bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is Multifocality an Indicator of Aggressive Behavior in Small Bowel Neuroendocrine Tumors?
Authors: Choi Allen B. , Maxwell Jessica E. , Keck Kendall J. , Bellizzi Andrew J. , Dillon Joseph S. , O'Dorisio Thomas M. , Howe James R. 
Published: September 2017

Objectives
Many patients with small bowel neuroendocrine tumors (SBNETs) have multifocal tumors (MFTs), but the frequency of MFTs has varied widely across SBNET studies. It is also unclear whether patients with MFTs have more advanced disease or worse clinical course than do those with unifocal SBNETs. We set out to determine the frequency of multifocal and unifocal SBNETs and compare clinicopathologic factors, somatostatin receptor 2 expression, and survival.

Methods
Clinicopathologic variables from 179 patients with surgically managed SBNETs were collected. Statistical comparisons were made using Welch t-test, Wilcoxon test, and Fisher’s exact test. Survival was assessed using the Kaplan-Meier method. Somatostatin receptor 2 expression was analyzed by quantitative polymerase chain reaction, and Ki-67 expression by immunohistochemistry.

Results
Multifocal tumors were found in 45% of patients with SBNETs. Clinicopathologic factors such as grade, TNM stage, presence of distant metastases, mean somatostatin receptor 2 expression, success of imaging modalities, and preoperative and postoperative hormone levels were not significantly different between multifocal and unifocal groups. Progression-free survival and overall survival were also not significantly affected by multifocality.

Conclusions
Clinicopathologic features and survival of patients with MFTs and unifocal tumors are remarkably similar. Although the etiology of MFTs is unclear, patients with MFTs do not have a more aggressive clinical course than patients with unifocal SBNETs.
Magnetic Resonance Imaging of Neuroendocrine Tumor Hepatic Metastases
Authors: Morse Brian , Jeong Daniel , Thomas Kerry , Diallo Dalanda , Strosberg Jonathan R. 
Published: September 2017

Objective
The aim of this study was to determine if magnetic resonance imaging (MRI) performed with hepatobiliary phase imaging results in higher lesion conspicuity and produces lesion measurements with higher interobserver agreement than other MRI sequences when imaging neuroendocrine hepatic metastases.

Methods
Patients who had MRIs with both gadoxetate disodium and gadopentetate dimeglumine contrast within a 6-month span were identified, and 23 hepatic lesions were selected. Three radiologists and 1 oncologist measured the greatest diameter of each lesion on the following sequences: T2 weighted, T1 weighted, postcontrast (dynamic, delayed, and hepatobiliary phase), and diffusion weighted. Signal intensity ratio (SIlesion/SIliver) and contrast-to-noise ratio ([SIlesion – SIliver]/noise) were calculated for all lesions on each sequence. The interobserver agreement of measurements on each sequence was calculated using concordance correlation coefficient.

Results
Diffusion-weighted sequences had the highest signal intensity ratio ranging from 147% to 187% (vs other sequences range of 19.6%–130%). One hepatobiliary sequence had the highest contrast-to-noise ratio with a value of 41 (vs other sequences range of 3.2–28.1). Lesion measurements on all sequences showed high-interobserver agreement, with hepatobiliary sequences showing some of the highest levels of agreement.

Conclusions
Our results support the use of contrast agents with hepatobiliary excretion when imaging neuroendocrine tumors metastatic to liver.
Age-Specific Pattern of Anogenital Wart in Men Who Have Sex With Men
Authors: Ong Jason J. , Fairley Christopher K. , Read Tim R.H. , Chen Marcus Y. , Zhang Lei , Chow Eric P.F. 
Published: September 2017

Abstract
We examined the proportion of anogenital warts in men who have sex with men attending a sexual health center. Anal warts were most common in younger men who have sex with men (5.8% for age <21 years) and became less common with age (2.8% in age >50 years), but penile warts occurred at approximately the same proportion (~1.5%) over all age groups.
Selecting an HIV Test: A Narrative Review for Clinicians and Researchers
Authors: Hurt Christopher B. , Nelson Julie A.E. , Hightow-Weidman Lisa B. , Miller William C. 
Published: September 2017

Abstract
Given the many options available, selecting an HIV test for a particular clinical or research setting can be daunting. Making an informed decision requires an assessment of the likelihood of acute infection in the test population and an understanding of key aspects of the tests themselves. The ability of individual tests to reliably detect HIV infection depends on the target(s) being detected, when they can be expected to be present after infection, and the concentration of stable target in test specimens, all of which are explained by the virologic and serologic events after infection. The purpose of this article is to review the timeline of HIV infection, nomenclature, and characteristics of different tests; compare point-of-care and laboratory-based tests; discuss the impact of different specimens on test performance; and provide practical advice to help clinicians and researchers new to the field select a test that best suits their needs.
The Interaction of Sexual Validation, Criminal Justice Involvement, and Sexually Transmitted Infection Risk Among Adolescent and Young Adult Males
Authors: Matson Pamela A. , Towe Vivian , Ellen Jonathan M. , Chung Shang-en , Sherman Susan G. 
Published: September 2017

Background
Young men who have been involved with the criminal justice system are more likely to have concurrent sexual partners, a key driver of sexually transmitted infections. The value men place on having sexual relationships to validate themselves may play an important role in understanding this association.

