Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk Factors and Outcomes for Ineffective Empiric Treatment of Sepsis Caused by Gram-Negative Pathogens: Stratification by Onset of Infection

ABSTRACT Sepsis and septic shock remain serious consequences of infections, with reported mortality rates in excess of 40 percent. Timely antibiotic therapy in cases of sepsis and septic shock is recognized as an important determinant of outcome. However, the administration of ineffective empirical treatment (IET) (an initial antibiotic regimen that is not active against the identified pathogen[s] based on in vitro susceptibility testing results) is associated with excess mortality compared to effective empirical treatment (EET). We examined all hospitalized patients at Barnes-Jewish Hospital with a sterile site (blood or pleural, abdominal, cerebrospinal, synovial, and pericardial fluid) culture positive for Gram-negative (GN) bacteria combined with a primary or secondary ICD-9-CM code for severe sepsis (995.92) or septic shock (785.52) between January 2010 and October 2015. Variables significantly associated with early-onset (<48 h of hospitalization) IET of GN sterile site sepsis and septic shock included age, recent hospitalization, and prior intravenous antibiotics. Late-onset IET was associated with increasing numbers of hospitalization days before infection onset and prior intravenous antibiotic administration. For patients with early-onset infection, we found no difference in rates of survival between patients receiving IET and EET. However, patients in the late-onset infection group receiving IET had a statistically lower rate of survival than those receiving EET. These data suggest that risk factors and outcomes for IET can vary based on the time of onset of infection. Our results also highlight the importance of prior intravenous antibiotic exposure as a risk factor for IET in infections by GN bacteria regardless of the time of onset of infection.
Hyperparameter Optimization: A Spectral Approach

We give a simple, fast algorithm for hyperparameter optimization inspired by techniques from the analysis of Boolean functions. We focus on the high-dimensional regime where the canonical example is training a neural network with a large number of hyperparameters. The algorithm --- an iterative application of compressed sensing techniques for orthogonal polynomials --- requires only uniform sampling of the hyperparameters and is thus easily parallelizable. Experiments for training deep neural networks on Cifar-10 show that compared to state-of-the-art tools (e.g., Hyperband and Spearmint), our algorithm finds significantly improved solutions, in some cases better than what is attainable by hand-tuning. In terms of overall running time (i.e., time required to sample various settings of hyperparameters plus additional computation time), we are at least an order of magnitude faster than Hyperband and Bayesian Optimization. We also outperform Random Search 8x. Additionally, our method comes with provable guarantees and yields the first improvements on the sample complexity of learning decision trees in over two decades. In particular, we obtain the first quasi-polynomial time algorithm for learning noisy decision trees with polynomial sample complexity.
Positive Natural Selection in the Human

www.sciencemag. org (this information is current as of May 18, 2007 ): The following resources related to this article are available online at http://www.sciencemag. org/cgi/content/full/312/5780/1614 version of this article at: including high-resolution figures, can be found in the online Updated information and services, http://www.sciencemag. org/cgi/content/full/312/5780/1614/DC1 can be found at: Supporting Online Material http://www.sciencemag. org/cgi/content/full/312/5780/1614#otherarticles , 25 of which can be accessed for free: cites 68 articles This article 19 article(s) on the ISI Web of Science. cited by This article has been http://www.sciencemag. org/cgi/content/full/312/5780/1614#otherarticles 8 articles hosted by HighWire Press; see: cited by This article has been http://www.sciencemag. org/cgi/collection/evolution Evolution : subject collections This article appears in the following http://www.sciencemag. org/about/permissions.dtl in whole or in part can be found at: this article permission to reproduce of this article or about obtaining reprints Information about obtaining
Management of the cervico‐petrous internal carotid artery in class C tympanojugular paragangliomas

Management of the cervical and petrous internal carotid artery (ICA) is frequently required in Fisch class C tympanojugular paragangliomas (TJPs). The purpose of this study was to discuss the perioperative intervention of the ICA in patients who underwent surgical resection of a TJP.
The relative burden of dry eye in patients' lives: comparisons to a U.S. normative sample.

