bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of tandem and interspersed segmental duplications using high-throughput sequencing
Authors: Soylev Arda , Le Thong Minh , Amini Hajar , Alkan Can , Hormozdiari Fereydoun 
Published: March 2019

Abstract

Motivation
Several algorithms have been developed that use high-throughput sequencing technology to characterize structural variations (SVs). Most of the existing approaches focus on detecting relatively simple types of SVs such as insertions, deletions and short inversions. In fact, complex SVs are of crucial importance and several have been associated with genomic disorders. To better understand the contribution of complex SVs to human disease, we need new algorithms to accurately discover and genotype such variants. Additionally, due to similar sequencing signatures, inverted duplications or gene conversion events that include inverted segmental duplications are often characterized as simple inversions, likewise, duplications and gene conversions in direct orientation may be called as simple deletions. Therefore, there is still a need for accurate algorithms to fully characterize complex SVs and thus improve calling accuracy of more simple variants.

Results
We developed novel algorithms to accurately characterize tandem, direct and inverted interspersed segmental duplications using short read whole genome sequencing datasets. We integrated these methods to our TARDIS tool, which is now capable of detecting various types of SVs using multiple sequence signatures such as read pair, read depth and split read. We evaluated the prediction performance of our algorithms through several experiments using both simulated and real datasets. In the simulation experiments, using a 30× coverage TARDIS achieved 96% sensitivity with only 4% false discovery rate. For experiments that involve real data, we used two haploid genomes (CHM1 and CHM13) and one human genome (NA12878) from the Illumina Platinum Genomes set. Comparison of our results with orthogonal PacBio call sets from the same genomes revealed higher accuracy for TARDIS than state-of-the-art methods. Furthermore, we showed a surprisingly low false discovery rate of our approach for discovery of tandem, direct and inverted interspersed segmental duplications prediction on CHM1 (&lt;5% for the top 50 predictions).

Availability and implementation
TARDIS source code is available at https://github.com/BilkentCompGen/tardis, and a corresponding Docker image is available at https://hub.docker.com/r/alkanlab/tardis/.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Framework of Historical Oppression, Resilience and Transcendence to Understand Disparities in Depression Amongst Indigenous Peoples
Authors: Burnette Catherine E , Renner Lynette M , Figley Charles R 
Published: March 2019

Abstract
Given chronic experiences of historical oppression, Indigenous peoples tend to experience much higher rates of depression than the general US population, which then, drives disproportionately high rates of suicide and other health disparities. The purpose of this research was to examine the core components of the culturally grounded Framework of Historical Oppression, Resilience, and Transcendence as they relate to depressive symptoms experienced by Indigenous peoples. As part of a larger convergent mixed-methods study, in this quantitative survey component, we utilised data from a sample of 127 Indigenous adults across two Southeastern US tribes. Regression analysis results signified support for the framework, indicating that historical oppression and proximal stress (daily stressors and lower incomes) were risk factors, whereas family resilience and life satisfaction (a measure of transcendence) were protective factors related to depressive symptoms. The results provide a foundation for future research to build upon in identifying culturally relevant risk and protective factors to ameliorate depression and other health disparities.
PS01.200: OPEN IVOR LEWIS ESOPHAGECTOMY WITH AN AGGRESSIVE UPPER MEDIASTINAL LYMPH NODE DISSECTION
Authors: Koike Masahiko , Kodera Yasuhiro 
Published: March 2019

Abstract

Background
The Ivor Lewis procedure consists of open subtotal esophagectomy and intrathoracic esophago-gastric anastomosis. Though this procedure is open surgery, it can minimize the risk of anastomotic leakage. This procedure combined with aggressive upper mediastinal lymph node dissection could achieve satisfactory short-term and long-term outcomes.

Methods
The cases with middle or lower thoracic cancer without metastasis at the cervical area are subjected to this Ivor Lewis procedure. To evade the demerit of thoracotomy, we have employed 1) the 3-field lymphadenectomy in selective patients, 2) the vertical muscle-sparing thoracotomy without transection of muscles and ribs, 3) paravertebral block for postoperative pain.