Methods
Data were from a household survey. Young men (N = 132), aged 16 to 24 years, self-reported whether they ever spent time in jail or juvenile detention and if they had sexual partnerships that overlapped in time. A novel scale, “Validation through Sex and Sexual Relationships” (VTSSR) assessed the importance young men place on sex and sexual relationships (α = 0.91). Weighted logistic regression accounted for the sampling design.

Results
The mean (SD) VTSSR score was 23.7 (8.8) with no differences by race. Both criminal justice involvement (CJI) (odds ratio [OR], 3.69; 95% confidence interval [CI], 1.12–12.1) and sexual validation (OR, 1.10; 95% CI, 1.04–1.16) were associated with an increased odds of concurrency; however, CJI did not remain associated with concurrency in the fully adjusted model. There was effect modification, CJI was associated with concurrency among those who scored high on sexual validation (OR, 9.18; 95% CI, 1.73–48.6]; however, there was no association among those who scored low on sexual validation. Racial differences were observed between CJI and concurrency, but not between sexual validation and concurrency.

Conclusions
Sexual validation may be an important driver of concurrency for men who have been involved with the criminal justice system. Study findings have important implications on how sexual validation may explain racial differences in rates of concurrency.
HIV Transmission Dynamics Among Foreign-Born Persons in the United States
Authors: Valverde Eduardo E. , Oster Alexandra M. , Xu Songli , Wertheim Joel O. , Hernandez Angela L. 
Published: September 2017

Background:
In the United States (US), foreign-born persons are disproportionately affected by HIV and differ epidemiologically from US-born persons with diagnosed HIV infection. Understanding HIV transmission dynamics among foreign-born persons is important to guide HIV prevention efforts for these populations. We conducted molecular transmission network analysis to describe HIV transmission dynamics among foreign-born persons with diagnosed HIV.

Methods:
Using HIV-1 polymerase nucleotide sequences reported to the US National HIV Surveillance System for persons with diagnosed HIV infection during 2001–2013, we constructed a genetic distance-based transmission network using HIV-TRACE and examined the birth region of potential transmission partners in this network.

Results:
Of 77,686 people, 12,064 (16%) were foreign born. Overall, 28% of foreign-born persons linked to at least one other person in the transmission network. Of potential transmission partners, 62% were born in the United States, 31% were born in the same region as the foreign-born person, and 7% were born in another region of the world. Most transmission partners of male foreign-born persons (63%) were born in the United States, whereas most transmission partners of female foreign-borns (57%) were born in their same world region.

Discussion:
These finding suggests that a majority of HIV infections among foreign-born persons in our network occurred after immigrating to the United States. Efforts to prevent HIV infection among foreign-born persons in the United States should include information of the transmission networks in which these individuals acquire or transmit HIV to develop more targeted HIV prevention interventions.
The 2016 WHO classification of central nervous system tumors: what neurologists need to know
Authors: DeWitt John C. , Mock Andreas , Louis David N. 
Published: September 2017

Purpose of review
The 2016 WHO classification of tumors of the central nervous system (2016 CNS WHO) features many changes that are relevant to neurologists treating patients with brain tumors as well as neurologists involved in basic, clinical, and epidemiological research. This review summarizes what neurologists need to know and will need to know in the next years.

Recent findings
The 2016 CNS WHO introduces diagnostic terms that ‘integrate’ histological and molecular information and suggests presenting diagnoses in a four-layered reporting format. In addition, it utilizes a ‘not otherwise specified’ designation to identify diagnostic categories that are not precisely defined. A better understanding of the biology of entities further led to changes in the tumor nosology, for example, diffuse gliomas based on IDH gene status. Meaningful molecular subgroups could also be identified in embryonal tumors and other entities. Given the pace of change in the field of brain tumor classification, there will likely be additional practical advances that emerge over the next few years. A new initiative entitled Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy intends to formulate recommendations between WHO updates.