PURPOSE To assess the relative burden of dry eye in daily life by comparing Short Form-36 (SF-36) responses from individuals with and without dry eye against U.S. norms. METHODS Assessment of 210 people, 130 with non-Sjogren's keratoconjunctivitis sicca (non-SS KCS), 32 with Sjogren's Syndrome (SS), and 48 control subjects. The study population data and published normative SF-36 data were compared. Dry eye severity was assessed by recruited severity (control, non-SS KCS, SS), patient self-report (none, very mild/mild, moderate, severe/extremely severe), and clinician-report (none, mild, moderate, severe). Age- and gender-matched norms were compared with all defined severity groups. RESULTS Compared with the norms, control subjects scored higher on all SF-36 scales. Effect size (ES) ranged from 0.15 to 0.52. Non-SS KCS patients had lower Role-Physical (ES=-0.07), Bodily Pain (ES=-0.08), and Vitality (ES=-0.11) scores, indicating more dry eye impact on those areas versus the norm. All SF-36 scale scores except Mental Health (ES=0.12) were lower in the SS group than the adjusted norm (ES range: -0.16 to -0.99). Regardless of severity classification, mild patients consistently had lower Role-Physical and Bodily Pain scores than the norm, suggesting impact on daily roles (ES < 0.2). Patients with moderately severe disease also experienced less vitality and poorer general health. The group with severe disease scored lower than the norm across all domains (ES range: -0.14 to -0.91) except Role-Emotional (ES=0.13) and Mental Health (ES=0.23). CONCLUSIONS These results indicate dry eye's negative impact on everyday life, particularly in daily activities. Further research using disease-specific measures to examine dry eye's impact is underway.
A Meta-Analysis of Unilateral versus Bilateral Pedicle Screw Fixation in Minimally Invasive Lumbar Interbody Fusion

Study Design Meta-analysis. Background Bilateral pedicle screw fixation (PS) after lumbar interbody fusion is a widely accepted method of managing various spinal diseases. Recently, unilateral PS fixation has been reported as effective as bilateral PS fixation. This meta-analysis aimed to comparatively assess the efficacy and safety of unilateral PS fixation and bilateral PS fixation in the minimally invasive (MIS) lumbar interbody fusion for one-level degenerative lumbar spine disease. Methods MEDLINE/PubMed, EMBASE, BIOSIS Previews, and Cochrane Library were searched through March 30, 2014. Randomized controlled trials (RCTs) and controlled clinical trials (CCTs) on unilateral versus bilateral PS fixation in MIS lumbar interbody fusion that met the inclusion criteria and the methodological quality standard were retrieved and reviewed. Data on participant characteristics, interventions, follow-up period, and outcomes were extracted from the included studies and analyzed by Review Manager 5.2. Results Six studies (5 RCTs and 1 CCT) involving 298 patients were selected. There were no significant differences between unilateral and bilateral PS fixation procedures in fusion rate, complications, visual analogue score (VAS) for leg pain, VAS for back pain, Oswestry disability index (ODI). Both fixation procedures had similar length of hospital stay (MD = 0.38, 95% CI = −0.83 to 1.58; P = 0.54). In contrast, bilateral PS fixation was associated with significantly more intra-operative blood loss (P = 0.002) and significantly longer operation time (P = 0.02) as compared with unilateral PS fixation. Conclusions Unilateral PS fixation appears as effective and safe as bilateral PS fixation in MIS lumbar interbody fusion but requires less operative time and causes less blood loss, thus offering a simple alternative approach for one-level lumbar degenerative disease.
Can Neural Networks Understand Logical Entailment?