Results
A total of 246 patients who underwent subtotal esophagectomy (2011.1–2016.12) were analyzed for short-time postoperative outcomes. In 135 patients of the Ivor-Lewis group, prevalence of anastomotic leakage, anastomotic stricture recurrent nerve palsy and the morbidity, defined as Clavien-Dindo classification 2 or further, was 0%, 0.7% and 21% respectively. On the other hand, the incidence of these increased significantly in 111 patients who underwent cervical anastomosis, 10%, 6.3% and 47% respectively. Though Ivor-Lewis was open surgery, 83% patients in the Ivor Lewis group achieved 30 m walking at the ward within postoperative day 2 and the median length of postoperative hospital stay was 16 days (10–83). The survival according to our therapeutic strategy was analyzed in 352 patients who underwent subtotal esophagectomy for thoracic esophageal cancer (2002.1–2012.12). The overall survival was 82.5/83.5/52.1/50.0/32.1% for stage0/I/II/III/IVa (JES10th). The solitary cervical lymph node recurrence was diagnosed in 5 patients of Ivor-Lewis group, but 4 of the patient could be cured by additional cervical lymph node dissection.

Conclusion
Discussion: Intrathoracic anastomosis could minimize the risk of anastomotic leakage, and consequently the total complication rate could be reduced. The strategy that the cervical lymphadenectomy is performed only through the thoracic cavity in the selected patients was acceptable because of our survival data.
Conclusion: Using our Ivor-Lewis procedure for the patients with thoracic esophageal cancer, even the open operation can minimize the risk of complication. Out therapeutic strategy could achieve satisfactory survival results.

Disclosure
All authors have declared no conflicts of interest.
PS02.247: TWO CASES OF NEUROENDOCRINE CARCINOMA OF ESOPHAGOGASTRIC JUNCTION
Authors: Yamada L E O , Ohki Shinji , Ujiie Daisuke , Tada Takeshi , Hanayama Hiroyuki , Saze Zenichiro , Momma Tomoyuki , Hayase Suguru , Gonda Kenji , Nirei Azuma , Okayama Hirokazu , Sakamoto Wataru , Endo Hisahito , Fujita Shotaro , Kikuchi Tomohiro , Saito Motonobu , Kono Koji , Marubashi Shigeru 
Published: March 2019

Abstract

Background
Neuroendocrine cell carcinoma (NEC) of the esophagogastric junction is rare and usually has a very poor prognosis.

Methods
Here we present two cases of NEC occurred in the esophagogastric junction.

Results
Case 1
A 50-year-old man was admitted to the introduction origin medical institute with an abdominal pain and dysphagia. Upper gastrointestinal endoscopy revealed a type 2 tumor at the esophagogastric junction, and the pathological examination showed the diffuse proliferation of relatively homogeneous tumor cell with chromatin-enriched nuclear and immunohistologically, the tumor cells were positive for Chromogranin A, CD56, AE1/3. MIB-1 index was 80%, we diagnosed neuroendocrine carcinoma (small cell type).
TNM Stage was GE, Type 3, cT4, cN1, cM0 cStage IIIB (ENETS TNM classification) He had undergone total gastrectomy and lower esophagectomy with transhiatal approach and 2 field of lymph node dissection.
Pathological examination revealed NEC component developed under the muscularis mucosa, differentiated adenocarcinoma localized upper the muscularis mucosa and Chromogranin A positive cells were scattered inside.
Pathological findings showed NEC (MIB-1 72.5%) with tub1, 70 × 56 mm, pT3 pN1(7/36), stage IIIB (HER2 score0). Adjuvant chemotherapy using S-1 was started, but the follow up CT showed recurrence in mediastinum, left subclavian and paraaortic lymph nodes 7 months after surgery. S-1 followed by CPT-11 + CDDP, CT showed the shrinkage of paraaortic lymph nodes metastasis. The patient alive for 55 months without any evidence ofprogression being continued chemotherapy.
Case 2
A 57-year-old man was admitted to the introduction origin medical institute with dysphagia. Upper gastrointestinal endoscopy revealed a type 2 tumor at the esophagogastric junction, and the pathological examination showed NEC (small cell type). CT and PET revealed mediastinal lymph node metastasis, aortic invasion and adrenal metastasis. TNM stage was NEC, EG, cT3, cN1, cM1 cStage IV. We performed a systemic chemotherapy with CPT-11 + CDDP, the evaluation of treatment effect after 5 course chemotherapy revealed partial response. However the patient underwent the endoscopic stent graft due to stenosis, and died due to progressive disease 18months after chemotherapy induction.

