Miracle-dz/UniFAR-FTUs huggingface dataset:
Machine Learning for Survival Analysis

Survival analysis is a subfield of statistics where the goal is to analyze and model data where the outcome is the time until an event of interest occurs. One of the main challenges in this context is the presence of instances whose event outcomes become unobservable after a certain time point or when some instances do not experience any event during the monitoring period. This so-called censoring can be handled most effectively using survival analysis techniques. Traditionally, statistical approaches have been widely developed in the literature to overcome the issue of censoring. In addition, many machine learning algorithms have been adapted to deal with such censored data and tackle other challenging problems that arise in real-world data. In this survey, we provide a comprehensive and structured review of the statistical methods typically used and the machine learning techniques developed for survival analysis, along with a detailed taxonomy of the existing methods. We also discuss several topics that are closely related to survival analysis and describe several successful applications in a variety of real-world application domains. We hope that this article will give readers a more comprehensive understanding of recent advances in survival analysis and offer some guidelines for applying these approaches to solve new problems arising in applications involving censored data.
Correction: ICAP-1 monoubiquitylation coordinates matrix density and rigidity sensing for cell migration through ROCK2–MRCKα balance

Cell migration is a complex process requiring density and rigidity sensing of the microenvironment to adapt cell migratory speed through focal adhesion and actin cytoskeleton regulation. ICAP-1 (also known as ITGB1BP1), a β1 integrin partner, is essential for ensuring integrin activation cycle and focal adhesion formation. We show that ICAP-1 is monoubiquitylated bySmurf1, preventing ICAP-1binding to β1 integrin. The non-ubiquitylatable form of ICAP-1 modifies β1 integrin focal adhesion organization and interferes with fibronectin density sensing. ICAP-1 is also required for adapting cell migration in response to substrate stiffness in a β1-integrin-independent manner. ICAP-1 monoubiquitylation regulates rigidity sensing by increasing MRCKα (also known as CDC42BPA)-dependent cell contractility through myosin phosphorylation independently of substrate rigidity. We provide evidence that ICAP-1 monoubiquitylation helps in switching from ROCK2-mediated to MRCKα-mediated cell contractility. ICAP-1 monoubiquitylation serves as a molecular switch to coordinate extracellular matrix density and rigidity sensing thus acting as a crucial modulator of cell migration and mechanosensing.
Arsenic Contamination of Drinking Water and Mental Health

This paper investigates the effect of drinking arsenic contaminated water on mental health. Drinking water with an unsafe arsenic level for a prolonged period can lead to arsenicosis and associated illness. Based on rich and newly collected household survey data from Bangladesh, we construct several measures for arsenic contamination that include the actual arsenic level in the respondent’s tubewell (TW), and past institutional arsenic test results as well as their physical and mental health. To account for potential endogeneity of water source, we take advantage of the quasi-randomness of arsenic distribution and employ the pre-1999 use of TW as an instrument and structural modelling as alternatives for robustness checks. We find that suffering from an arsenicosis symptom is strongly negatively related to mental health, even more so than from other illnesses. Calculations of the costs of arsenic contamination reveal that the average individual would need to be compensated for suffering from an arsenicosis symptom by an amount of money over 10 percent of annual household income.
Modeling Grouping Cues for Auditory Scene Analysis Using a Spectral Clustering Formulation

Computational Auditory Scene Analysis (CASA) is challenging problem for which many different approaches have been proposed. These approaches can be based on statistical and signal processing methods such as Independent Component Analysis or can be based on our current knowledge about human auditory perception. Learning happens at the boundary interactions between prior knowledge and incoming data. Separating complex mixtures of sound sources such as music requires a complex interplay between prior knowledge and analysis of incoming data. Many approaches to CASA can also be broadly categorized as either model-based or grouping-based. Although it is known that our perceptual-system utilizes both of these types of processing, building such systems computationally has been challenging. As a result most existing systems either rely on prior source models or are solely based on grouping cues. In this chapter the authors argue that formulating this integration problem as clustering based on similari- ties between time-frequency atoms provides an expressive yet disciplined approach to building sound source characterization and separation systems and evaluating their performance. After describing the main components of such an architecture, the authors describe a concrete realization that is based on spectral clustering of a sinusoidal representation. They show how this approach can be used to model both traditional grouping cues such as frequency and amplitude continuity as well as other types of in- formation and prior knowledge such as onsets, harmonicity and timbre-models for specific instruments.
Lesbian, Gay, and Bisexual Identities and Youth: Psychological Perspectives