We introduce a new dataset of logical entailments for the purpose of measuring models' ability to capture and exploit the structure of logical expressions against an entailment prediction task. We use this task to compare a series of architectures which are ubiquitous in the sequence-processing literature, in addition to a new model class---PossibleWorldNets---which computes entailment as a "convolution over possible worlds". Results show that convolutional networks present the wrong inductive bias for this class of problems relative to LSTM RNNs, tree-structured neural networks outperform LSTM RNNs due to their enhanced ability to exploit the syntax of logic, and PossibleWorldNets outperform all benchmarks.
Influence of Gestational Age, Secretor, and Lewis Blood Group Status on the Oligosaccharide Content of Human Milk

Objectives: Human milk oligosaccharides (HMOs) are considered to play an important role for the infant. As the biotechnical production of some HMOs is feasible today and clinical studies are being designed, the individual variation of the total amount of HMOs and of single components is of particular importance. Our objectives were to investigate whether differences exist between term and preterm milk, milk from mothers with secretor or nonsecretor status, and a Lewis blood group (a+b−), (a−b+), or (a−b−) pattern. Methods: Within a longitudinal study 96 milk samples (colostrum, transitional, and mature milk) from 32 mothers with preterm (n = 18) and term (n = 14) infants were collected. Delipidated and deproteinized milk was subjected to porous graphitized carbon cartridges followed by high pH anion exchange chromatography with pulsed amperometric detection. Results: Quantitation of 16 single HMOs revealed changes during the first weeks of lactation without discrepancies between term and preterm milk. Significant differences occurred between “secretor” and “nonsecretor” milk (median approximately 10 vs 5 g/L total HMOs). Lacto-N-tetraose (LNT) and lacto-N-fucopentaose (LNFP) II comprised > 55% of the total HMO content in Lewis blood group (a+b−), “nonsecretor” milk and LNT together with 2’fucosyllactose, LNFP I, and difucosyllactose approximately 60% in Lewis (a−b+), “secretor” milk. In Lewis (a−b−), “secretor” milk 80% of oligosaccharides are due to LNT, 2’fucosyllactose, and LNFP I. Conclusions: There are marked differences in total HMOs and single HMOs in milk depending on Lewis blood group and secretor status, which need to be taken into account in clinical studies.
Robustness of the Theory of Planned Behavior in Predicting Entrepreneurial Intentions and Actions

This analysis demonstrates the relevance and robustness of the theory of planned behavior in the prediction of business start–up intentions and subsequent behavior based on longitudinal survey data (2011 and 2012; n = 969) from the adult population in Austria and Finland. By doing so, the study addresses two weaknesses in current research: the limited scope of samples used in the majority of prior studies and the scarcity of investigations studying the translation of entrepreneurial intentions into behavior. The paper discusses conceptual and methodological issues related to studying the intention–behavior relationship and outlines avenues for future research.
Perianal Crohn Disease in a Large Multicenter Pediatric Collaborative

Background: Although perianal complications of Crohn disease (CD) are commonly encountered in clinical practice, the epidemiology of perianal CD among populations of children is poorly understood. We sought to characterize the prevalence of perianal disease in a large and diverse population of pediatric patients with CD. Methods: We conducted retrospective analyses from a prospective observational cohort, the ImproveCareNow Network (May 2006–October 2014), a multicenter pediatric inflammatory bowel disease quality improvement collaborative. Clinicians prospectively documented physical examination and phenotype classification at outpatient visits. Perianal examination findings and concomitant phenotype change were used to corroborate time of new-onset perianal disease. Results were stratified by age, sex, and race and compared across groups with logistic regression. Cumulative incidence was estimated using Kaplan-Meier analyses and compared between groups with Cox proportional hazard regression models. Results: The registry included 7076 patients with CD (41% girls). Missing/conflicting entries resulted in 397 (6%) patient exclusions. Among the remaining 6679 cases, 1399 (21%) developed perianal disease. Perianal disease was more common among boys (22%) than girls (20%; P = 0.013) and developed sooner after diagnosis among those with later rather than early onset disease (P < 0.001). Perianal disease was also more common among blacks (26%) compared with whites (20%; P = 0.017). Asians with later onset CD developed perianal disease earlier in their disease course (P = 0.01). There was no association between disease location or nutritional status at diagnosis and later development of perianal disease. Conclusions: In this large multicenter collaborative, we found that perianal disease is more common among children with CD than previously recognized. Differences in the development of perianal disease were found across racial and other subgroups. Treatment strategies are needed to prevent perianal disease development.
Prior event rate ratio adjustment for hidden confounding in observational studies of treatment effectiveness: a pairwise Cox likelihood approach