Conclusion
We reported here two cases of NEC occurring in the esophagogastric junction. It's clinical behavior remains unclear and the treatment strategy for NEC of esophagogastric junction is not established. Further investigation of accumulated cases of this rare entity is necessary.

Disclosure
All authors have declared no conflicts of interest.
PS02.251: TWO CASES OF THE ADVANCED ESOPHAGEAL CANCER WHICH WAS ABLE TO IMPROVE QOL BY VATS- E AS PALLIATIVE OPERATION
Authors: Yoshida Takayoshi , Lee Chunyong , Chouchi Takeshi , Komekami Yusuke , Konishi Humio 
Published: March 2019

Abstract

Background
We often troubled with the choice of the treatment for unresctable or elderly advanced esophageal cancer on the keeping of quality of life (QOL) . There are few cases to impair QOL remarkably, because of dysphagia with esophageal stenosis or esophago-tracheal fistula after Chemo-Radiation Therapy. Esophageal bypass including palliative esopagectomy and esophageal stenting are used for the oral intake of these cases.

Methods
We reported two cases of the elderly advanced esophageal cancer which were effective for QOL improvement by palliative Video-Assisted Thoracic Surgery of Esophagus (VATS-E).

Results
Case 1: A 72-year-old woman admitted with dysphagia was found to have advanced esophageal carcinoma, clinical stage IV (T3N2M1). We initiated definitive chemotherapy with combined 5-fluorouracil and cisplatin, to which the patient showed confirmed partial response. Dysphagia was not improved enough. Therefore, she received esophageal stenting with the antireflex valve. She was not able to have enough oral ingestion after stenting. So VATS-esophageal bypass was performed four months after initial treatment. At 2 years after surgery, she was alive and underwent outpatients chemotherapy. She can have normal diet.
Case 2: A 79-year-old woman admitted with vomiting and body weight loss. The diagnosis was advanced esophageal carcinoma, clinical stage IV (T4N3M0). She received definitive Docetaxel chemotherapy because of renal dysfunction, malnutrition, to which patient showed progressive disease. So, VATS-esophageal resection (D0) was performed about 1 months after chemotherapy. There were not postoperative complications. She can have rice gruel diet.

Conclusion
It is difficult to determine which treatment is better esophageal stenting and esophageal palliative operation, because there are few reports that compared the esophageal palliative operation. In late years, VATS become able to be carried out safely. It is lower invasive treatment than thoracotomy. VATS is one of the palliative therapy, but it is necessary to decide the indication carefully in the case that a prognosis is limited. We think that it is useful to have satisfaction of the oral ingestion for cases with the severe stenosis and refractory cases of stenting. It is thought that VATS-E have possibilities to become the useful choice as one means of the palliative operation in consideration of the general status and the prognosis of the patients.

Disclosure
All authors have declared no conflicts of interest.
Long-term proarrhythmic pharmacotherapy among patients with congenital long QT syndrome and risk of arrhythmia and mortality
Authors: Weeke Peter E , Kellemann Jesper S , Jespersen Camilla Bang , Theilade Juliane , Kanters Jørgen K , Hansen Michael Skov , Christiansen Michael , Marstrand Peter , Gislason Gunnar H , Torp-Pedersen Christian , Bundgaard Henning , Jensen Henrik K , Tfelt-Hansen Jacob 
Published: March 2019

Abstract

Aims
It is Class I recommendation that congenital long QT syndrome (cLQTS) patients should avoid drugs that can cause torsades de pointes (TdP). We determined use of TdP risk drugs after cLQTS diagnosis and associated risk of ventricular arrhythmia and all-cause mortality.

