bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased Leucocyte–Platelet Complex Formation in Recently Symptomatic versus Asymptomatic Carotid Stenosis Patients and in Micro-emboli Negative Subgroups
Authors: Murphy Stephen , Lim Soon , Kinsella Justin , Tierney Sean , Egan Bridget , Feeley T. , Murphy Sinead , Walsh Richard , Collins D. , Coughlan Tara , O'Neill Desmond , Harbison Joseph , Madhavan Prakash , O'Neill Sean , Colgan Mary , Cox Dermot , Moran Niamh , Hamilton George , McCabe Dominick 
Published: February 2019

Introduction Cerebral micro-embolic signals (MES) predict risk of stroke in carotid stenosis patients. However, MES-negative ‘recently symptomatic patients’ also have a higher stroke risk than ‘asymptomatic patients’. Differences in platelet activation status may contribute to this disparity in risk.
Methods This prospective, observational study assessed platelet biomarkers and their relationship with MES in asymptomatic versus symptomatic moderate (≥50–69%) or severe (≥70–99%) carotid stenosis patients. Full blood count parameters were measured and whole-blood flow cytometry was used to quantify platelet surface CD62P and CD63 expression and leucocyte–platelet complex formation. Bilateral simultaneous transcranial Doppler ultrasound of the middle cerebral arteries classified patients as ‘MES positive’ or ‘MES negative’.
Results Data from 34 asymptomatic patients were compared with those from 43 symptomatic patients in the ‘early phase’ (≤ 4 weeks) and 37 of these symptomatic patients in the ‘late phase’ (≥ 3 months) after transient ischaemic attack/ischaemic stroke. There were no differences in %CD62P or %CD63 expression between early or late symptomatic and asymptomatic patients overall (p > 0.05). The percentage of lymphocyte–platelet complexes was higher in early symptomatic than in asymptomatic patients (2.8 vs. 2.16%; p < 0.001). MES were more commonly observed in early symptomatic (31.4%; p = 0.027) but not in late symptomatic (6.7%; p = 0.996) versus asymptomatic patients (7.1%). The percentage of lymphocyte–platelet complexes was higher in early symptomatic than in asymptomatic MES-negative patients (2.7 vs. 2.17%; p = 0.02).
Conclusion These data add to the evidence that leucocyte–platelet complex formation/platelet activation is increased in recently symptomatic versus asymptomatic patients, and may contribute to the pathogenesis of first and subsequent strokes in carotid stenosis patients, including those who are MES negative.
Generalizing the effects of chirality on block copolymer assembly
Authors: Wang Hsiao-Fang , Yang Kai-Chieh , Hsu Wen-Chun , Lee Jing-Yu , Hsu Jung-Tzu , Grason Gregory M. , Thomas Edwin L. , Tsai Jing-Cherng , Ho Rong-Ming 
Published: February 2019

Significance
Chirality is a measure of asymmetry that is important in many branches of science. Homochiral evolution at different length scales is critical for molecular processes in nature (such as communication, replication, and enzyme catalysis) that rely on a delicate balance between molecular and conformational chirality and, most importantly, control the nature of the self-assembly of superstructures of constituent molecules. Here, we compare the homochiral evolution from molecular, to intrachain, to interchain, and, ultimately, to mesodomain chirality from the self-assembly of a pair of block copolymers possessing a chiral block that exhibits one of the two different stereochemistries. The comparison sheds light on the physical mechanisms that link chiral structure across these length scales in this prototypical class of self-assembling materials.
A humanitarian disaster or invasion of Europe?
Authors: Koca-Helvacı Zeynep Cihan 
Published: February 2019

Abstract
This study sought to find out how language resources were employed to reflect the changing media attitude towards immigrants during the 2015 Migrant Crisis. Combining relevant analytical categories of the Socio-Cognitive Approach (Van Dijk 1991), the Discourse-Historical Approach (Wodak 2001) and the Social Actor Analysis (van Leeuwen 2008) with Corpus Linguistic techniques, it compared the British media coverage of two critical cases; the Death of Aylan Kurdi, and the Cologne Sexual Assaults. The findings show that in both cases, regardless of news content, immigration was problematized as a crisis, controversy, and catastrophe. The scale of the tragedy and the possibility of an immigrant influx to the UK deeply influenced the media representation of the immigrants.
The great wall of Europe
Authors: Silaški Nadežda , Đurović Tatjana 
Published: February 2019

