bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and application of a high throughput natural language processing architecture to convert all clinical documents in a clinical data warehouse into standardized medical vocabularies
Authors: Afshar Majid , Dligach Dmitriy , Sharma Brihat , Cai Xiaoyuan , Boyda Jason , Birch Steven , Valdez Daniel , Zelisko Suzan , Joyce Cara , Modave François , Price Ron 
Published: April 2019

Abstract

Objective
Natural language processing (NLP) engines such as the clinical Text Analysis and Knowledge Extraction System are a solution for processing notes for research, but optimizing their performance for a clinical data warehouse remains a challenge. We aim to develop a high throughput NLP architecture using the clinical Text Analysis and Knowledge Extraction System and present a predictive model use case.

Materials and Methods
The CDW was comprised of 1 103 038 patients across 10 years. The architecture was constructed using the Hadoop data repository for source data and 3 large-scale symmetric processing servers for NLP. Each named entity mention in a clinical document was mapped to the Unified Medical Language System concept unique identifier (CUI).

Results
The NLP architecture processed 83 867 802 clinical documents in 13.33 days and produced 37 721 886 606 CUIs across 8 standardized medical vocabularies. Performance of the architecture exceeded 500 000 documents per hour across 30 parallel instances of the clinical Text Analysis and Knowledge Extraction System including 10 instances dedicated to documents greater than 20 000 bytes. In a use–case example for predicting 30-day hospital readmission, a CUI-based model had similar discrimination to n-grams with an area under the curve receiver operating characteristic of 0.75 (95% CI, 0.74–0.76).

Discussion and Conclusion
Our health system’s high throughput NLP architecture may serve as a benchmark for large-scale clinical research using a CUI-based approach.
The Galician Paradigm? Post-war Voices of German-Speaking Polish Jewish Survivors1
Authors: Aleksiun Natalia 
Published: April 2019

Abstract
This paper examines the experience of Galician-Jewish survivors who were fluent in German and who had developed close ties to German culture before the Second World War. It suggests that looking through the German linguistic lens highlights the multilayered nature of Jewish cultural identity in Galicia and offers an important critical tool with which to understand the distinct ways in which Galician Jews experienced the Holocaust. Using personal accounts, this article analyzes the ways in which complex cultural biographies of Galician Jews shaped their identities as eastern European Jews, Polish citizens, and Holocaust survivors. On the basis of testimonies included in early accounts for the Jewish historical commissions, statements by Jewish witnesses in post-war trials, oral interviews, and memoirs, this article discusses the ways in which Galician Jews remembered their relationship with German culture and how their complex cultural identity shaped their personal trajectories after the liberation.
Simulations and difficult problems
Authors: Hoover David L 
Published: April 2019

AbstractAn authorship attribution investigation ideally begins with a well-defined set of possible authors and an adequate number of firmly attributed roughly contemporaneous long texts in the same genre by those authors. Many significant or intriguing problems, however, suffer from deficiencies or limitations that reduce the effectiveness or validity of some kinds of analysis and make others impossible. These problematic situations can be approached by creating simulations that are designed to overcome or mitigate the difficulties of the problems. The results of the simulations can be used to suggest at least tentative solutions. Here, simulations are used to investigate four difficult problems. One involves fewer and shorter texts than would be ideal–texts that are also chronologically earlier than the known texts by the target author. The second involves too small a number of well attributed texts by the authors in question, and initial uncertainty about the genres of the texts, the number of authors involved, and their genders. The third is a tricky case of co-authorship with only relatively vague and uncertain evidence about the nature and extent of each author’s contribution; here simulations with sections of well-attributed texts by the two authors are used to test Rolling Classify. The fourth addresses the sparsity of well-attributed and confidently-dated Early Modern plays, using simulations to evaluate Brian Vickers’ rare n-gram approach to the attribution of such plays.
Molecular Evolution in Large Steps—Codon Substitutions under Positive Selection
Authors: Chen Qingjian , He Ziwen , Lan Ao , Shen Xu , Wen Haijun , Wu Chung-I 
Published: April 2019

