bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning how to know
Authors: San Roque Lila , Schieffelin Bambi B. 
Published: April 2018

Abstract
Languages with egophoric systems require their users to pay special attention to who knows what in the speech situation, providing formal marking of whether the speaker or addressee has personal knowledge of the event being discussed. Such systems have only recently come to be studied in cross-linguistic perspective. This chapter has two aims in regard to contributing to our understanding of egophoric marking. Firstly, it presents relevant data from a relatively under-described and endangered language, Kaluli (aka Bosavi), spoken in Papua New Guinea. Unusually, Kaluli tense inflections appear to show a mix of both egophoric and first vs non-first person-marking features, as well as other contrasts that are broadly relevant to a typology of egophoricity, such as special constructions for the expression of involuntary experience. Secondly, the chapter makes a preliminary foray into issues concerning egophoric marking and child language, drawing on a naturalistic corpus of child-caregiver interactions. Questions for future investigation raised by the Kaluli data concern, for example, the potentially challenging nature of mastering inflections that are sensitive to both person and speech act type, the possible role of question-answer pairs in children’s acquisition of egophoric morphology, and whether there are special features of epistemic access and authority that relate particularly to child-adult interactions.
Chronic iliofemoral vein obstruction – an under‐recognized cause of exercise limitation‡
Authors: Segel Michael J. , Reuveny Ronen , Luboshitz Jacob , Shlomi Dekel , Ben‐Dov Issahar 
Published: April 2018

AbstractLocal symptoms of chronic venous insufficiency after deep vein thrombosis (DVT) are well described, but little is known about the effect of residual venous obstruction on exercise capacity. We tested our hypothesis that chronic residual iliofemoral vein occlusion (IFVO) after DVT may impair exercise capacity. Nine post‐DVT patients with residual IFVO and effort intolerance were studied; a comparison cohort consisted of 11 healthy volunteers. Exercise tolerance was assessed by bimodality incremental symptom‐limited cardiopulmonary testing, using leg and arm ergometers. In healthy subjects, leg vein obstruction was modelled by application to the thighs of cuff tourniquets inflated to 30–40 mmHg. Leg exercise tolerance as measured by oxygen uptake at peak exercise (peak ⩒’O2) was reduced in patients (median 50% predicted (range 36–83%) vs. 88% predicted (67–129%) in normal subjects, p < 0.001). Arm exercise tolerance was also reduced in patients, but less severely than in the legs – the median arm: leg ratio of peak ⩒’O2 was 0.95 (0.77–1.43) in patients vs. a normal ratio of 0.73 (0.6–1.0) in healthy subjects (p < 0.003). In healthy subjects, bilateral leg vein obstruction by tourniquets reduced peak ⩒’O2 in leg exercise to 76% predicted (range 55–108%; p < 0.001 vs. standard test). In conclusion, the comparison of arm vs. leg exercise capacity in post‐DVT patients with residual IFVO and the effect of experimental venous obstruction (thigh tourniquets) in healthy subjects suggest that reduced exercise capacity in patients was at least partially caused by reduced venous return. Chronic venous obstruction should be recognized as a cause of exercise limitation.
Asymptotically optimal minimizers schemes
Authors: Marçais Guillaume , DeBlasio Dan , Kingsford Carl 
Published: April 2018

Abstract

Motivation
The minimizers technique is a method to sample k-mers that is used in many bioinformatics software to reduce computation, memory usage and run time. The number of applications using minimizers keeps on growing steadily. Despite its many uses, the theoretical understanding of minimizers is still very limited. In many applications, selecting as few k-mers as possible (i.e. having a low density) is beneficial. The density is highly dependent on the choice of the order on the k-mers. Different applications use different orders, but none of these orders are optimal. A better understanding of minimizers schemes, and the related local and forward schemes, will allow designing schemes with lower density and thereby making existing and future bioinformatics tools even more efficient.

