Miracle-dz/UniFAR-FTUs huggingface dataset:
Posterior Regularization for Learning with Side Information and Weak Supervision

Supervised machine learning techniques have been very successful for a variety of tasks and domains including natural language processing, computer vision, and computational biology. Unfortunately, their use often requires creation of large problem-specific training corpora that can make these methods prohibitively expensive. At the same time, we often have access to external problem-specific information that we cannot alway easily incorporate. We might know how to solve the problem in another domain (e.g. for a different language); we might have access to cheap but noisy training data; or a domain expert might be available who would be able to guide a human learner much more efficiently than by simply creating an IID training corpus. A key challenge for weakly supervised learning is then how to incorporate such kinds of auxiliary information arising from indirect supervision. In this thesis, we present Posterior Regularization, a probabilistic framework for structured, weakly supervised learning. Posterior Regularization is applicable to probabilistic models with latent variables and exports a language for specifying constraints or preferences about posterior distributions of latent variables. We show that this language is powerful enough to specify realistic prior knowledge for a variety applications in natural language processing. Additionally, because Posterior Regularization separates model complexity from the complexity of structural constraints, it can be used for structured problems with relatively little computational overhead. We apply Posterior Regularization to several problems in natural language processing including word alignment for machine translation, transfer of linguistic resources across languages and grammar induction. Additionally, we find that we can apply Posterior Regularization to the problem of multi-view learning, achieving particularly good results for transfer learning. We also explore the theoretical relationship between Posterior Regularization and other proposed frameworks for encoding this kind of prior knowledge, and show a close relationship to Constraint Driven Learning as well as to Generalized Expectation Constraints. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Computer and Information Science First Advisor Fernando Pereira Second Advisor Ben Taskar This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/265
Microbiota, Disease, and Back to Health: A Metastable Journey

The gut microbiota affects many immune-related diseases; the next step is to harness this knowledge for therapeutics. Alterations in the composition of the commensal microbiota have been observed in many complex diseases. Understanding the basis for these changes, how they relate to disease risk or activity, and the mechanisms by which the symbiotic state of colonization resistance and host homeostasis is restored is critical for future therapies aimed at manipulating the microbiota.
OpenThinning: Fast 3D Thinning based on Local Neighborhood Lookups

3D Thinning is an often required image processing task in order to perform shape analysis in various applications. For researchers in these domains, a fast, ﬂexible and easy to access implementation is required. Open source solutions, as the Insights Segmentation and Registration Toolkit (ITK), are often used for image processing and visualization tasks, due to their wide range of provided algorithms. Unfortunately, ITK’s thinning implementation is computational ex- pensive and allows solely one speciﬁc thinning approach. Therefore, this work presents OpenThinning, an open source thinning solution for 3D image data. The implemented algorithm evaluates a moving local neighborhood to ﬁnd deletable voxels, according to different sets of criteria. In order to reduce the computational ef-fort, all possible local neighborhood setting outputs are stored in a lookup table. To show the effectiveness of OpenThinning, the implementation is compared to the performance of the ITK library.
Interobserver agreement in hepatitis C grading and staging and in the Banff grading schema for acute cellular rejection: the "hepatitis C 3" multi-institutional trial experience.