AbstractMolecular evolution is believed to proceed in small steps. The step size can be defined by a distance reflecting physico-chemical disparities between amino acid (AA) pairs that can be exchanged by single 1-bp mutations. We show that AA substitution rates are strongly and negatively correlated with this distance but only when positive selection is relatively weak. We use the McDonald and Kreitman test to separate the influences of positive and negative selection. While negative selection is indeed stronger on AA substitutions generating larger changes in chemical properties of AAs, positive selection operates by different rules. For 65 of the 75 possible pairs, positive selection is comparable in strength regardless of AA distance. However, the ten pairs under the strongest positive selection all exhibit large leaps in chemical properties. Five of the ten pairs are shared between Drosophila and Hominoids, thus hinting at a common but modest biochemical basis of adaptation across taxa. The hypothesis that adaptive changes often take large functional steps will need to be extensively tested. If validated, molecular models will need to better integrate positive and negative selection in the search for adaptive signal.
Increased mortality risk associated with serum sodium variations and borderline hypo- and hypernatremia in hospitalized adults
Authors: Thongprayoon Charat , Cheungpasitporn Wisit , Yap John Q , Qian Qi 
Published: April 2019

Abstract

Background
This study aimed to evaluate short-term and long-term mortalities in a cohort of unselected hospitalized patients with serum sodium concentration ([Na+]) variations within and outside of reference range.

Methods
All adult patients admitted to the Mayo Clinic, Rochester, MN, USA from January 2011 to December 2013 (n = 147358) were retrospectively screened. Unique patients admitted during the study period were examined. The main exposure was serum [Na+] variation. Outcome measures were hospital and 1-year all-cause mortalities.

Results
A total of 60944 patients, mean age 63 ± 17 years, were studied. On admission, 17% (n = 10066) and 1.4% (n = 852) had hypo- and hypernatremia, respectively. During the hospital stay, 11044 and 4128 developed hypo- and hypernatremia, respectively, accounting for 52.3 and 82.9% of the total hypo- and hypernatremic patients. Serum [Na+] variations of ≥6 mEq/L occurred in 40.6% (n = 24 740) of the 60 944 patients and were significantly associated with hospital and 1-year mortalities after adjusting potential confounders (including demographics, comorbidities, estimated glomerular filtration rate, admission serum [Na+], number of [Na+] measurements and length of hospital stay). Adjusted odds ratios for hospital and 1-year mortalities increased with increasing [Na+] variations in a dose-dependent manner, from 1.47 to 5.48 (all 95% confidence intervals &gt;1.0). Moreover, in fully adjusted models, [Na+] variations (≥6 mEq/L) within the reference range (135–145 mEq/L) or borderline hypo- or hypernatremia (133–137 and 143–147 mEq/L, respectively) compared with 138–142 mEq/L were associated with increased hospital and 1-year mortalities.

Conclusion
In hospitalized adults, [Na+] fluctuation (≥6 mEq/L) irrespective of admission [Na+] and borderline hypo- or hypernatremia are independent predictors of progressively increasing short- and long-term mortality burdens.
Inequality and its discontents
Authors: Nolan Brian , Valenzuela Luis 
Published: April 2019

AbstractInequality in the distribution of income and wealth has come to the fore as a core concern across the industrialized world. Here we examine what has happened to income inequality across the rich countries in recent decades. We discuss the range of factors that appear to be driving inequality upwards, notably the role of technological change, globalization, and national institutions and policies. We look at how rising inequality might undermine economic growth and squeeze the middle, and assess the extent to which it has actually done so. We assess whether rising inequality is associated with worsening outcomes and inequalities across various social domains. Finally, we review emerging evidence on the role that rising inequality may be playing in the ‘revolt of the angry’ and rise of populism.
Explaining local variation in referrals from health services to children’s social care in England 2013–16: a study using ‘children in need’ administrative data
Authors: Emmott E H , Mc Grath-Lone L , Harron K , Woodman J 
Published: April 2019

Abstract

Background
Referral rates from Health service to Children’s Social Care (CSC) services vary across England. In 2019, the National Audit Office (re)iterated the urgent need to understand the drivers of such variation.