Results
From the analysis of the asymptotic behavior of minimizers, forward and local schemes, we show that the previously believed lower bound on minimizers schemes does not hold, and that schemes with density lower than thought possible actually exist. The proof is constructive and leads to an efficient algorithm to compare k-mers. These orders are the first known orders that are asymptotically optimal. Additionally, we give improved bounds on the density achievable by the three type of schemes.
Parapred: antibody paratope prediction using convolutional and recurrent neural networks
Authors: Liberis Edgar , Veličković Petar , Sormanni Pietro , Vendruscolo Michele , Liò Pietro 
Published: April 2018

Abstract

Motivation
Antibodies play essential roles in the immune system of vertebrates and are powerful tools in research and diagnostics. While hypervariable regions of antibodies, which are responsible for binding, can be readily identified from their amino acid sequence, it remains challenging to accurately pinpoint which amino acids will be in contact with the antigen (the paratope).

Results
In this work, we present a sequence-based probabilistic machine learning algorithm for paratope prediction, named Parapred. Parapred uses a deep-learning architecture to leverage features from both local residue neighbourhoods and across the entire sequence. The method significantly improves on the current state-of-the-art methodology, and only requires a stretch of amino acid sequence corresponding to a hypervariable region as an input, without any information about the antigen. We further show that our predictions can be used to improve both speed and accuracy of a rigid docking algorithm.

Availability and implementation
The Parapred method is freely available as a webserver at http://www-mvsoftware.ch.cam.ac.uk/and for download at https://github.com/eliberis/parapred.

Supplementary information
Supplementary information is available at Bioinformatics online.
Initial Assessment of the Risk Assessment and Prediction Tool in a Heterogeneous Neurosurgical Patient Population
Authors: Piazza Matthew , Sharma Nikhil , Osiemo Benjamin , McClintock Scott , Missimer Emily , Gardiner Diana , Maloney Eileen , Callahan Danielle , Smith J Lachlan , Welch William , Schuster James , Grady M Sean , Malhotra Neil R 
Published: April 2018

Abstract

BACKGROUND
Bundled care payments are increasingly being explored for neurosurgical interventions. In this setting, skilled nursing facility (SNF) is less desirable from a cost perspective than discharge to home, underscoring the need for better preoperative prediction of postoperative disposition.

OBJECTIVE
To assess the capability of the Risk Assessment and Prediction Tool (RAPT) and other preoperative variables to determine expected disposition prior to surgery in a heterogeneous neurosurgical cohort, through observational study.

METHODS
Patients aged 50 yr or more undergoing elective neurosurgery were enrolled from June 2016 to February 2017 (n = 623). Logistic regression was used to identify preoperative characteristics predictive of discharge disposition. Results from multivariate analysis were used to create novel grading scales for the prediction of discharge disposition that were subsequently compared to the RAPT Score using Receiver Operating Characteristic analysis.

RESULTS
Higher RAPT Score significantly predicted home disposition (P < .001). Age 65 and greater, dichotomized RAPT walk score, and spinal surgery below L2 were independent predictors of SNF discharge in multivariate analysis. A grading scale utilizing these variables had superior discriminatory power between SNF and home/rehab discharge when compared with RAPT score alone (P = .004).

CONCLUSION
Our analysis identified age, lower lumbar/lumbosacral surgery, and RAPT walk score as independent predictors of discharge to SNF, and demonstrated superior predictive power compared with the total RAPT Score when combined in a novel grading scale. These tools may identify patients who may benefit from expedited discharge to subacute care facilities and decrease inpatient hospital resource utilization following surgery.
Impact of diet deprivation and subsequent overallowance during gestation on lactation performance of primiparous sows1
Authors: Farmer Chantal , Herkelman Kevin , James Brad , Lessard Pierre , Samson Arnaud , Cormier Isabelle 
Published: April 2018