CONTEXT Establishing adequate interobserver agreement is crucial not only for standardization of patient care but also to ensure validity of findings in multi-institutional trials. OBJECTIVE To evaluate interobserver agreement in assessing chronic hepatitis C (HCV) and acute cellular rejection (ACR) among 17 hepatopathologists involved in the "Hepatitis C 3" trial. DESIGN The trial is a randomized multicenter (17 institutions) study involving 312 patients undergoing transplantation for HCV. Patients are randomized to 3 treatment arms. For final data analysis, all biopsy specimens are reviewed by a central pathologist (G.J.N.). Recurrence of HCV is evaluated according to the Batts and Ludwig schema. The 1997 Banff schema is used to evaluate ACR. To assess interobserver agreement, hematoxylin-eosin-stained sections from 11 liver biopsy specimens (6 HCV and 5 ACR) were sent by the central pathologist to 16 local pathologists from 13 institutions. Statistical analysis was performed on raw ACR/HCV data as well as data grouped according to clinically significant primary endpoint cutoffs. RESULTS Statistically significant agreement was found among all participating pathologists (P < .001). On kappa analysis, the degree of agreement was rated "moderate" for HCV grade and stage and ACR global grading (kappa = 0.30, 0.33, and 0.37, respectively). Interobserver agreement was weaker for rejection activity index scoring of ACR (kappa = 0.15). A stronger degree of agreement was found when scores were grouped based on endpoint cutoffs (kappa = 0.76 "almost perfect" for HCV and 0.62 "substantial" for ACR). CONCLUSIONS An overall statistically significant interobserver agreement was found among 17 pathologists using the 1997 Banff schema and the Batts and Ludwig schema.
Workplace Experiences of Individuals Who Are HIV+ and Individuals with Cancer

Maintaining one's role in the workplace despite significant health concerns can be important in meeting an individual's emotional and economic needs. This qualitative research study reviewed the workplace experiences of 18 individuals who are HIV+ and 14 people who have cancer. Questions in the study addressed the following issues: the impact of the illness on their work life; whether they disclosed their health status and, if so, the reactions of co-workers and supervisors; and what accommodations, if any, they received. Recommendations for individuals with significant health concerns, employers, and rehabilitation counselors are discussed.
Body fat, fitness and level of everyday physical activity in adolescents and young adults with meningomyelocele.

OBJECTIVE Data on body fat and fitness in adolescents and young adults with meningomyelocele are scarce. The aim of this study was to assess body fat and fitness in this patient group. In addition, we explored whether the level of everyday physical activity is related to body fat and fitness. SUBJECTS AND METHODS Body fat (skinfold thickness), fitness (VO2peak), and everyday physical activity (Activity Monitor, based on accelerometry) were measured in 14 patients with meningomyelocele (8 men, 6 women; age range 14-26 years). RESULTS Peak VO2 was 20-30% lower than reference values and 4 patients were obese. Level of everyday activity was related to fitness (rs = 0.65, p = 0.01) but not to body fat. CONCLUSION Young patients with meningomyelocele are at risk for developing obesity and have a distinctly subnormal fitness. Level of everyday physical activity is related to fitness in this patient group.
Behavior, Expectations and Status

We predict effects of behavior patterns and status on performance expectations and group inequality using an integrated theory developed by Fişek, Berger and Norman (1991). We next test those predictions using new experimental techniques we developed to control behavior patterns as independent variables. In a 10-condition experiment, predictions accounted for about 72 percent of variance in the data, with closer fit for women than for men. The gender difference may be related to features of the experiment, especially to the experimental design that counters cultural gender prescriptions in some conditions. We suggest ways to improve the experiment by more precisely separating behavior from inferred performance competence in later research. Applications include using behavior to reduce undesirable effects of status generalization.
THE IMPACT OF MOTIVATION AND LEADER BEHAVIOR ON SATISFACTION IN NONPROFITS

How employees of nonprofit organizations are motivated and satisfied may still be unclear. If the nonprofit environment attracts different employees than for-profits, is it safe to view motivation the same? The impact of extrinsic and intrinsic motivation and supervisor style is examined in several nonprofit social service organizations. Surprising results indicate that intrinsically motivated employees were the least satisfied but were more likely to be able to clearly describe their supervisor’s style, while extrinsically motivated employees were more satisfied with their supervisor regardless of style.
Fuzzy-trace theory and children's false memories.