Methods
Using administrative data (Children in Need Census, 2013–16), we calculated annual referral rates from Health to CSC services (Health referral rate) by Local Authority (LA) areas. We used multilevel linear regression to investigate the relationship between age-adjusted Health referral rates and local need (demand factors) and local practice/systems (supply factors). We present a tool to compare unadjusted and adjusted LA rates.

Results
There was high LA variation in Health referral rates, particularly for infants (mean = 29.0/1000 children &lt; 1 y; range = 6.5–101.8; sd = 12.4). LA variation persisted after age-adjustment. Child poverty (local need) and overall referral rate (local practice/systems) explained 60% of variation in age-adjusted Health referral rates. Overall referral rate was the strongest predictor. Adjusted referral rates were substantially different from unadjusted rates. After adjustment, 57.7% of LAs had higher/lower Health referral rates than expected.

Conclusions
While higher levels of local need are associated with higher Health referrals, some areas have high Health referrals irrespective of local need. Our tool demonstrates the benefits of using adjusted rates to compare LAs.
Association of smokeless tobacco and cerebrovascular accident: a systematic review and meta-analysis of global data
Authors: Gupta R , Gupta S , Sharma S , Sinha D N , Mehrotra R 
Published: April 2019

Abstract

Background
The association of smokeless tobacco (SLT) with stroke has been dealt with in only a few reviews. The present meta-analysis aims to present the updated comprehensive summary risk of stroke in adult SLT users along with sub group analysis.

Methods
A systematic literature search for articles evaluating risk of stroke in SLT users was conducted. The study characteristics and risk estimates were extracted independently by two authors (RG and SG). Random-effect model was used to estimate the summary relative risks.

Results
The overall risk of stroke in SLT users was found to be significantly higher (1.17, 95% CI 1.04–1.30) compared to non-users, especially for users in Southeast Asian region. The results remained unchanged even after strict adjustment for smoking (1.18, 95% CI 1.04–1.32). SLT users had 1.34 times or 13.4% higher risk of fatal stroke, though risk of nonfatal stroke was not enhanced. Significantly higher risk of stroke was seen in users of chewing tobacco (1.35, 95% CI 1.20–1.50) in comparison to non-chewers. Gender-based analysis showed enhanced risk of fatal stroke in both male and female users. SLT-attributable fraction of fatal stroke was highest for India at 14.8%.

Conclusion
The significant higher risk of stroke with SLT use, even after adjustment for smoking, emphasizes the imperative need to include SLT cessation advice for control and prevention of stroke.
Increased Reactivity of the Mesolimbic Reward System after Ketamine Injection in Patients with Treatment-resistant Major Depressive Disorder
Authors: Sterpenich Virginie , Vidal Sonia , Hofmeister Jeremy , Michalopoulos Giorgio , Bancila Victor , Warrot Delphine , Dayer Alexandre , Desseilles Martin , Aubry Jean-Michel , Kosel Markus , Schwartz Sophie , Vutskits Laszlo 
Published: April 2019

Abstract

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New

Background
Ketamine rapidly improves maladaptive mood states in major depressive disorder, and some of the neural substrates underlying this therapeutic effect have been identified. This study aimed to identify functional changes within neural networks that may underlie the impact of ketamine on both reward and emotional processing in patients with treatment-resistant major depression.

Methods
Ten adult patients with a Montgomery–Åsberg Depression Rating Scale score above 25 were enrolled to receive a single intravenous administration of ketamine (0.5 mg/kg). Patients’ performance along with related neural network activations were analyzed in a game-like reward task and in an emotional judgment task using functional magnetic resonance imaging 1 day before and 1 and 7 days after ketamine administration.

Results
A significant correlation (R
2 = 0.46, P = 0.03) between the improvement of depression scores and the enhanced reaction time for positive items was found in the game-like reward task 1 day after ketamine administration. This enhanced sensitivity for rewarded items was accompanied by increased activity of reward-related brain regions, including the orbitofrontal cortex, ventral striatum, and the ventral tegmental area, an effect that persisted up to 1 week after ketamine injection. In the emotional judgment task, it was found that ketamine rapidly modified local brain activities in response to emotionally negative, positive, or neutral stimuli in the amygdala, insula, anterior cingulate cortex, and in the ventral tegmental area.