Abstract
The impact of diet deprivation followed by overallowance during gestation on metabolic status of pregnant gilts and their lactation performance was determined. Gilts were fed a standard diet until day 27 of gestation and were subsequently reared under a control (CTL; n = 28) or an experimental (treatment, TRT; n = 26) dietary regimen. The experimental regimen provided 70% (restriction diet, RES) and 115% (overallowance diet, OVER) of the protein and NE contents provided by the CTL diet. The RES diet was given from days 28 to 74 of gestation followed by the OVER diet from day 75 until farrowing. Blood samples were obtained from all gilts on days 28, 75, and 110 of gestation, and on days 3 and 20 of lactation to measure concentrations of IGF-1, urea, FFA, and glucose. Milk samples were collected from 12 sows per treatment on day 19 of lactation and sow feed intake was recorded daily throughout lactation. Piglets were weighed at 24 h (after standardization of litter size), and on days 7, 14, and 21 (weaning). The TRT gilts gained less BW than CTL gilts (17.3 vs. 31.7 kg; P &lt; 0.01) from days 28 to 75 of gestation and more BW (29.5 vs. 21.9 kg; P &lt; 0.01) from days 75 to 110, but their overall gain from mating to day 110 was lower (61.4 vs. 67.2 kg; P &lt; 0.05). Metabolic status during gestation was affected, with TRT gilts having less IGF-1 and urea, and more FFA than CTL gilts on day 75 (P &lt; 0.01), and more urea on day 110 (P &lt; 0.01). Growth rate of suckling piglets, sow lactation feed intake, and standard milk composition in late lactation (DM, fat, protein, lactose) were not affected by treatment (P &gt; 0.10). In conclusion, diet deprivation of gilts as of day 28 of gestation followed by overfeeding from day 75 of gestation until farrowing did not improve lactation performance. It is likely that the compensatory growth that took place in late gestation was not adequate to illicit beneficial effects.
Is the Current Management of Patients Presenting With Spinal Trauma to District General Hospitals Fit for Purpose?
Authors: Hill Daniel S. , Marynissen Hans 
Published: April 2018

Study Design.
A retrospective cross-sectional analysis.

Objective.
The aim of this study was to describe the provision of a spinal service using an electronic platform to direct management from an external spinal unit, and to quantify the time taken to obtain definitive management plans while under prescribed spinal immobilization.

Summary of Background Data.
Most attending district general hospitals following spinal trauma will have stable injuries and normal neurology, with only a small proportion requiring urgent transfer to a specialist center.

Methods.
A retrospective review of 104 patients admitted following vertebral trauma during a 12-month period. The British Orthopaedic Association Standards for Trauma consensus that “spinal immobilisation is not recommended for more than 48 hours” was the standard of care measured against.

Results.
One hundred patients occupied a total of 975 hospital inpatient bed days. One hundred and seventeen radiological investigations were requested after the point of external referral [47 computed tomography (CT)-scans, 37 magnetic resonance imaging (MRI)-scans, and 33 weight-bearing radiographs]. The period between initial referral to the regional spinal service and then receiving a definitive final management plan had a median value of 72 hours and a range of 0 and 33 days. Patients will have been under some form of prescribed spinal immobilization until the definitive management plan was communicated. Thirty-four patients (34% of the overall cohort) had a definitive management plan in place within 48 hours. Eighty patients had vertebral injuries (73 stable, six unstable), three patients had prolapsed intervertebral disks, one had metastatic disease, and 17 did not have evidence of an acute injury following evaluation.

Conclusion.
Patients are being placed under prescribed immobilization for longer than is recommended. Delays in obtaining radiological imaging were an important factor, together with the time taken to receive a definitive management plan. Limitations in social care provision and delays in arranging this were additional barriers to hospital discharge following the final management plan.

Level of Evidence: 4
Complexities and potential pitfalls of clinical study design and data analysis in assisted reproduction
Authors: Patounakis George , Hill Micah J. 
Published: April 2018

Purpose of review
The purpose of the current review is to describe the common pitfalls in design and statistical analysis of reproductive medicine studies. It serves to guide both authors and reviewers toward reducing the incidence of spurious statistical results and erroneous conclusions.

Recent findings
The large amount of data gathered in IVF cycles leads to problems with multiplicity, multicollinearity, and over fitting of regression models. Furthermore, the use of the word ‘trend’ to describe nonsignificant results has increased in recent years. Finally, methods to accurately account for female age in infertility research models are becoming more common and necessary.

Summary
The pitfalls of study design and analysis reviewed provide a framework for authors and reviewers to approach clinical research in the field of reproductive medicine. By providing a more rigorous approach to study design and analysis, the literature in reproductive medicine will have more reliable conclusions that can stand the test of time.
VISUAL ACUITY IN PSEUDOXANTHOMA ELASTICUM
Authors: Risseeuw Sara , Ossewaarde-van Norel Jeannette , Klaver Caroline C. W. , Colijn Johanna M. , Imhof Saskia M. , van Leeuwen Redmer 
Published: April 2018

Purpose:
To assess the age-specific proportion of visual impairment in patients with pseudoxanthoma elasticum (PXE) and to compare this with foveal abnormality and similar data of late age-related macular degeneration patients.