PART I: CONCEPTUAL FRAMEWORKS 1. Psychosocial Change at Puberty and Beyond: Understanding Adolescent Sexuality and Sexual Orientation 2. Biological Factors in the Development of Sexual Orientation 3. Exotic becomes Erotic: Integrating Biological and Experiential Antecedents of Sexual Orientation PART II: PSYCHOLOGICAL CHALLENGES 4. Toward a Reconceptualization of the Coming-Out Process for Adolescent Females 5. Developmental Trajectories of Gay, Lesbian, and Bisexual Youths 6. Intimacy Development, Gender, and Ethnicity among Sexual-Minority Youths PART III: ISSUES FOR INTERVENTION AND SOCIAL CHANGE 7. Avoiding HIV/AIDS and the Challenge of Growing Up Gay, Lesbian, and Bisexual 8. The Experiences of Lesbian, Gay, and Bisexual Youths in University Communities 9. The Victimization of Lesbian, Gay, and Bisexual Youths 10. Counseling Lesbian, Gay, and Bisexual Youths 11. Educational Reform and Sexual Identity: Conflicts and Challenges 12. Social Change, Sexual Diversity, and Tolerance for Bisexuality in the United States Index
Differences in neural crest sensitivity to ethanol account for the infrequency of anterior segment defects in the eye compared with craniofacial anomalies in a zebrafish model of fetal alcohol syndrome.

BACKGROUND Ethanol (ETOH) exposure during pregnancy is associated with craniofacial and neurologic abnormalities, but infrequently disrupts the anterior segment of the eye. In these studies, we used zebrafish to investigate differences in the teratogenic effect of ETOH on craniofacial, periocular, and ocular neural crest. METHODS Zebrafish eye and neural crest development was analyzed by means of live imaging, TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling) assay, immunostaining, detection of reactive oxygen species, and in situ hybridization. RESULTS Our studies demonstrated that foxd3-positive neural crest cells in the periocular mesenchyme and developing eye were less sensitive to ETOH than sox10-positive craniofacial neural crest cells that form the pharyngeal arches and jaw. ETOH increased apoptosis in the retina, but did not affect survival of periocular and ocular neural crest cells. ETOH also did not increase reactive oxygen species within the eye. In contrast, ETOH increased ventral neural crest apoptosis and reactive oxygen species production in the facial mesenchyme. In the eye and craniofacial region, sod2 showed high levels of expression in the anterior segment and in the setting of Sod2 knockdown, low levels of ETOH decreased migration of foxd3-positive neural crest cells into the developing eye. However, ETOH had minimal effect on the periocular and ocular expression of transcription factors (pitx2 and foxc1) that regulate anterior segment development. CONCLUSION Neural crest cells contributing to the anterior segment of the eye exhibit increased ability to withstand ETOH-induced oxidative stress and apoptosis. These studies explain the rarity of anterior segment dysgenesis despite the frequent craniofacial abnormalities in fetal alcohol syndrome. Birth Defects Research 109:1212-1227, 2017. © 2017 Wiley Periodicals, Inc.
The pollination niche and its role in the diversification and maintenance of the southern African flora

The flora of southern Africa has exceptional species richness and endemism, making it an ideal system for studying the patterns and processes of evolutionary diversification. Using a wealth of recent case studies, I examine the evidence for pollinator-driven diversification in this flora. Pollination systems, which represent available niches for ecological diversification, are characterized in southern Africa by a high level of ecological and evolutionary specialization on the part of plants, and, in some cases, by pollinators as well. These systems are asymmetric, with entire plant guilds commonly specialized for a particular pollinator species or functional type, resulting in obvious convergent floral evolution among guild members. Identified modes of plant lineage diversification involving adaptation to pollinators in these guilds include (i) shifts between pollination systems, (ii) divergent use of the same pollinator, (iii) coevolution, (iv) trait tracking, and (v) floral mimicry of different model species. Microevolutionary studies confirm that pollinator shifts can be precipitated when a plant species encounters a novel pollinator fauna on its range margin, and macroevolutionary studies confirm frequent pollinator shifts associated with lineage diversification. As Darwin first noted, evolutionary specialization for particular pollinators, when resulting in ecological dependency, may increase the risk of plant extinction. I thus also consider the evidence that disturbance provokes pollination failure in some southern African plants with specialized pollination systems.
Model driven development of a generic data control engine: An industrial experience: Short paper

