WDM optical networks - performance analysis

The paper develops a theoretical performance analysis model for the online single-hop traffic grooming algorithm in the mesh topology wavelength division multiplexing (WDM) optical network. This is done by developing a link blocking model for traffic grooming based on the continuous time Markov chain and queueing theory, and by extending the Erlang fixed-point approximation for traffic grooming analysis. The results obtained from the analytic model are shown to match well with the numerical results obtained from simulations.
Comparative Analysis of the Hematopoietic Progenitor Cells from Placenta, Cord Blood, and Fetal Liver, Based on Their Immunophenotype

We have investigated the characteristics of human hematopoietic progenitor cells (HPCs) with the CD34+CD45lowSSClow phenotype from full-term placental tissue (FTPT) as compared to cord blood (CB) and fetal liver (FL) cells. We demonstrated the presence of cell subpopulations at various stages of the differentiation with such immunophenotypes as CD34+/lowCD45low/−, CD34++CD45low/−, CD34+++CD45low/−, CD34+/lowCD45hi, and CD34++CD45hi in both first trimester placental tissue (FiTPT) and FTPT which implies their higher phenotypic heterogeneity compared to CB. HPCs of the FTPT origin expressed the CD90 antigen at a higher level compared to its expression by the CB HPCs and the CD133 antigen expression being at the same level in both cases. The HPCs compartment of FTPT versus CB contained higher number of myeloid and erythroid committed cells but lower number of myeloid and lymphoid ones compared to FL HPCs. HPCs of the FTPT and CB origin possess similar potentials for the multilineage differentiation in vitro and similar ratios of myeloid and erythroid progenitors among the committed cells. This observation suggests that the active hematopoiesis occurs in the FTPT. We obtained viable HPCs from cryopreserved placental tissue fragments allowing us to develop procedures for banking and testing of placenta-derived HPCs for clinical use.
Adaptação e validação do Drinking Motives Questionnaire-Revised – (DMQ-R)

31 O presente estudo 34 ESTUDO I: ANALISE EXPLORATORIA DA ESTRUTURA DO DMQ-R 36 Objetivos 36 METODO 36 Traducao dos itens para o portugues 36 Participantes 36 Procedimentos 37 Instrumento 37 Analise dos dados 37 RESULTADOS 38 DISCUSSAO 41 ESTUDO II: ANALISE CONFIRMATORIA DA ESTRUTURA DO DMQ-R 43 Objetivos 43 METODO 43 Participantes 43 Instrumentos 43 Intensidade de uso de alcool 43 Problemas relacionados ao uso de bebidas alcoolicas. 43 Preferencia por tipos de bebidas. 44 Contextos e situacoes de uso. 44 Motivos para uso de bebidas alcoolicas. 44 Analise dos dados 44 RESULTADOS 46 Teste confirmatorio da estrutura do DMQ-R 46 Motivos como preditores de uso de alcool e variaveis relacionadas 49 DISCUSSAO 52 CONSIDERACOES FINAIS 54 CAPITULO III 56 DISCUSSAO GERAL 56 Consideracoes finais 57 REFERENCIAS 59 Anexo A: Termo de consentimento utilizado com os participantes dos Estudos I e II . 66 Anexo B: Folha de aprovacao do projeto de pesquisa pelo Comite de Etica em Pesquisa do Instituto de Psicologia da UFRGS 67 Anexo C: versao de aplicacao do DMQ-R 68 Anexo D: itens utilizados do AUDIT para avaliar frequencia de consumo, quantidade e frequencia de episodios de uso pesado 69 Anexo E: itens empregados para avaliar problemas relacionados ao uso do alcool 70 Anexo F: itens utilizados para avaliar preferencia por de tipos de bebidas 71 Anexo G: itens utilizados para avaliar contextos e situacoes de uso de bebidas alcoolicas 72 Anexo H: Pareceres dos professores da banca de defesa da dissertacao 73 LISTA DE TABELAS E FIGURAS CAPITULO I Figura 1. Estudos na area nos ultimos 20 anos 11 CAPITULO I Tabela 1. Instrumentos que avaliam motivos para usar alcool e seus itens e dimensoes 21 CAPITULO II Figura 1. Grafico da curva de declividade (Screeplot) 38 Tabela 1. Resultados da analise de componentes principais 39 Tabela 2. Medias, desvios-padrao, fidedignidade e correlacoes entre as escalas do DMQR 40 Tabela 3. Estruturas do DMQ-R eleitas para teste confirmatorio 45 Tabela 4. Resultados das analises fatoriais confirmatorias do DMQ-R 46 Figura 2. Modelo confirmatorio de quatro fatores e 19 itens 48 Tabela 5. Medias, desvios-padrao, fidedignidade, correlacoes item-restante e correlacoes entre subescalas 49 Tabela 6. Motivos para uso de alcool como preditores de variaveis relacionadas ao uso 50
Pinworm Infestation Mimicking Crohns' Disease