Fuzzy-trace theory's concepts of identity judgment, nonidentity judgment, and similarity judgment provide a unified account of the false-memory phenomena that have been most commonly studied in children: false-recognition effects and misinformation effects. False-recognition effects (elevated false-alarm rates for unpresented distractors that preserve the meanings of presented targets) are due to increased rates of similarity or false identity judgment about distractors or to decreased rates of nonidentity judgment. Misinformation effects (erroneous acceptance of misleading postevent information and erroneous rejection of actual events) are also due to variability in rates of similarity, identity, and nonidentity judgment. Two experimental paradigms are presented, one for false recognition (conjoint recognition) and one for misinformation (conjoint misinformation), that allow investigators to tease apart the contributions of these processes to children's false-memory reports. Each paradigm is implemented in a mathematical model that provides numerical estimates of the processes.
Sleeping difficulties in relation to depression and anxiety in elderly adults

This study examines the prevalence of sleeping difficulties and their relationship to depression and anxiety in 1328 subjects aged 57? 79 years by means of a questionnaire. Difficulties initiating sleep (DIS), difficulties maintaining sleep (DMS), early morning awakenings (EMA), and nightmares were assessed with The Uppsala Sleep Inventory (USI) and depression and anxiety with The Hospital Anxiety and Depression Scale (HAD scale). A total of 20.4% reported severe sleeping difficulties (DIS, DMS, or EMA), with a female preponderance. On the basis of the HAD scale we found that 3.4% fulfilled the criteria for ''definite depression'' and 10.1% fulfilled the criteria for ''possible depression''. The prevalence of ''definite'' and ''possible pure anxiety'' (anxiety without depression) was 2.7% and 8.1%, respectively. There was no sex difference in reports of depression, but women more often reported pure anxiety. Altogether, 24.3% of the sample had either depression or anxiety. Nightmares were reported by 2.2% .
Characterization of Ergodic Hidden Markov Sources

An algebraic criterion for the ergodicity of discrete random sources is presented. For finite-dimensional sources, which contain hidden Markov sources as a subclass, the criterion can be effectively computed. This result is obtained on the background of a novel, elementary theory of discrete random sources, which is based on linear spaces spanned by word functions, and linear operators on these spaces. An outline of basic elements of this theory is provided.
Two Studies Investigating the Reliability and Validity of the English ACTFL OPIc ® with Korean Test Takers The ACTFL OPIc ® Validation Project Technical Report

Two studies were conducted with Korean test takers to assess initial psychometric evidence for the English ACTFL OPIc ® as a measure of speaking proficiency in English. The initial study (Study 1) established evidence of reliability and validity for the assessment, specifically interrater reliability, testretest reliability, and construct validity evidence. Study 1 led to several recommendations to improve the assessment, which were implemented by ACTFL. A smaller, second study (Study 2) was conducted after the modifications were implemented and yielded further evidence of the reliability and validity of the ACTFL OPIc ® . Although they use different interview modalities, the results suggest both assessments measure the same construct, have similar reliabilities, and provide similar inferences. The findings from the two studies provide sufficient evidence to justify the initial use of the ACTFL OPIc ® for commercial testing. However, ACTFL should maintain its commitment to using research to inform the test development and validation process as it extends the computerized interview format to other languages and test takers. This technical report describes both English studies and presents and discusses the results.
The Offender Personality Disorder Pathway: Expansion in the Face of Failure?

In 2011, the current government announced plans to overhaul the Dangerous and Severe Personality Disorder (DSPD) programme, renaming it the Offender Personality Disorder Pathway (OPDP). This article questions the government's dedication to continuing, and potentially expanding, a costly and controversial initiative in the face of its apparent failure to treat the offenders in its care effectively and facilitate their progress through the prison system. It suggests that these unfulfilled promises are ancillary to another aim: preventively detaining troublesome prisoners. The plans are of particular concern for prisoners on indeterminate sentences for public protection (IPP), whose release may be further impeded.
Effects of Strength Training and Vascular Occlusion