Abstract
Complementing the theoretical framework of Critical Metaphor Analysis (Charteris-Black 2004; Musolff 2004, 2011) with research on multimodality from a cognitive viewpoint (Bounegru and Forceville 2011), in this chapter we deal with both linguistic and multimodal instantiations of the wall metaphor in Serbian media texts published in 2015 in an attempt to identify the most frequent metaphor scenarios modelled around this concept in a critical period during the European migrant crisis. Two major metaphor scenarios (Musolff 2006) triggered by the wall metaphor arise – fortress europe and berlin wall, both appearing to be instrumental in communicating the notions of marginalisation and non-belongingness to the EU space, emanating from verbally and visually constructed image of both migrants and the Serbian nation.
Expressing ‘possession’
Authors: Aikhenvald Alexandra Y. 
Published: February 2019

Abstract
Competing motivations are often at work in the choice of form and meaning of possessive and associative noun phrases. The article offers a broad typological review of the ways of expressing possession at the NP-internal level. In particular, it discusses how iconicity and economic motivations interact in determining the shape of NP-internal possessive expressions, also addressing the topics of how socio-cultural factors affect the grammar of possession and how societal changes are reflected in language variation.
Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data
Authors: Rashid Sabrina , Shah Sohrab , Bar-Joseph Ziv , Pandya Ravi 
Published: February 2019

Abstract

Motivation
Intra-tumor heterogeneity is one of the key confounding factors in deciphering tumor evolution. Malignant cells exhibit variations in their gene expression, copy numbers and mutation even when originating from a single progenitor cell. Single cell sequencing of tumor cells has recently emerged as a viable option for unmasking the underlying tumor heterogeneity. However, extracting features from single cell genomic data in order to infer their evolutionary trajectory remains computationally challenging due to the extremely noisy and sparse nature of the data.

Results
Here we describe ‘Dhaka’, a variational autoencoder method which transforms single cell genomic data to a reduced dimension feature space that is more efficient in differentiating between (hidden) tumor subpopulations. Our method is general and can be applied to several different types of genomic data including copy number variation from scDNA-Seq and gene expression from scRNA-Seq experiments. We tested the method on synthetic and six single cell cancer datasets where the number of cells ranges from 250 to 6000 for each sample. Analysis of the resulting feature space revealed subpopulations of cells and their marker genes. The features are also able to infer the lineage and/or differentiation trajectory between cells greatly improving upon prior methods suggested for feature extraction and dimensionality reduction of such data.

Availability and implementation
All the datasets used in the paper are publicly available and developed software package and supporting info is available on Github https://github.com/MicrosoftGenomics/Dhaka.

Supplementary information
Supplementary data are available at Bioinformatics online.
Ultrasonographic Evaluation of Gastric Contents in Term Pregnant Women Fasted for 6 Hours
Authors: Hakak S. , McCaul C.L. , Crowley L. 
Published: February 2019

(Int J Obstet Anesth. 2018;34:15–20)
Fasting before elective anesthesia is intended to reduce gastric fluid volume and the risk of aspiration of gastric contents leading to aspiration pneumonitis, which can be life-threatening. Pregnant women are considered to be at increased risk of pulmonary aspiration due to some of the physiological changes of pregnancy, including relaxation of the lower esophageal sphincter and the upward displacement of the stomach by the gravid uterus. Current fasting guidelines vary among national anesthesiology organizations with most recommending at least 6 hours of fasting after a light meal and some suggesting 6 to 8 hours of fasting depending on the type of food consumed before anesthesia for elective procedures. This current prospective study was undertaken to analyze the stomach contents of nonlaboring term pregnant women after 6 hours of fasting, using ultrasonographic assessments.
Applying Surgical Antimicrobial Standards in Cesarean Deliveries
Authors: Fay K.E. , Yee L. 
Published: February 2019