We here report a case of a young man who presented to his general practitioner with diarrhea. Inflammatory bowel disease was suspected and a colonoscopy showed aphthous lesions suggestive of Crohns' disease but biopsies revealed eggs of Enterobius vermicularis. When treated for this parasite, his symptoms were alleviated and a followup colonoscopy revealed a normal colon and distal ileum. Enterobius vermicularis is the most common parasite worldwide and has been attributed with many different presentations and pathologies. It is therefore necessary to maintain vigilance, even in high-income countries, in order to diagnose patients with one of the many atypical presentations of pinworms.
Converting hybrid wire-frames to B-rep models

Solid reconstruction from engineering drawings is one of the efficient technologies to product solid models. The B-rep oriented approach provides a practical way for reconstructing a wide range of objects. However, its major limitation is the computational complexity involved in the search for all valid faces from the intermediate wire-frame, especially for objects with complicated face topologies. In previous work, we presented a hint-based algorithm to recognize quadric surfaces from orthographic views and generate a hybrid wire-frame as the intermediate model of our B-rep oriented method. As a key stage in the process of solid reconstructing, we propose an algorithm to convert the hybrid wire-frame to the final B-rep model by extracting all the rest faces of planes based on graph theory. The entities lying on the same planar surface are first collected in a plane graph. After all the cycles are traced in a simplified edge-adjacency matrix of the graph, the face loops of the plane are formed by testing loop containment and assigning loop directions. Finally, the B-rep model is constructed by sewing all the plane faces based on the Möbius rule. The method can efficiently construct 2-manifold objects with a variety of face topologies, which is illustrated by results of implementation.
Efficiency of Leptotrombidium Chiggers (Acari: Trombiculidae) at Transmitting Orientia tsutsugamushi to Laboratory Mice

Abstract Thirteen different laboratory colonies of Leptotrombidium chiggers [L. chiangraiensis Tanskul & Linthicum, L. deliense Walch and L. imphalum (Vercammen-Grandjean & Langston)] were evaluated for their ability to transmit Orientia tsutsugamushi (Hyashi) to mice. Of 4,372 transmission attempts using individual chiggers from all 13 colonies, 75% (n = 3,275) successfully infected mice. Transmission rates for the individual chigger colonies ranged from 7 to 80%. Increasing the number of chiggers that fed on a given mouse generally increased transmission rates. Transmission of O. tsutsugamushi to mice by different generations (F1–F11) of certain chigger colonies was stable; however, transmission rates varied greatly in other colonies. Transmission rates (both vertical and horizontal) of several L. chiangraiensis colonies and the L. deliense colony were the highest, suggesting that these colonies may be useful for the development of a chigger-challenge model that can be used to evaluate the efficacy of candidate scrub typhus vaccines or therapeutic agents in laboratory mice.
Document Visualization using Topic Clouds