Observational studies provide a rich source of information for assessing effectiveness of treatment interventions in many situations where it is not ethical or practical to perform randomized controlled trials. However, such studies are prone to bias from hidden (unmeasured) confounding. A promising approach to identifying and reducing the impact of unmeasured confounding is prior event rate ratio (PERR) adjustment, a quasi‐experimental analytic method proposed in the context of electronic medical record database studies. In this paper, we present a statistical framework for using a pairwise approach to PERR adjustment that removes bias inherent in the original PERR method. A flexible pairwise Cox likelihood function is derived and used to demonstrate the consistency of the simple and convenient alternative PERR (PERR‐ALT) estimator. We show how to estimate standard errors and confidence intervals for treatment effect estimates based on the observed information and provide R code to illustrate how to implement the method. Assumptions required for the pairwise approach (as well as PERR) are clarified, and the consequences of model misspecification are explored. Our results confirm the need for researchers to consider carefully the suitability of the method in the context of each problem. Extensions of the pairwise likelihood to more complex designs involving time‐varying covariates or more than two periods are considered. We illustrate the application of the method using data from a longitudinal cohort study of enzyme replacement therapy for lysosomal storage disorders. © 2016 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.
Stem cells as an emerging paradigm in stroke 3: enhancing the development of clinical trials.

Cell-based therapy continues to grow as a new field to explore investigational treatments for stroke. Leaders from academia and industry convened an inaugural meeting in 2007 with members of the National Institutes of Health and Food and Drug Administration (FDA) to generate consensus-based guidelines on the development of cell therapies for stroke, entitled “Stem Cells as an Emerging Paradigm in Stroke” (STEPS). 1 These guidelines focused on preclinical studies that are considered important as part of a development program to support clinical testing of cell therapies. The STEPS meeting also provided recommendations on the conduct of early-stage clinical trials. Given the rapid advances in the field, a second meeting was held in 2009 to update and expand these guidelines, which were published as STEPS 2.2 In December 2011, investigators in academia, industry leaders, and members of the National Institutes of Health and FDA gathered at a third meeting, STEPS 3, to discuss emerging data on the mechanisms of action of cell therapy, the barriers to successful translation from animal models to patients, and the design of current clinical trials for acute and chronic stroke. Since the prior STEPS meeting, there are now several active cell therapy platforms for stroke and other neurological disorders, in stages that range from preclinical to clinical trials, and with sponsors that include industry, the National Institutes of Health, and the California Institute of Regenerative Medicine. As the field continues to progress and as pilot clinical studies are starting to show safety for some cell types, it has become necessary to formulate a new set of guidelines that address topics not covered in prior STEPS publications. Specifically, the current document reflects a compilation of recommendations that focus on more advanced stages of clinical testing, as well as the testing of cell therapies in a broader …
Life quality assessment of patients after phacoemulsification or extracapsular cataract extraction.