Summary
The 2016 CNS WHO includes major changes in the way brain tumors are classified, with molecular parameters being incorporated into diagnostic criteria for a substantial number of such entities.
Allosteric signalling paths in hemoglobin: a protein dynamics network analysis
Authors: Monza Emanuele , Blouin George , Spiro Thomas G. , Guallar Victor 
Published: September 2017

AbstractHemoglobin is the paradigm of cooperative protein-ligand binding. Cooperativity is the consequence of inter-subunit allosteric communication: binding at one site increases the affinity of the others. Despite half a century of studies, the mechanism behind oxygen binding in hemoglobin is not fully understood yet. In particular, it is not clear if cooperativity arises from preferential inter-subunit channels and which residues propagate the allosteric signal from one heme to the others. In this work, the heme-heme dynamical interactions have been mapped through a network-based analysis of residue conformational fluctuations, as described by molecular dynamics simulations. In particular, it was possible to suggest which inter-subunit interactions are mostly responsible of allosteric signalling and, within each pair of subunits, which protein fragments convey such signalling process.
Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques
Authors: Semler Matthew R. , Wiseman Roger W. , Karl Julie A. , Graham Michael E. , Gieger Samantha M. , O’Connor David H. 
Published: September 2017

AbstractPig-tailed macaques (Macaca nemestrina, Mane) are important models for human immunodeficiency virus (HIV) studies. Their infectability with minimally modified HIV makes them a uniquely valuable animal model to mimic human infection with HIV and progression to acquired immunodeficiency syndrome (AIDS). However, variation in the pig-tailed macaque major histocompatibility complex (MHC) and the impact of individual transcripts on the pathogenesis of HIV and other infectious diseases is understudied compared to rhesus and cynomolgus macaques. In this study, we used Pacific Biosciences single-molecule real-time circular consensus sequencing to describe full-length MHC class I (MHC-I) transcripts for 194 pig-tailed macaques from three breeding centers. We then used the full-length sequences to inferMane-AandMane-Bhaplotypes containing groups of MHC-I transcripts that co-segregate due to physical linkage. In total, we characterized full-length open reading frames (ORFs) for 313Mane-A,Mane-B, andMane-Isequences that defined 86Mane-Aand 106Mane-BMHC-I haplotypes. Pacific Biosciences technology allows us to resolve theseMane-AandMane-Bhaplotypes to the level of synonymous allelic variants. The newly defined haplotypes and transcript sequences containing full-length ORFs provide an important resource for infectious disease researchers as certain MHC haplotypes have been shown to provide exceptional control of simian immunodeficiency virus (SIV) replication and prevention of AIDS-like disease in nonhuman primates. The increased allelic resolution provided by Pacific Biosciences sequencing also benefits transplant research by allowing researchers to more specifically match haplotypes between donors and recipients to the level of nonsynonymous allelic variation, thus reducing the risk of graft-versus-host disease.
Positional encoding in cotton-top tamarins (Saguinus oedipus)
Authors: Versace Elisabetta , Rogge Jessica R. , Shelton-May Natalie , Ravignani Andrea 
Published: September 2017

AbstractStrategies used in artificial grammar learning can shed light into the abilities of different species to extract regularities from the environment. In theA(X)nBrule,AandBitems are linked but assigned to different positional categories and separated by distractor items. Open questions are how widespread is the ability to extract positional regularities fromA(X)nBpatterns, which strategies are used to encode positional regularities and whether individuals exhibit preferences for absolute or relative position encoding. We used visual arrays to investigate whether cotton-top tamarins (Saguinus oedipus) can learn this rule and which strategies they use. After training on a subset of exemplars, half of the tested monkeys successfully generalized to novel combinations. These tamarins discriminated between categories of tokens with different properties (A,B,X) and detected a positional relationship between non-adjacent items even in the presence of novel distractors. Generalization, though, was incomplete, since we observed a failure with items that during training had always been presented in reinforced arrays. The pattern of errors revealed that successful subjects used visual similarity with training stimuli to solve the task, and that tamarins extracted the relative position ofAsandBsrather than their absolute position, similarly to what observed in other species. Relative position encoding appears to be the default strategy in different tasks and taxa.
Viable But Non-Culturable Cells Are Persister Cells
Authors: Kim Jun-Seob , Chowdhury Nityananda , Wood Thomas K. 
Published: September 2017