Conclusions
Single bolus ketamine administration rapidly triggers lasting changes in mesolimbic neural networks to improve pathologic reward and emotional processing in patients with major depressive disorder.
Iontophoretic Transepithelial Collagen Cross-Linking Versus Epithelium-Off Collagen Cross-Linking in Pediatric Patients: 3-Year Follow-Up
Authors: Buzzonetti Luca , Petrocelli Gianni , Valente Paola , Iarossi Giancarlo , Ardia Roberta , Petroni Sergio , Parrilla Rosa 
Published: April 2019

Purpose:
To compare 3-year iontophoretic transepithelial corneal cross-linking (I-ON CXL) outcomes with epithelium-off collagen cross-linking (epi-off CXL) in pediatric patients.

Methods:
Forty eyes of 28 consecutive pediatric patients [mean age 14.3 ± 2.5 (SD) years; range, 9–18 years] with keratoconus were evaluated. Twenty eyes of 15 patients underwent I-ON and 20 eyes of 13 patients epi-off CXL. Mean corrected distance visual acuity, spherical equivalent, maximum keratometry (Kmax), posterior elevation of the thinnest point, and thickness of the thinnest point were evaluated. The Student t test was used to compare baseline and postoperative data. Keratoconus progression as a function of preoperative Kmax and cone location was evaluated.

Results:
At 36 months, corrected distance visual acuity statistically improved (from 0.18 ± 0.1 to 0.10 ± 0.1 logarithm of the minimum angle of resolution) in epi­off CXL, whereas spherical equivalent and posterior elevation of the thinnest point did not significantly change. Mean Kmax increased from the baseline +0.8 diopters (D) in epi-off and +2.9D in I-ON. In both groups, the thinnest point decreased. Keratoconus progression, defined by an increase of Kmax reading of the anterior corneal surface of at least 1.00D, occurred in 25% of epi-off and 50% of I-ON CXL over the 3-year period. Kmax value in I-ON, and cone location in both groups, seemed to be factors influencing the disease progression.

Conclusions:
In pediatric patients, 3 years after treatment, epi-off CXL halted keratoconus progression in 75% of eyes, whereas I-ON CXL seemed to slow down keratoconus progression in 50% of eyes, mainly in those with highest Kmax and paracentral cone.
Inconsistency Between Contrast-Enhanced CT and Bone Scintigraphy in Revealing Radiation Nephritis
Authors: Zhu Wenjia , Zhen Hongnan , Ding Ning , Jing Hongli , Huo Li 
Published: April 2019

Abstract
A 34-year-old woman with pancreatic acinar cell carcinoma underwent a 99mTc-MDP bone scan to rule out potential bone metastasis because of back pain 18 months after radiation therapy. The bone scintigraphy revealed increased uptake over the upper pole of both kidneys corresponding to the portions of the kidneys included within the radiation field, consisting with radiation nephritis.
Synchronous Paraganglioma Masquerading as 68Ga-PSMA PET/CT–Avid Metastasis in Carcinoma Prostate—How Specific Is 68Ga-PSMA PET/CT?
Authors: Tyagi Shantanu , Singh Shrawan Kumar , Narain Tushar Aditya , Singh Harmandeep , Kumar Rajender , Vadi Shelvin Kumar 
Published: April 2019

Abstract
We present a case of biopsy-proven prostatic adenocarcinoma with a tracer-avid left paravertebral location at D4 to D5 vertebrae, suggestive of metastasis. However, in view of uncommon location of single-site metastasis at paravertebral region with no tracer-avid regional lymphadenopathy, image-guided biopsy was done, which was suggestive of paraganglioma. 68Ga-PSMA is known to have variable tracer avidity in multiple nonprostatic benign as well as malignant lesions, and our case adds to the list of nonspecific uptake by this once considered “specific” to prostate PET radiotracer.
Alloreactive T Cells Display a Distinct Chemokine Profile in Response to Conditioning in Xenogeneic GVHD Models
Authors: Kawasaki Yasufumi , Sato Kazuya , Nakano Hirofumi , Hayakawa Hiroko , Izawa Junko , Takayama Norihito , Mashima Kiyomi , Oh Iekuni , Minakata Daisuke , Yamasaki Ryoko , Morita Kaoru , Ashizawa Masahiro , Yamamoto Chihiro , Hatano Kaoru , Fujiwara Shin-ichiro , Ohmine Ken , Muroi Kazuo , Ito Ryoji , Hayakawa Morisada , Ohmori Tsukasa , Kanda Yoshinobu 
Published: April 2019