PURPOSE To study the quality of life, treatment outcomes, and satisfaction in patients who have undergone cataract surgery Methods: This comparative case series study was conducted at the Ophthalmology Service of the Bettina Ferro de Souza University Hospital, Belém, Pará, Brazil. Totally, 60 patients with cataract were included; 50% underwent conventional extracapsular cataract extraction (ECEE) and 50% underwent cataract extraction by phacoemulsification (PHACO). Patients were interviewed using the Visual Function 14 (VF-14) questionnaire to determine the quality of life before and 30 days after surgery. The results of ophthalmological examination were recorded in the patients' files and were available throughout this study. One-way ANOVA, Tukey's post-hoc comparison, and the sign test were used for statistical analyses. RESULTS The mean VF-14 satisfaction index was 38.0 and 89.4 before and after surgery, respectively, for the ECEE group and 47.0 and 94.1, respectively, for the PHACO group. The improvement in patient quality of life after surgery was significant in both groups (p<0.0001), with a similar amount of improvement in both groups. CONCLUSIONS The observed improvement in quality of life was significant (p<0.0001) and directly related to patient satisfaction with surgical outcomes, which was also significant (p<0.0001) as assessed using the VF-14. Satisfaction and quality of life are individual factors; consequently, patient responses to questions regarding improvements in the ability to perform each activity are subjective and depend uniquely on individual perception.
School of Chemical Technology Degree Programme of Materials Science and Engineering Petri Hirvonen PHASE FIELD CRYSTAL MODELING OF GRAIN BOUNDARIES IN GRAPHENE Master’s thesis for the degree of Master of Science in Technology

Graphene is a two-dimensional allotrope of carbon that exhibits extraordinary crystalline, mechanical, electrical, thermal and optical properties. The material has been studied for over a decade, but the details of its atomic ordering and microstructural evolution are still incomplete. The phase field crystal model for modeling crystalline systems at atomic length and diffusive time scales is suited for studying such complex phenomena. The phase field crystal model has not previously been applied to quantitatively model two-dimensional materials. In the present work, three variants of the original phase field crystal model are assessed to find a good description for microstructural evolution in graphene. Performance of the three models is evaluated by investigating the symmetric tilt grain boundary structures and related energies they predict in free-standing, planar graphene. Two of the three models produce realistic grain boundary structures, namely those comprised of pentagon-heptagon, or 5|7 dislocations. First of these two models gives a rich variety of other structures as well. Some such structures are presumably metastable or even unphysical and tools to better control the relaxation of the modeled grain boundary structures are presented. This first model yields grain boundary energy as a function of the tilt angle in the approximate range of 0 5 eV/nm which is in quantitative agreement with other numerical works. The second model captures qualitatively the essential features of the grain boundary energy curve (ca. 0 11 eV/nm). The third model gives a similar range for the grain boundary energy (ca. 0 10 eV/nm) but captures its features poorly as a function of the tilt angle. The phase field crystal technique is shown applicable to quantitative modeling of graphene microstructures. This approach benefits the study of atomic structures in real world graphene and may help unlock novel applications.
Propensity of marine reserves to reduce the evolutionary effects of fishing in a migratory species

Evolutionary effects of fishing can have unwanted consequences diminishing a fishery's value and sustainability. Reserves, or no-take areas, have been proposed as a management tool for reducing fisheries-induced selection, but their effectiveness for migratory species has remained unexplored. Here we develop an eco-genetic model to predict the effects of marine reserves on fisheries-induced evolution under migration. To represent a stock that undergoes an annual migration between feeding and spawning grounds, we draw model parameters from Atlantic cod (Gadus morhua) in the northern part of its range. Our analysis leads to the following conclusions: (i) a reserve in a stock's feeding grounds, protecting immature and mature fish alike, reduces fisheries-induced evolution, even though protected and unprotected population components mix on the spawning grounds; (ii) in contrast, a reserve in a stock's spawning grounds, protecting only mature fish, has little mitigating effects on fisheries-induced evolution and can sometimes even exacerbate its magnitude; (iii) evolutionary changes that are already underway may be difficult to reverse with a reserve; (iv) directly after a reserve is created or enlarged, most reserve scenarios result in yield losses; and (v) timescale is very important: short-term yield losses immediately after a reserve's creation can give way to long-term gains.