Methods:
Cross-sectional data of 195 patients with PXE were reviewed, including best-corrected visual acuity and imaging. The World Health Organisation criteria were used to categorize bilateral visual impairment. These results were compared with similar data of 131 patients with late age-related macular degeneration from the Rotterdam study.

Results:
Overall, 50 PXE patients (26.0%) were visually impaired, including 21 (11%) with legal blindness. Visual functioning declined with increasing age. In patients older than 50 years, 37% was visually impaired and 15% legally blind. Foveal choroidal neovascularization was found in 84% of eyes with a best-corrected visual acuity lower than 20/70 (0.30) and macular atrophy in the fovea in 16%. In late age-related macular degeneration patients, 40% were visually impaired and 13% legally blind. Visual impairment started approximately 20 years later as compared with PXE patients.

Conclusion:
Visual impairment and blindness are frequent in PXE, particularly in patients older than 50 years. Although choroidal neovascularization is associated with the majority of vision loss, macular atrophy is also common. The proportion of visual impairment in PXE is comparable with late age-related macular degeneration but manifests earlier in life.
ENDOPHTHALMITIS AFTER PARS PLANA VITRECTOMY
Authors: Weiss Stephanie J. , Adam Murtaza K. , Gao Xinxiao , Obeid Anthony , Sivalingam Arunan , Fineman Mitchell S. , Maguire Joseph I. , Garg Sunir J. , Haller Julia , Fischer David H. , Hsu Jason 
Published: April 2018

Purpose:
To examine rates of acute infectious endophthalmitis after pars plana vitrectomy (PPV) in eyes that received intraoperative subconjunctival antibiotics versus eyes that did not.

Methods:
A retrospective, nonrandomized, comparative case series of 18,886 consecutive cases of transconjunctival 23-, 25-, and 27-gauge PPV over a 5-year period was performed. The impact of prophylactic intraoperative subconjunctival antibiotics on the development of acute infectious postoperative endophthalmitis was examined.

Results:
Of 18,886 cases of PPV, 14,068 (74.5%) received intraoperative subconjunctival antibiotics, whereas 4,818 (25.5%) did not. Sixteen cases (0.085%, 1/1,176) of post-PPV endophthalmitis were identified. The incidence of endophthalmitis in eyes that received subconjunctival antibiotics was 0.078% (11/14,068 cases, 1/1,282), whereas the incidence in those that did not receive subconjunctival antibiotics was 0.10% (5/4,818 cases, 1/1,000). No statistically significant difference was identified in the incidence of endophthalmitis between those that received subconjunctival antibiotics and those that did not (P = 0.598). Microbial culture was performed in 11 cases with 6 culture-positive cases (5/8 cases that received subconjunctival antibiotics and 1/3 cases that did not).

Conclusion:
Prophylactic subconjunctival antibiotics were not associated with a significantly reduced rate of post-PPV endophthalmitis. With consideration of emerging multidrug-resistant bacteria, routine prophylactic subconjunctival antibiotics may not be justified.
Safety and Efficacy of Oki Stenting Used to Treat Obstructions in the Right Mainstem Bronchus
Authors: Dalar Levent , Abul Yasin 
Published: April 2018

Background:
Silicone stenting has been used to palliatively manage respiratory symptoms in patients with airway stenoses. Oki and Saka recently developed stents that can be used to manage stenoses around the carina between the bronchus to the right upper lobe and the bronchus intermedius (termed the primary right carina). The aim of this study was to assess the efficacy and safety of Oki stenting used to treat airway stenosis around the primary right carina.

Methods:
We included 5 patients with airway stenoses. All Oki stenting procedures were performed with the patients under general anesthesia using either rigid or flexible bronchoscopy.

Results:
Oki stents were successfully placed in all 5 patients, and the dyspnea index improved in all. Modified Oki stenting was performed at the anastomotic site of 1 patient who had undergone sleeve resection. Four patients had airway obstructions caused by malignant disease. No serious procedural or early complication was noted. One patient died of liver insufficiency, and another with a malignancy died from cranial metastasis of the primary tumor.