(Am J Obstet Gynecol. 2018;218(4):416.e1–416.e4)
Surgical site infections are costly and common in the United States. Most surgical guidelines for antimicrobial prophylaxis endorse repeat antibiotic administration after an estimated blood loss (EBL) of 1500 mL or following 1 to 2 half-lives of the agent. The American College of Obstetricians and Gynecologists have not made recommendations for redosing antibiotics in obstetric surgeries, and currently a single dose of preoperative antibiotics is considered standard of care. Parturients have increased renal clearance and may benefit from antimicrobial redosing.
Ethical Problems in Decision Making in the Neonatal ICU
Authors: Lantos J.D. 
Published: February 2019

(N Engl J Med. 2018;379:1851–1860)
Disagreements regarding life-sustaining treatments in the neonatal intensive care unit (NICU) are not uncommon, especially when parental requests conflict with doctor recommendations. Cases that are intractable often end up in court, where outcomes can vary depending on state statutes. Ethicists have developed a general framework, first articulated in 1983, for balancing the child’s interest with the scope of parental authority. When benefits of treatment are clear, the baby’s right to treatment outweighs parental rights. When benefits of treatment are less clear, ethicists and courts often defer to parental choice. Nevertheless, gray zones still exist in conflict resolution. A new approach, emerging in the early 2000s, proposes that rather than only providing detailed, objective information, doctors help parents discern their own values and ethical commitments in these unanticipated situations. In this review, the author discussed this shift in approach and how advances in both prenatal diagnosis and neonatal therapeutics can change treatments and perspectives in the NICU.
A 36-Year-Old Pregnant Woman With Newly Diagnosed Adenocarcinoma
Authors: Murphy J.E. , Shampain K. , Riley L.E. , Clark J.W. , Basnet K.M. 
Published: February 2019

(N Engl J Med. 2018;379:1562–1570)
A 36-year-old pregnant woman was evaluated at 33 weeks gestation because of newly diagnosed adenocarcinoma. At 32 weeks’ admission, the patient had presented to another hospital with a history of 3 days of nonradiating, severe pain accompanied by nausea in her lower back that rated 10 on a scale of 10 and originated in the epigastric region and migrated to the upper right quadrant and lower back. On examination, there was tenderness in the right upper quadrant. The gravid uterus was soft, and no abnormal fetal findings were observed. An incidental finding of renal ultrasonography showed the liver to be diffusely heterogenous and nodular, and to contain numerous masses. Abdominal magnetic resonance imaging without contrast revealed multiple lesions in the liver, some with central necrosis and with the largest being 7.4×3.9 cm. Computed tomography also revealed multiple hypoattenuating hepatic lesions, with the largest measuring 8.2 cm in diameter, with the presence of multiple enlarged periaortic and portocaval lymph nodes. Percutaneous liver biopsy revealed metastatic adenocarcinoma, poorly differentiated with widespread involvement of the liver and lymph nodes. Plans for chemotherapy and early fetal delivery were discussed with the patient, but at 32 weeks’ gestation, the patient left the first hospital because she thought her pain was undertreated and she and her spouse wanted to identify the primary cancer, understand treatment options, and obtain adequate pain relief. She presented to a second hospital at 33 weeks gestation, with continued ongoing severe back pain. No vaginal bleeding or contractions were found, and fetal movement was detectable in the gravid uterus.
Anaplastic Lymphoma Kinase (ALK)-positive Tumors
Authors: Gupta Rohan , Amanam Idoroenyi , Rahmanuddin Syed , Mambetsariev Isa , Wang Yingyu , Huang Charity , Reckamp Karen , Vora Lalit , Salgia Ravi 
Published: February 2019