The purpose of our study was to determine if vascular occlusion produced an additive effect on muscle hypertrophy and strength performance with high strength training loads. Sixteen physically active men were divided into two groups: high-intensity (HI = 6 RM) and moderate-intensity training (MI = 12 RM). An occlusion cuff was attached to the proximal end of the right thigh, so that blood flow was reduced during the exercise. The left leg served as a control, thus was trained without vascular occlusion. Knee extension 1 RM and quadriceps cross-sectional area (MRI) were evaluated pre- and post-8 weeks of training. We only found a main time effect for both strength gains and quadriceps hypertrophy (p < 0.001). Therefore, we conclude that vascular occlusion in combination with high-intensity strength training does not augment muscle strength or hypertrophy when compared to high-intensity strength training alone.
Seasonal variations in black‐faced black spider monkey (Ateles chamek) habitat use and ranging behavior in a southern Amazonian tropical forest

Data are presented regarding the habitat use and ranging behavior of a spider monkey (Ateles chamek) community at Lago Caiman in northeastern Bolivia. Habitat use was driven primarily by fruit availability and distribution across the community home range. Strong seasonal variations occurred in fruit availability within all five of the floristically and phenologically distinct habitat types identified within the study site, and the spider monkeys dramatically shifted their ranging according to which habitat was richest in fleshy fruits. This use of local habitat diversity resulted in an unusually elongated shape for the home range that was otherwise typical of previous Ateles studies in terms of size. Ranging behavior was clumped and community core areas shifted seasonally across the focal community home range. Individual core areas were not relevant to the study due to dramatic community‐wide shifts in ranging patterns. Day journey lengths were highly variable (460–5,690 m) and the distribution and abundance of fleshy fruit resources explained 81% of the monthly variations in mean day journey length. Keystone habitats for forest frugivores are identified and results are discussed with reference to previous studies on this genus, and the importance of considering keystone habitats and local habitat diversity within the management of forestry concessions in the region. Results are also discussed with reference to the behavioral ecology of the genus Ateles. Am. J. Primatol. 68:313–332, 2006. © 2006 Wiley‐Liss, Inc.
Virtual Reality Cognitive-Behavior Therapy for Public Speaking Anxiety

Public speaking anxiety (PSA) is a common social phobia. Although cognitive-behavior therapy (CBT) is the treatment of choice, difficulties arise with both in vivo and in vitro exposure (lack of therapist control, patient’s inability to imagine, self-flooding, and a lack of confidentiality resulting from public exposure). Virtual reality CBT (VRCBT) enables a high degree of therapist control, thus overcoming these difficulties. In a previous publication, the authors reported on their findings that VRCBT (n = 28) and CBT (n = 30) groups were significantly more effective than a wait-list control (WLC; n = 30) group in anxiety reduction on four of five anxiety measures as well as on participant’s self-rating of anxiety during a behavioral task. No significant differences were found between VRCBT and CBT. However, twice as many clients dropped out of CBT (15) than from VRCBT (6). Results demonstrated that VRCBT is an effective and brief treatment regimen, equal to CBT. This brief report examined durability of these changes. They found that both VRCBT (25) and CBT (24) groups maintained their improvement from post treatment to follow-up, on all five measures. In addition, they found that the CBT group continued to improve from post treatment to follow-up on Liebowitz Social Anxiety Scale (LSAS) fear. Thus, treatment gains were maintained at a 1-year follow-up.
Encephalomyelitis in SJL/J Mice Suppresses Experimental Allergic Administration of Dehydroepiandrosterone