The Model Driven Development of a generic control engine for Electronic Data Interchange (EDI) has led to the development of a line of products to handle and document models. In the long run the problem is to strike the proper balance between genericity and specificity, between the return in productivity provided by code generation and the rigidities inherent to the underlying models.
The expressivity of turn-taking: Understanding children pragmatics by hybrid classifiers

We analyze the effect of children age on pragmatic skills, i.e. on the way children manage the conversation dynamics. In particular, we focus exclusively on the turn-taking (who talks when and how much), reducing conversations as sequences of simple speech/silence periods. Employing a hybrid (generative + discriminative) classification framework, we demonstrate that such a simple signature is very informative, allowing to separate 22 “pre-School” conversations (between 3-4 years old children) and 24 “School” conversations (between 6-8 years old children) subjects, with 78% of accuracy. The framework exploits Steady Conversational Periods and Observed Influence Models as feature extractors, plus LASSO regression as feature selector and classifier. The generative nature of our method permits, as byproduct, to identify the pragmatic skills that better discriminate the two groups: no-tably, scholar children tend to have more frequent periods of sustained conversation, in a statistically significant way.
Histaminase release from human granulocytes

Histaminase (EC-1.4.3.6), one of the two catabolic enzymes for histamine, is contained in human granulocytes. Opsonized zymosan or the calcium ionophore A-23187 induce a dose-dependent release of histaminase from human granulocytes in vitro. Release is completed within 30 min, is temperature dependent, and requires divalent cations. Opsonized zymosan-induced histaminase release was maximal in the presence of both calcium and magnesium, whereas ionophore release was magnesium independent. The total cellular content of histaminase could be released by both opsonized zymosan and ionophore. In contrast, only 25% of the cellular beta glucuronidase, a lysosomal enzyme, was released after maximal stimulation with opsonized zymosan; there was minimal release of beta glucuronidase with ionophore. Zymosan- and ionophore-induced histaminase release was inhibited by agents that are presumed to interfere with cell metabolism and disrupt microtubules. Human granulocytes therefore may modulate the effect of histamine by releasing histaminase at a site of inflammation. Studies of granulocyte histaminase release in vitro may also provide a new model to explore granulocyte function and secretion.
Microvascular Obstruction and the No-Reflow Phenomenon After Percutaneous Coronary Intervention

C ase presentation A: A 50-year-old diabetic man presented to the hospital after 8 hours of continuous chest pain. Because of acute myocardial infarction of the anterior wall, he underwent direct stenting to an occlusion in the left anterior descending coronary artery. Despite revascularization, suboptimal coronary flow was achieved, and he subsequently developed heart failure. Case presentation B: A 77-year-old man underwent elective stenting of a significant stenosis in a degenerated saphenous vein coronary bypass graft. After the procedure, coronary flow in the graft was severely reduced, and he sustained a myocardial infarction in the subtended myocardial territory. The concept of “no reflow” refers to a state of myocardial tissue hypoperfusion in the presence of a patent epicardial coronary artery. The underlying cause of no reflow is microvascular obstruction, which may be produced by various mechanisms. No reflow can be classified according to the duration of the preceding myocardial ischemia (Figure 1). “Reperfusion no reflow” occurs after primary percutaneous coronary intervention (PCI) for reperfusion of an infarct artery in the setting of acute myocardial infarction (AMI) and may be asymptomatic or may present clinically with continued chest pain and ST-segment elevation. Reperfusion no reflow is preceded by ischemic cell injury, is confined to the irreversibly damaged necrotic zone, and may be exacerbated at the time of reperfusion. Reperfusion no reflow is an independent predictor of adverse clinical outcome after AMI regardless of infarct size and is associated with heart failure and increased mortality.1 Figure 1. Schematic illustrating the effect of duration of preceding myocardial ischemia on mechanism of no reflow (NR). “Interventional no reflow” follows noninfarct PCI and affects myocardium that was not subjected to prolonged ischemia before the procedure. Clinically recognized interventional no reflow that complicates PCI is typically sudden in onset, presenting as acute ischemia with chest …
Predictors of Time to Completion of Graduate Degrees.