Introduction:Anaplastic lymphoma kinase (ALK)gene rearrangements are observed in about 4% to 8% non–small cell lung cancer (NSCLC).ALK+ tumors have been associated with increased pleural and pericardial disease. Our primary objective was to determine the uncommon sites of metastasis ofALK+ NSCLC. Secondary objectives included study of coexisting mutations and factors impacting survival ofALK+ NSCLC.Methods:All patients with metastaticALK+ NSCLC at the City of Hope Cancer Center in Duarte, California from 2010 to 2017 were selected for retrospective chart review. The demographic variables were collected. The molecular statuses of patients were evaluated through commercially available platforms for next-generation sequencing. Three-dimensional volumetric images were generated for the primary lesion and different sites of metastasis.Results:Sixty two patients withALK+ NSCLC were identified from 2010 to 2017. The median age was 59 with 36 (58%) female individuals and only 20 (32%) smokers. Twenty four patients had uncommon sites of metastasis which were thyroid, soft tissue, chest and abdominal wall, spleen, peritoneum, omentum, kidney, and ovary. Common characteristics of the primary lesions were right upper lobe location (N=23 [37%]), oval shape (N=22 [35%]), irregular margins (N=26 [42%]), solid lesions (N=27 [44%]), presence of pleural contact or effusion (N=22 [35%]). Twenty four patients had next-generation sequencing testing which showed coexisting mutations such asTP53(N=8),EGFR(N=5),KRAS(N=3). Patients with uncommon sites of metastasis had a decreased median survival compared with common sites (39 vs. 82 m,P=0.046).Conclusion:In NSCLC,ALKrearrangements may not be mutually exclusive mutations and can present with unique radiographic patterns. Patients with uncommon sites of metastasis may have worse outcomes.
Early Routine Use of Upper GI Contrast Series Post Paraesophageal Hernia Repair: A Single Institution Consecutive Case Series
Authors: Robertson-More Connal , Prasad Shalvin , Gill Richdeep , Church Neal , Mitchell Philip , Debru Estifanos 
Published: February 2019

Introduction:
There is conflicting evidence with regard to the routine use of upper gastrointestinal contrast series in detecting early complications post paraesophageal hernia repair (PEHR).

Methods:
All cases booked for a PEHR between January 2007 and September 2015 were identified using hospital records. Standard demographic, operation, and imaging data were extracted.

Results:
We retrospectively identified 391 PEHR cases between January 2007 and September 2015. The mean age at the index operation was 66.7 years with a female predominance. The majority of index operations were elective and completed for a large paraesophageal hernia. Contrast studies were reported as normal in 70.6%, a leak in 0.3%, an obstruction in 27.9%, and early recurrence in 1.0%. Reoperation was required in 1.8% of cases.

Conclusion:
Routine upper gastrointestinal contrast studies post-PEHR changed management in 0.8% of cases and were unhelpful in determining the need for early reoperation in 57.1% of cases requiring reoperation.
Pediatric blunt renal trauma practice management guidelines: Collaboration between the Eastern Association for the Surgery of Trauma and the Pediatric Trauma Society
Authors: Hagedorn Judith C. , Fox Nicole , Ellison Jonathan S. , Russell Robert , Witt Cordelie E. , Zeller Kristen , Ferrada Paula , Draus John M. 
Published: February 2019

BACKGROUND
Injury to the kidney from either blunt or penetrating trauma is the most common urinary tract injury. Children are at higher risk of renal injury from blunt trauma than adults, but no pediatric renal trauma guidelines have been established. The authors reviewed the literature to guide clinicians in the appropriate methods of management of pediatric renal trauma.

METHODS
Grading of Recommendations Assessment, Development and Evaluation methodology was used to aid with the development of these evidence-based practice management guidelines. A systematic review of the literature including citations published between 1990 and 2016 was performed. Fifty-one articles were used to inform the statements presented in the guidelines. When possible, a meta-analysis with forest plots was created, and the evidence was graded.

RESULTS
When comparing nonoperative management versus operative management in hemodynamically stable pediatric patient with blunt renal trauma, evidence suggests that there is a reduced rate of renal loss and blood transfusion in patients managed nonoperatively. We found that in pediatric patients with high-grade American Association for the Surgery of Trauma grade III-V (AAST III-V) renal injuries and ongoing bleeding or delayed bleeding, angioembolization has a decreased rate of renal loss compared with surgical intervention. We found the rate of posttraumatic renal hypertension to be 4.2%.

CONCLUSION
Based on the completed meta-analyses and Grading of Recommendations Assessment, Development and Evaluation profile, we are making the following recommendations: (1) In pediatric patients with blunt renal trauma of all grades, we strongly recommend nonoperative management versus operative management in hemodynamically stable patients. (2) In hemodynamically stable pediatric patients with high-grade (AAST grade III-V) renal injuries, we strongly recommend angioembolization versus surgical intervention for ongoing or delayed bleeding. (3) In pediatric patients with renal trauma, we strongly recommend routine blood pressure checks to diagnose hypertension. This review of the literature reveals limitations and the need for additional research on diagnosis and management of pediatric renal trauma.