Methods and results
Congenital long QT syndrome patients (1995–2015) were identified from four inherited cardiac disease clinics in Denmark. Individual-level linkage of nation-wide registries was performed to determine TdP risk drugs usage (www.crediblemeds.org) and associated risk of ventricular arrhythmias and all-cause mortality. Risk analyses were performed using Cox-hazards analyses. During follow-up, 167/279 (60%) cLQTS patients were treated with a TdP risk drug after diagnosis. Most common TdP risk drugs were antibiotics (34.1%), proton-pump inhibitors (15.0%), antidepressants (12.0%), and antifungals (10.2%). Treatment with a TdP risk drug decreased 1 year after diagnosis compared with 1 year before (28.4% and 23.2%, respectively, P &lt; 0.001). Five years after diagnosis, 33.5% were in treatment (P &lt; 0.001). Risk factors for TdP risk drug treatment were age at diagnosis (5-year increment) [hazard ratio (HR) = 1.07, confidence interval (CI) 1.03–1.11] and previous TdP risk drug treatment (HR = 2.57, CI 1.83–3.61). During follow-up, nine patients were admitted with ventricular arrhythmia (three were in treatment with a TdP risk drug). Eight patients died (four were in treatment with a TdP risk drug). No significant association between TdP risk drug use and ventricular arrhythmias or all-cause mortality was found (P = 0.53 and P = 0.93, respectively), but events were few.

Conclusion
Torsades de pointes risk drug usage was common among cLQTS patients after time of diagnosis and increased over time. A critical need for more awareness in prescribing patterns for this high-risk patient group is needed.
Biofilm development in L. fermentum under shear flow & sequential GIT digestion
Authors: Aziz Kanwal , Tariq Muhammad , Zaidi Arsalan 
Published: March 2019

ABSTRACT
The objective of this study was to investigate biofilm formation by Lactobacillus fermentum under physiologically relevant shear conditions both in the presence and absence of a food matrix and under simulated conditions of digestion. This was done using batch and flow biofilms of L. fermentum strains under conditions simulating digestion in the human gastrointestinal tract and shear flow using a high throughput platform BioFlux 1000Z system. The putative probiotic strain, PL29, was found to be capable of adhesion and biofilm formation in mucin-coated microfluidic channels under liquid flow conditions mimicking those of the GIT. Based on these in vitro measurements, we conclude that L. fermentum strain PL29 could be an effective probiotic for human consumption.
Opioids and Infectious Diseases: A Converging Public Health Crisis
Authors: Schwetz Tara A , Calder Thomas , Rosenthal Elana , Kattakuzhy Sarah , Fauci Anthony S 
Published: March 2019

Abstract
A converging public health crisis is emerging because the opioid epidemic is fueling a surge in infectious diseases, such as human immunodeficiency virus infection with or without AIDS, the viral hepatitides, infective endocarditis, and skin and soft-tissue infections. An integrated strategy is needed to tailor preventive and therapeutic approaches toward infectious diseases in people who misuse and/or are addicted to opioids and to concurrently address the underlying predisposing factor for the infections—opioid use disorder. This commentary highlights the unique and complementary roles that the infectious diseases and substance use disorder communities can play in addressing this crisis of dual public health concerns.
Differential role of MyD88 signaling in Streptococcus suis serotype 2-induced systemic and central nervous system diseases
Authors: Auger Jean-Philippe , Benoit-Biancamano Marie-Odile , Bédard Christian , Segura Mariela , Gottschalk Marcelo 
Published: March 2019

Abstract
Streptococcus suis serotype 2 is an important porcine bacterial pathogen and a zoonotic agent responsible for sudden death, septic shock and meningitis, with exacerbated inflammation being a hallmark of the systemic and central nervous system (CNS) infections. However, S. suis serotype 2 strains are genetically and phenotypically heterogeneous, being composed of a multitude of sequence types (STs) whose virulence greatly varies. Yet, most studies have used ‘classical’ virulent Eurasian ST1 or ST7 strains, even though ST25 and ST28 strains account for most isolates in North America. While recognition of S. suis by innate immune cells has been associated with the myeloid differentiation primary response 88 (MyD88)-dependent Toll-like receptor (TLR) pathway in vitro, particularly surface-associated TLR2, little information is available regarding its role in vivo. This study demonstrates for the first time a differential role of MyD88 signaling in S. suis-induced systemic and CNS diseases, regardless of strain background diversity. The MyD88-dependent pathway is critical for the development of systemic disease via its role in inflammation, which subsequently controls bacterial burden. However, and differently from what has been described in vitro, TLR2 and TLR4 individually do not contribute to systemic disease, suggesting possible compensation in their absence and/or a collaborative role with other MyD88-dependent TLRs. On the other hand, CNS disease does not necessarily require MyD88 signaling and, consequently, neither TLR2 nor TLR4, suggesting a partial implication of other pathways. Finally, regardless of its notable heterogeneity, recognition of S. suis serotype 2 appears to be similar, indicating that recognized components are conserved motifs.
ASN-ASAS SYMPOSIUM: FUTURE OF DATA ANALYTICS IN NUTRITION: Modeling complex problems with system dynamics: applications in animal agriculture1
Authors: Nicholson Charles F , Peixoto Simões Andre Rozemberg , LaPierre Paul Andrew , Van Amburgh Michael E 
Published: March 2019