A multiple regression procedure was utilized to predict the time taken to complete graduate degree requirements for 395 master's and 79 doctoral students at a large Canadian university. Selected demographic (e.g., sex, age, marital status, registration status, citizenship), academic (e.g., undergraduate and graduate GPA, discipline, type of program) and financial support variables (funding received from internal and external scholarships and from research, graduate and teaching assistantships) were used as independent variables. Results for master's students indicate that full-time registration, increased financial support, higher graduate GPA and enrolment in a humanities discipline significantly decrease time to completion. Conversely, a thesis requirement and Canadian citizenship are associated with significantly slower degree progress. For doctoral students, enrolment in a natural sciences discipline, Canadian citizenship, full-time registration and increased funding significantly decrease the time taken to complete the doctorate.
Genetic Regulation of Dna2 Localization During the DNA Damage Response

DNA damage response pathways are crucial for protecting genome stability in all eukaryotes. Saccharomyces cerevisiae Dna2 has both helicase and nuclease activities that are essential for Okazaki fragment maturation, and Dna2 is involved in long-range DNA end resection at double-strand breaks. Dna2 forms nuclear foci in response to DNA replication stress and to double-strand breaks. We find that Dna2-GFP focus formation occurs mainly during S phase in unperturbed cells. Dna2 colocalizes in nuclear foci with 25 DNA repair proteins that define recombination repair centers in response to phleomycin-induced DNA damage. To systematically identify genes that affect Dna2 focus formation, we crossed Dna2-GFP into 4293 nonessential gene deletion mutants and assessed Dna2-GFP nuclear focus formation after phleomycin treatment. We identified 37 gene deletions that affect Dna2-GFP focus formation, 12 with fewer foci and 25 with increased foci. Together these data comprise a useful resource for understanding Dna2 regulation in response to DNA damage.
Colorectal Cancer Stem Cells Are Enriched in Xenogeneic Tumors Following Chemotherapy

Background Patients generally die of cancer after the failure of current therapies to eliminate residual disease. A subpopulation of tumor cells, termed cancer stem cells (CSC), appears uniquely able to fuel the growth of phenotypically and histologically diverse tumors. It has been proposed, therefore, that failure to effectively treat cancer may in part be due to preferential resistance of these CSC to chemotherapeutic agents. The subpopulation of human colorectal tumor cells with an ESA+CD44+ phenotype are uniquely responsible for tumorigenesis and have the capacity to generate heterogeneous tumors in a xenograft setting (i.e. CoCSC). We hypothesized that if non-tumorigenic cells are more susceptible to chemotherapeutic agents, then residual tumors might be expected to contain a higher frequency of CoCSC. Methods and Findings Xenogeneic tumors initiated with CoCSC were allowed to reach ∼400 mm3, at which point mice were randomized and chemotherapeutic regimens involving cyclophosphamide or Irinotecan were initiated. Data from individual tumor phenotypic analysis and serial transplants performed in limiting dilution show that residual tumors are enriched for cells with the CoCSC phenotype and have increased tumorigenic cell frequency. Moreover, the inherent ability of residual CoCSC to generate tumors appears preserved. Aldehyde dehydrogenase 1 gene expression and enzymatic activity are elevated in CoCSC and using an in vitro culture system that maintains CoCSC as demonstrated by serial transplants and lentiviral marking of single cell-derived clones, we further show that ALDH1 enzymatic activity is a major mediator of resistance to cyclophosphamide: a classical chemotherapeutic agent. Conclusions CoCSC are enriched in colon tumors following chemotherapy and remain capable of rapidly regenerating tumors from which they originated. By focusing on the biology of CoCSC, major resistance mechanisms to specific chemotherapeutic agents can be attributed to specific genes, thereby suggesting avenues for improving cancer therapy.
Thoracic and lumbar spinal surgery under local anesthesia for patients with multiple comorbidities: A consecutive case series