Conclusion:
Oki stenting of the primary right carina is safe, efficient, and acceptable when used for palliative management of airway obstruction, even after sleeve resection; in the latter case, some procedural modifications are required.
Bending of an Aspirated Pin During Rigid Bronchoscopy
Authors: Elsayed Abdelrahman A.A. , Mansour Albaraa A. , Amin Ahmed A.A. , Ahmed Mohsen S.M. 
Published: April 2018

Background:
Pin aspiration is a common problem in Muslim countries, where many women wear veils (hijab). This condition is usually treated using either a rigid or a flexible bronchoscope, and yet occasionally requires surgical approach. Pin bending may be necessary to extract impacted pins during the therapeutic rigid bronchoscopy.

Methods:
Medical records of patients who had pins extracted with a bending technique during the period from January 2012 to December 2016 in 1 institution were analyzed. Information on intraoperative and postoperative complications was collected.

Results:
Between 2012 and 2016, 315 rigid bronchoscopies were performed for pin extraction; in 38 cases, bending of the pin was required for the extraction because they were in a position that did not allow simple extraction. The procedure was successful in cases and there were no major complications.

Conclusion:
The extraction of visible, distally located or impacted pins can be safely performed by experienced bronchoscopists using the bending technique. Some safeguards and pitfalls must be noted to ensure maximum safety.
Tenofovir Versus Entecavir for the Treatment of Acute-on-Chronic Liver Failure due to Reactivation of Chronic Hepatitis B With Genotypes B and C
Authors: Wan Yue-Meng , Li Yu-Hua , Xu Zhi-Yuan , Wu Hua-Mei , Xu Ying , Wu Xi-Nan , Yang Jin-Hui 
Published: April 2018

Background and Aims:
Acute-on-chronic liver failure (ACLF) can be triggered by reactivation of chronic hepatitis B (CHB). Tenofovir disoproxil fumarate (TDF) and entecavir (ETV) are now the most potent antiviral agents for CHB. This study aimed to compare the short-term safety and efficacy of TDF with ETV in the treatment of ACLF due to reactivation of CHB [hepatitis B virus (HBV)-ACLF].

Patients and Methods:
In total, 67 consecutive patients with HBV-ACLF were divided into TDF group (n=32) receiving daily TDF (300 mg/d) and ETV group (n=35) receiving daily ETV (0.5 mg/d). They were prospectively followed-up and the primary endpoint was overall survival at 3 months.

Results:
At 2 weeks, the TDF group had significantly higher HBV-DNA reduction (P=0.003), lower HBV-DNA level (P=0.001), higher rate of HBV-DNA undetectbility (P=0.007), lower Child-Turcotte-Pugh (CTP; P=0.003), and model for end-stage liver disease (P=0.002) scores than the ETV group. At 3 months, HBV-DNA was undetectable in all survived patients; CTP (P=0.970) and model for end-stage liver disease (P=0.192) scores were comparable between the 2 groups, but markedly lower than at baseline (P<0.01); the TDF group had significantly higher cumulative survival rate than the ETV group (P=0.025). The white blood cell count (hazard ratio, 2.726; 95% confidence interval, 2.691-7.897; P=0.000), and HBV-DNA reduction (hazard ratio, 0.266; 95% confidence interval, 0.033-0.629; P=0.013) at 2 weeks were independent predictors for mortality. Both drugs were well tolerated.

Conclusions:
The short-term efficacy of TDF was superior to ETV for the treatment of HBV-ACLF. The white blood cell count and HBV-DNA reduction at 2 weeks were independent predictors for mortality at 3 months.
Psychiatric Services and “the Homeless”
Authors: Glick Ira D. , Olfson Mark 
Published: April 2018

Abstract
Given the changes in our society and worldwide massive migrations across borders, this article argues that we need to change the paradigm of how we think about “the homeless,” that is, to rethink our approach to not only those who cannot afford housing, the “economically homeless,” but especially important also the larger group—those with chronic, serious medical-psychiatric-addictive disorders, the “medically/mentally ill homeless.” We must place a greater emphasis on providing mental health services along with housing, legal, general medical, employment, and other services. The first and most crucial step toward adequate care is to understand these individuals and their lives as well as how we react to them. Second, we must become more proactive in helping those who live on the streets to receive adequate and coordinated services. And finally, for those who are unable to live independently in the community, we need to reinvent long-term, structured, humane residential, and inpatient settings.