Traditionally a document is visualized by a word cloud. Recently, distributed representation methods for documents have been developed, which map a document to a set of topic embeddings. Visualizing such a representation is useful to present the semantics of a document in higher granularity; it is also challenging, as there are multiple topics, each containing multiple words. We propose to visualize a set of topics using Topic Cloud, which is a pie chart consisting of topic slices, where each slice contains important words in this topic. To make important topics/words visually prominent, the sizes of topic slices and word fonts are proportional to their importance in the document. A topic cloud can help the user quickly evaluate the quality of derived document representations. For NLP practitioners, It can be used to qualitatively compare the topic quality of different document representation algorithms, or to inspect how model parameters impact the derived representations.
Consecutive tracking and segmentation using adaptive mean-shift and graph cut

We present an effective tracking and segmentation algorithm in which tracking and segmentation are carried out consecutively. Object tracking in video sequences is difficult since the appearance of an object tends to change. An adaptive tracker that employs color and shape features is adopted to conquer this problem. The target is modeled based on discriminative features selected using foreground/background contrast analysis. Tracking provides overall motion of the target for the segmentation module. Based on the overall motion, we segment object out using the effective graph cut algorithm. Markov Random Fields, which are the foundation of the graph cut algorithm, provide poor prior for specific shape. It is necessary to embed shape priors into the graph cut algorithm to achieve reasonable segmentation results. The object shape obtained by segmentation is used as shape priors to improve segmentation in next frame. We have verified the proposed approach and got positive results on challenging video sequences.
Cellular automaton model simulating spatiotemporal patterns, phase transitions and evolution concavity in traffic flow

This paper firstly show that a recent model (Tian et al., Transpn. Res. B 71, 138-157, 2015) is not able to well replicate the evolution concavity in traffic flow, i.e. the standard deviation of vehicles increases in a concave/linear way along the platoon. Then we propose an improved model by introducing the safe speed, the logistic function of the randomization probability, and small randomization deceleration for low-speed vehicles into the model. Simulations show that the improved model can well reproduce the metastable states, the spatiotemporal patterns, the phase transition behaviors of traffic flow, and the evolution concavity of traffic oscillations. Validating results show that the empirical time series of traffic speed obtained from Floating Car Data can be well simulated as well.
Choosing the Level of Stream Adaptation in TCP-Friendly Congestion Controlled Video Streaming Servers

In this paper we investigate stream adaptation policies for video streaming servers which use smooth TCP-friendly congestion controls to compute the transmission rate. TCP-friendly congestion controls compute, by specific means, the rate at which the streaming server can send video data (i.e. available bandwidth in the network). Of course, this rate must be supported at application level by an appropriate stream adaptation mechanism. We seek an optimal adaptation policy which maximizes the perceived quality at the client side and tries to avoid an empty prefetch buffer at the client side, in the given TCP-friendly conditions. We formulate our problem in an optimization framework and then devise a gradient ascend algorithm to solve it. The solution is an adaptation policy that can be used to support TCP-friendly rate control at codec (application) level.
Adhesion-preventing properties of 4% icodextrin and canola oil: a comparative experimental study