Background: Although some patients with symptomatic spinal disease may benefit greatly from surgery, their multiple attendant comorbidities may make general anesthesia risky or contraindicated. However, there is scarce literature describing the efficacy and safety of local anesthesia to perform these operations. Here we report seven patients who successfully underwent spinal surgery utilizing local anesthesia to limit the risks and complications of general anesthesia. Methods: Seven patients for whom general anesthesia was contraindicated were prospectively followed for a minimum of 3 months following spinal surgery performed under local anesthesia. Pain and functional improvement were assessed utilizing the Visual Analog Scores (VAS) and Oswestry Disability Index (ODI) scores. Results: Five patients had interlaminar decompressions for stenosis alone, while two patients had laminectomies for debulking of tumors. The mean duration of surgery was 79.8 ± 16.6 min, the mean estimated blood loss was 157.1 ± 53.4 ml, the mean dose of local anesthetic was 1.9 ± 0.7 mg/kg, and the mean length of hospital stay after surgery was 3.2 ± 1.2 days. There were no intraoperative complications. The surgery resulted in improved VAS and ODI scores consistent with significant improvement in pain (P = 0.017) and functionality (P = 0.011). Conclusions: Performing spinal surgery under local anesthesia is a safe and effective alternative when patient's major comorbidities preclude a general anesthetic. For all the seven patients studied, spinal surgery, performed under a local anesthetic, resulted in a statistically significant reduction in pain and improvement in function.
Competing understandings of the intersection between society and environment in the climate change debate

The failure of the Copenhagen Conference to produce a legally binding agreement marks an impasse. It also poses difficulties for sociology. This paper will not attempt to directly explain why no agreement could be reached in Copenhagen. Rather, it will sketch the sociological difficulties faced by this and other such mechanisms to use politics and law to facilitate the long term stability of the interface between natural environments and modern societies. In particular, the paper will indicate the role of each of science, morality, law, politics, and economy in producing competing understandings of „environment‟ and „society‟, competing understandings which are drawn on by many participants in the climate change debate. Our appreciation of how and why it presents a crisis, how it might have occurred, its consequences, and the fact that it is an environmental problem is a product of a certain type of specifically „environmental‟ thinking. Our project is to undertake a close exposition of how various understandings of the potential threat of climate change are generated.
The APC/C activator FZR1 coordinates the timing of meiotic resumption during prophase I arrest in mammalian oocytes

FZR1, an activator of the anaphase-promoting complex/cyclosome (APC/C), is recognized for its roles in the mitotic cell cycle. To examine its meiotic function in females we generated an oocyte-specific knockout of the Fzr1 gene (Fzr1Δ/Δ). The total number of fully grown oocytes enclosed in cumulus complexes was 35-40% lower in oocytes from Fzr1Δ/Δ mice and there was a commensurate rise in denuded, meiotically advanced and/or fragmented oocytes. The ability of Fzr1Δ/Δ oocytes to remain prophase I/germinal vesicle (GV) arrested in vitro was also compromised, despite the addition of the phosphodiesterase milrinone. Meiotic competency of smaller diameter oocytes was also accelerated by Fzr1 loss. Cyclin B1 levels were elevated ~5-fold in Fzr1Δ/Δ oocytes, whereas securin and CDC25B, two other APC/CFZR1 substrates, were unchanged. Cyclin B1 overexpression can mimic the effects of Fzr1 loss on GV arrest and here we show that cyclin B1 knockdown in Fzr1Δ/Δ oocytes affects the timing of meiotic resumption. Therefore, the effects of Fzr1 loss are mediated, at least in part, by raised cyclin B1. Thus, APC/CFZR1 activity is required to repress cyclin B1 levels in oocytes during prophase I arrest in the ovary, thereby maintaining meiotic quiescence until hormonal cues trigger resumption.