Background.
Chemokines and chemokine receptors are potential targets for the prevention and treatment of graft-versus-host disease (GVHD). The objective of the current study is to determine the clinical relevance of xenogeneic transplantation models in terms of host and donor chemokine profiles and, if this is the case, to assess the clinical efficacy of C–C chemokine receptor (CCR) 5 antagonist maraviroc for the prevention of GVHD using this model.

Methods.
Xenogeneic GVHD was induced by intravenous injection of 5 × 106 human pan T cells into NOD/Shi-scid-IL2rγ
null
(NOG) mice or MHC class I/II-deficient NOG mice in the presence or absence of total body irradiation before transplantation.

Results.
Extensive tissue destruction with human T-cell infiltration was observed throughout the body, particularly in lungs and liver, but relatively mild in gut. Consistent with this finding, quantitative polymerase chain reaction confirmed the upregulation of mouse CXC chemokine ligand (CXCL) 9 and CXCL10 in lungs and CCL4 in lungs and liver but not in gut. The addition of total body irradiation (1) led to the early release of mouse CCL4 and CXCL10, (2) upregulated a number of chemokine-related genes in human T cells, (3) induced higher expression of CCR5 on human CD4+ and CD8+ T cells and CXCR3 on human CD4+ T cells, and (4) promoted their migration and proliferation in organs, resulting in more severe tissue damage. In this context, pharmacological CCR5 blockade neither ameliorated GVHD nor prolonged survival in NOG mice.

Conclusions.
Our experimental data do not demonstrate clinical benefit of CCR5 antagonist for the prevention of GVHD in a myeloablative setting.
Impact of Induction Immunosuppression Strategies in Simultaneous Liver/Kidney Transplantation
Authors: Kamal Layla , Yu Jonathan W. , Reichman Trevor W. , Kang Le , Bandyopadhyay Dipankar , Kumar Dhiren , King Anne , Gautam Ujwal , Bhati Chandra , Yakubu Idris , Lacy Kevin , Levy Marlon , Gupta Gaurav 
Published: April 2019

Background.
There is scant data on the use of induction immunosuppression for simultaneous liver/kidney transplantation (SLKT).

Methods.
We analyzed the Organ Procurement and Transplant Network registry from 1996 to 2016 to compare outcomes of SLKT, based on induction immunosuppression.

Results.
Of 5172 patients, 941 (18%) received T-cell depletion induction, 1635 (32%) received interleukin 2 receptor antagonist (IL2-RA), and 2596 (50%) received no induction (NI). At 5 years, patient survivals were 68% in the T-cell group, 74% in the IL2-RA group, and 71% in the NI group (P = 0.0006). Five-year liver and kidney allograft survivals were 67% and 64% in the T-cell group, 73% and 70% in the IL2-RA group, and 70% and 68% in the NI group (P = 0.001 and 0.003), respectively. On multivariate analysis, the type of induction had no impact on patient or allograft survival. Maintenance steroids and calcineurin inhibitors (CNIs) at discharge were associated with improved patient and graft survival (steroids: patient survival hazard ratio [HR] 0.37 [0.27–0.52], liver survival HR 0.43 [0.31–0.59], kidney survival HR 0.46 [0.34–0.63]; P < 0.0001, CNI: patient survival HR 0.3 [0.21–0.43], liver survival HR 0.3 [0.2–0.44], kidney survival HR 0.4 [0.26–0.59]; P < 0.0001). CNI maintenance in patients who received T-cell induction was associated with decreased patient, liver, and kidney allograft survivals (respective HR: 1.4 [1.1, 1.8]; 1.5 [1.1, 1.9]; 1.3 [1.08, 1.7]; P < 0.05)

Conclusion.
Induction immunosuppression had no impact on patient and allograft survival in SLKT, while maintenance steroids and CNI were associated with improved patient and graft survivals. Given the inherent limitations of a registry analysis, these findings should be interpreted with caution.