OBJECTIVE: Postsurgical abdominal adhesions are common, serious postoperative complications. The present study compared the usefulness of 4% icodextrin and canola oil in preventing postoperative peritoneal adhesions. METHODS: Twenty-four Wistar albino rats were divided into three groups. Following a laparotomy, a serosal abrasion was made by brushing the cecum, and 3 mL of 0.9% NaCl, 4% icodextrin, or 3 mL of canola oil were intraperitoneally administered for the control, icodextrin, and canola oil groups, respectively. The abdomen was then closed. All of the rats were sacrificed at day 10. Macroscopic, histopathological, and biochemical evaluations were performed. The results were statistically analyzed using Kruskal–Wallis and ANOVA tests. RESULTS: Macroscopic analyses revealed that both canola oil and 4% icodextrin reduced adhesion formation, but the difference was not statistically significant (p = 0.17). The histopathological examinations revealed no significant differences in terms of giant cell, lymphocyte/plasmocyte, neutrophil, ICAM1, or PECAM1 scores. However, both canola oil and 4% icodextrin significantly reduced fibrosis (p = 0.025). In the canola oil group, the histiocytic reactions were significantly increased (p = 0.001), and the hydroxyproline levels were significantly lower than those in the other groups (p = 0.034). CONCLUSIONS: In the present study, canola oil was determined to be superior to 4% icodextrin in lowering hydroxyproline levels and increasing histiocytic reactions. Considering these results, we believe that canola oil is a promising agent for preventing adhesion formation.
Toxin variability during the cell cycle of the dinoflagellate Alexandrium fundyense

Cultures of the toxic dinoflagellate Alexandrium fundyense Balech were subjected to conditions that induced two synchronized divisions over a period of 48 h. Before, during, and after this interval, toxin content, toxin composition, and several other physiological parameters were monitored every 2 h for 94 h. Toxin production was discontinuous, induced by light, and always occurred during a defined time frame within the G1 phase of the cell cycle. Specific toxin production rates were positive for a period of ∼8–10 h in early G1 and dropped to zero for the remainder of the interphase and mitosis. Analysis of toxin composition showed that cellular concentrations of all the saxitoxin derivatives followed a similar pattern of increase, stabilization, and decrease throughout one generation time. A putative sequence of interconversions between the derivatives could be established, with C2 as the first compound to appear. Division of a subset of the population during the first 24 h of the experiment and the ensuing total synchrony of the culture suggest the existence of two transition points in the cell cycle of this dinoflagellate. The first transition point, at the beginning of G1, is light‐dependent and holds the cells in a G0‐like period. The second block point at the end of G1 is size‐dependent and arrests the cells in G1. We propose a model of the cell cycle of A. fundyense in which progression through the cell cycle can be arrested at two different transition points located in G1 and toxin production is induced by light during G1. The restriction off toxin production to a relatively short segment of the cell cycle provides a tool for comparing cells that are and are not synthesizing toxin.
An Examination of the HBB Gene in Various African Populations

Malarial resistance serves as a prime example of how infectious disease and parasite loads have affected human evolutionary biology. Claiming over 1 million deaths worldwide every year, malaria's wide and severe effects on the human condition are undeniably strong. However, studies on populations existing in malaria endemic areas have revealed numerous biological adaptations that confer resistance against the disease. Major forms of genetic resistance to malaria are seen through variants involved in sickle cell disease, Duffy blood antigens, glycophorins, blood type groupings, and glucose-6-dehydrogenase deficiency. Of these the best studied are the genetic variants in the HBB gene, which is responsible for the construction of hemoglobin in erythrocytes. Variants of the HBB gene include HbS, HbC, HbE, and variants involved in beta-thalassemias, which are present at varying frequencies in different areas of the world in response to the pressure of malarial disease. African populations in particular are of great interest due to their greater genetic diversity and the high rates of malarial diseases reported in African countries. As such, sequencing the genotypes of multiple African populations would give a greater understanding to the frequencies of the two major HBB variants present in Africa, HbS and HbC. Furthermore, given the strong selective pressure an infectious disease such as malaria would place on populations in malaria-endemic regions, it is possible that multiple variants may have evolved in these populations in attempt to combat the disease. By sequencing the HBB gene and its corresponding upstream region in 260 individuals from 15 different African populations, the frequencies of the HbS and HbC SNPs have been determined. Disciplines Anthropology This thesis or dissertation is available at ScholarlyCommons: http://repository.upenn. edu/anthro_seniortheses/135 An Examination of the HBB Gene in Various African Populations Charles Washington III University of Pennsylvania Department of Anthropology