Experimental allergic encephalomyelitis (EAE) is a Th1-mediated inﬂammatory demyelinating disease in the CNS, an animal model of multiple sclerosis. We have examined the effect of dehydroepiandrosterone (DHEA) on the development of EAE in mice. The addition of DHEA to cultures of myelin basic protein-primed splenocytes resulted in a signiﬁcant decrease in T cell proliferation and secretion of (pro)inﬂammatory cytokines (IFN- (cid:1) , IL-12 p40, and TNF- (cid:2) ) and NO in response to myelin basic protein. These effects were associated with a decrease in activation and translocation of NF- (cid:3) B. In vivo administration of DHEA signif-icantly reduced the severity and incidence of acute EAE, along with a decrease in demyelination/inﬂammation and expressions of (pro)inﬂammatory cytokines in the CNS. These studies suggest that DHEA has potent anti-inﬂammatory properties, which at least are in part mediated by its inhibition of NF- (cid:3) B activation. The Journal of Immunology, 2001, 167: 7094–7101. and
High-efficacy targeting of colon-cancer liver metastasis with Salmonella typhimurium A1-R via intra-portal-vein injection in orthotopic nude-mouse models

Liver metastasis is the main cause of colon cancer-related death and is a recalcitrant disease. We report here the efficacy and safety of intra-portal-vein (iPV) targeting of Salmonella typhimurium A1-R on colon cancer liver metastasis in a nude-mouse orthotopic model. Nude mice with HT29 human colon cancer cells, expressing red fluorescent protein (RFP) (HT29-RFP), growing in the liver were administered S. typhimurium A1-R by either iPV (1×104 colony forming units (CFU)/100 μl) or, for comparison, intra-venous injection (iv; 5×107 CFU/100 μl). Similar amounts of bacteria were delivered to the liver with the two doses, indicating that iPV delivery is 5×103 times more efficient than iv delivery. Treatment efficacy was evaluated by tumor fluorescent area (mm2) and total fluorescence intensity. Tumor fluorescent area and fluorescence intensity highly correlated (p<0.0001). iPV treatment was more effective compared to both untreated control and iv treatment (p<0.01 and p<0.05, respectively with iPV treatment with S. typhimurium arresting metastatic growth). There were no significant differences in body weight between all groups. The results of this study suggest that S. typhimurium A1-R administered iPV has potential for peri-operative adjuvant treatment of colon cancer liver metastasis.
[In-hospital prognosis of right ventricular myocardial infarction].

AIM To identify prognostic risk factors for in-hospital outcome of right ventricular myocardial infarction (RVI). METHODS A retrospective study of 20 patients admitted with acute myocardial infarction with a RVI defined by ST segment elevation > or = 1 mm in V3R and V4R leads. RESULTS The mean age was 62 years. RVI was associated with an inferior myocardial infarction in 18 patients. Half of the patients had hemodynamic complication on admission (cardiogenic shock in 4 cases, right ventricular failure in 6 cases) and third degree atrio-ventricular block was present in 5 patients. Sixteen patients (80%) received thrombolysis and 3 went to an emergency angioplasty. The in-hospital mortality was 25% caused by a cardiogenic shock in 4 patients and a ventricular fibrillation in 1 patient. Statistic analysis showed that cardiogenic shock on admission, the absence of thrombolytic therapy and the low ejection fraction of the left ventricle were associated with a high in-hospital mortality (p = 0.004, p = 0.03, p = 0.03 respectively). CONCLUSION In-hospital outcome of RVI is characterized by hemodynamic complications leading to a high incidence of mortality. Thus RVI must be diagnosed quickly and maximal therapeutic efforts must be done to procure the opening of the occluded coronary artery.
"What Do You Mean I Wrote a C Paper?" Writing, Revision, and Self-Regulation.

Students often express surprise at their grades on papers. This gap between expectation and achievement may stem in part from lack of facility with revision strategies. How, then, can teachers work with their students to foster more effective revisions? This question in teaching and learning has inspired an interdisciplinary collaboration: one of us is a management and leadership professor (Sharen), and the other is an English/communication professor (Feltham). In this essay, we describe a research study from winter 2013 in which we explored how a series of interventions improved students’ mindsets about the process of drafting and revising reports for a second-year-university course entitled “Women and Leadership. ” After outlining key aspects of this study that we feel are of general interest, we then present a series of reflective suggestions about how to teach revision derived from both our experiences and a selective survey of the literature on both revision and self-regulation.