AbstractMany problematic outcomes in agricultural and food systems have important dynamic dimensions and arise due to underlying system structure. Thus, understanding the linkages between system structure and dynamic behavior often is important for the design and implementation of interventions to achieve sustained improvements. System dynamics (SD) modeling represents system structure using stock-flow-feedback structures expressed as systems of differential equations solved by numerical integration methods. System dynamics methods also encompass a broader methodological approach that emphasizes model structural development and data inputs to replicate one of a limited number of problematic behavioral modes, anticipates dynamic complexity, and focuses on feedback processes arising from endogenous system elements. This paper highlights the process of SD modeling using 2 examples from animal agriculture at different scales. A dynamic version of the Cornell Net Carbohydrate and Protein System (CNCPS) that represents outcomes for an individual dairy cow is formulated as an SD model illustrates the benefits of the SD approach in modeling rumen fill and animal performance. At a very different scale, an SD model of the Brazilian dairy supply chain (farms, processing, and consumers) illustrates the country-level impacts of efforts to improve cow productivity and how impacts differ if productivity improvement occurs on small farms rather than large farms. The paper concludes with recommendations about how to increase awareness and training in SD methods to enhance their appropriate use in research and instruction.
A Tool for Automatic Correction of Endogenous Concentrations: Application to BHB Analysis by LC–MS-MS and GC-MS
Authors: Desharnais Brigitte , Lajoie Marie-Jo , Laquerre Julie , Savard Stéphanie , Mireault Pascal , Skinner Cameron D 
Published: March 2019

Abstract
Several substances relevant for forensic toxicology purposes have an endogenous presence in biological matrices: beta-hydroxybutyric acid (BHB), gamma-hydroxybutyric acid (GHB), steroids and human insulin, to name only a few. The presence of significant amounts of these endogenous substances in the biological matrix used to prepare calibration standards and quality control samples (QCs) can compromise validation steps and quantitative analyses. Several approaches to overcome this problem have been suggested, including using an analog matrix or analyte, relying entirely on standard addition analyses for these analytes, or simply ignoring the endogenous contribution provided that it is small enough. Although these approaches side-step the issue of endogenous analyte presence in spiked matrix-matched samples, they create serious problems with regards to the accuracy of the analyses or production capacity. We present here a solution that addresses head-on the problem of endogenous concentrations in matrices used for calibration standards and quality control purposes. The endogenous analyte concentration is estimated via a standard-addition type process. This estimated concentration, plus the spiked concentration are then used as the de facto analyte concentration present in the sample. These de facto concentrations are then used in data analysis software (MultiQuant, Mass Hunter, etc.) as the sample’s concentration. This yields an accurate quantification of the analyte, free from interference of the endogenous contribution. This de facto correction has been applied in a production setting on two BHB quantification methods (GC-MS and LC–MS-MS), allowing the rectification of BHB biases of up to 30 μg/mL. The additional error introduced by this correction procedure is minimal, although the exact amount will be highly method-dependent. The endogenous concentration correction process has been automated with an R script. The final procedure is therefore highly efficient, only adding four mouse clicks to the data analysis operations.
The inventories of the Madre de Deus
Authors: van Kessel Elsje 
Published: March 2019

Abstract
This article examines the impact made by the taking of the ship Madre de Deus in 1592 on the circulation of Asian material culture in England. As a Portuguese cargo ship on its way from Goa, the Madre de Deus was filled with precious and exotic objects – an immense treasure for the English privateers who seized it. An examination of the extensive archival record generated by the ship’s capture allows for a reconstruction of the cargo. Probing inventories and other documents for their material and formal qualities as much as for their contents, the article argues that written documents became an instrument with which the English authorities tried to control the uncontrollable movements of the booty. The pathways subsequently followed by some of the items recovered are traced, and the question of how they affected England’s artistic culture is addressed.