LEVEL OF EVIDENCE
Guidelines study, level III.
Non-motor effects of subthalamic nucleus stimulation in Parkinson’s patients
Authors: Sammartino Francesco , Marsh Rachel , Rezai Ali , Krishna Vibhor 
Published: February 2019

AbstractIntroductionThe existing white matter connectivity analyses of the subthalamic region have mainly included the motor effects of deep brain stimulation.We investigate white matter connectivity associated with the stimulation-induced non-motor acute clinical effects in three domains: mood changes, dizziness and sweating.MethodsUsing whole brain probabilistic tractography and seeding from the volumes of tissue activation, connectivity maps were generated and statistically compared across patients. The cortical voxels associated with each non-motor domain were compared with stimulation-induced motor improvements in a multivariate model. The resulting voxels maps were thresholded for false discovery (FDR q<0.05) and clustered using a multimodal atlas. To understand the role of local pathways in the subthalamic region, a group level parcellation was performed for each non-motor domain.ResultsThe non-motor effects are rarely observed during stimulation titration: from 1100 acute clinical effects, mood change was observed in 14, dizziness in 23, and sweating in 20. Distinct cortical clusters were associated with each domain, notably mood change was associated with voxels in salience network and dizziness with voxels in visual association cortex. The subthalamic parcellation yielded a medio-lateral gradient with motor parcel being lateral and the non-motor parcels being medial. We also observed an antero-posterior organization in the medial non-motor clusters with mood changes (anterior), dizziness and sweating (posterior).ConclusionWe interpret these findings based on the literature and foresee these to be useful for shaping the electrical field with the imminent use of steerable DBS electrodes.
Ohana: detecting selection in multiple populations by modelling ancestral admixture components
Authors: Cheng Jade Yu , Racimo Fernando , Nielsen Rasmus 
Published: February 2019

AbstractOne of the most powerful and commonly used methods for detecting local adaptation in the genome is the identification of extreme allele frequency differences between populations. In this paper, we present a new maximum likelihood method for finding regions under positive selection. The method is based on a Gaussian approximation to allele frequency changes and it incorporates admixture between populations. The method can analyze multiple populations simultaneously and retains power to detect selection signatures specific to ancestry components that are not representative of any extant populations. We evaluate the method using simulated data and compare it to related methods based on summary statistics. We also apply it to human genomic data and identify loci with extreme genetic differentiation between major geographic groups. Many of the genes identified are previously known selected loci relating to hair pigmentation and morphology, skin and eye pigmentation. We also identify new candidate regions, including various selected loci in the Native American component of admixed Mexican-Americans. These involve diverse biological functions, like immunity, fat distribution, food intake, vision and hair development.
ICONIC MANAKINS AND DESPICABLE GRACKLES: COMPARING BIRD-RELATED CULTURAL ECOSYSTEM SERVICES ACROSS BIRDWATCHERS, FARMERS, AND URBANITES IN NORTHWESTERN COSTA RICA
Authors: Echeverri Alejandra , Naidoo Robin , Karp Daniel S. , Chan Kai M.A. , Zhao Jiaying 
Published: February 2019

AbstractDespite the great cultural and economic benefits associated with birdwatching and other bird-related cultural ecosystem services (CES), little is known about the bird-related CES perceived by people, and how they differ across stakeholder groups and species. The goal of this study was to explore CES across three stakeholder groups in northwestern Costa Rica. We conducted surveys (n=404 total) in which we presented farmers (n=140), urbanites (n=149), and birdwatchers (n=115) with pictures and songs of bird species and collected participants’ ratings on items designed to measure multiple CES. We found bird-related CES were perceived as six different constructs: identity, bequest, education, birdwatching, acoustic aesthetic, and disservices. The three stakeholder groups varied across these constructs and across species. Specifically, birdwatchers ranked species higher in terms of their education scores and lower in disservices scores compared to the other two groups. Positive correlations across CES, and negative correlations with disservices, suggest that the affect heuristic (by which generalized positive or negative feelings sway judgements of risks and benefits) might be informing bird-related CES. Our approach represents a novel method for assessing CES that can be adapted and modified for different taxa and multiple geographical contexts.