ABSTRACTBacteria have two dormant phenotypes: the viable but non-culturable (VBNC) state and the persister state. Both resting stages arise without mutation and both have been linked to chronic infections; however, persister cells revive rapidly whereas the cell population called VBNC is reported to not resuscitate. Here we investigated the relatedness of the two stress-induced phenotypes at the single-cell level by using transmission electron microscopy and fluorescent microscopy to examine cell morphology and by quantifying cell resuscitation. Using the classic starvation conditions to create VBNC cells, we found that the majority of the remainingEscherichia colipopulation are spherical, have empty cytosol, and fail to resuscitate; however, some of the spherical cells under these classic VBNC-inducing conditions resuscitate immediately (most probably those with dense cytosol). Critically, all the culturable cells became persister cells within 14 days of starvation. We found that the persister cells initially are rodlike, have clear but limited membrane damage, can resuscitate immediately, and gradually become spherical by aging. After 24 h, only rod-shaped persister cells survive, and all the spherical cells lyse. Both cell populations formed under the VBNC-inducing conditions and the persister cells are metabolically inactive. Therefore, the bacterial population consists of dead cells and persister cells in the VBNC-inducing conditions; i.e., the non-lysed particles that do not resuscitate are dead, and the dormant cells that resuscitate are persister cells. Hence, “VBNC” and “persister” describe the same dormant phenotype.
Identification of DISE-inducing shRNAs by monitoring cellular responses
Authors: Patel Monal , Peter Marcus E. 
Published: September 2017

AbstractOff-target effects (OTE) are an undesired side effect of RNA interference (RNAi) caused by partial complementarity between the targeting siRNA and mRNAs other than the gene to be silenced. The death receptor CD95 and its ligand CD95L contain multiple sequences that when expressed as either si-or shRNAs kill cancer cells through a defined OTE that targets critical survival genes. Death induced by survival gene elimination (DISE) is characterized by specific morphological changes such as elongated cell shapes, senescence-like enlarged cells, appearance of large intracellular vesicles, release of mitochondrial ROS followed by activation of caspase-2, and induction of a necrotic form of mitotic catastrophe. Using genome-wide shRNA lethality screens with eight different cancer cell lines, we recently identified 651 genes as critical for the survival of cancer cells. To determine whether the toxic shRNAs targeting these 651 genes contained shRNAs that kill cancer cell through DISE rather than by silencing their respective target genes, we tested all shRNAs in the TRC library derived from a subset of these genes targeting tumor suppressors (TS). We now report that only by monitoring the responses of cancer cells following expression of shRNAs derived from these putative TS it was possible to identify DISE-inducing shRNAs in five of the genes. These data indicate that DISE in general is not an undefined toxic response of cells caused by a random OTE but rather a specific cellular response with shared features that points at a specific biological function involving multiple genes in the genome.
Successful TS‐1 monotherapy as the second‐line treatment for advanced extramammary Paget's disease: A report of two cases
Authors: Kato Junji , Hida Tokimasa , Yamashita Toshiharu , Kamiya Shiori , Horimoto Kohei , Sato Sayuri , Takahashi Hitomi , Sawada Masahide , Yamada Mao , Uhara Hisashi 
Published: September 2017

AbstractThere is no standard chemotherapeutic treatment for advanced extramammary Paget's disease, though the effectiveness of some chemotherapy regimens, including docetaxel, has been reported. In this report, we report that TS‐1 monotherapy was effective in two patients with advanced extramammary Paget's disease after docetaxel treatment failure. TS‐1 monotherapy may be useful as the second‐line treatment for patients with advanced extramammary Paget's disease.
Mapping biopsy for Buruli ulcer self‐medicated with occlusive dressing
Authors: Hayami Takuma , Takahashi Toshifumi , Kato Takeshi , Tanaka Toshihiro , Fujimoto Noriki 
Published: September 2017

AbstractBuruli ulcer is the third most common mycobacterial infection next to tuberculosis and leprosy caused by Mycobacterium ulcerans. Although it affects the skin, subcutaneous tissues, muscles and sometimes bones, there is no reliable evidence to determine the extent of debridement. We present here a case of Buruli ulcer treated successfully with a preoperative mapping biopsy procedure, which had been self‐medicated with occlusive dressing. Because Buruli ulcer is accompanied by subtle pain, patients and clinicians tend to initially treat the ulcer with occlusive dressing therapy, which leads to the misdiagnosis of Buruli ulcer as a common bacterial infection only judging from bacterial culture of the surface of the ulcer. We propose the efficacy of mapping biopsy for treating Buruli ulcer.
Application of spectral decomposition and neural networks to characterise deep turbidite systems in the outer fold and thrust belt of the Niger Delta
Authors: Aminu Muslim B. , Ojo Samuel B. 
Published: September 2017

ABSTRACTWe have applied a wavelet‐based spectral decomposition scheme and a multi‐layered feed‐forward neural network to interpret turbidite depositional systems from three‐dimensional reflection seismic data and well logs for a prospective hydrocarbon zone in the outer fold and thrust belt of the Niger Delta. The goal was to overcome difficulties in interpreting depositional systems from deep sections of the Field, occasioned by loss of seismic resolution with depth and the sparse distribution of wells.The decomposition scheme allowed us to delineate multiple depositional systems not apparent on the conventional seismic amplitude display. These systems include linear channel systems with terminal splay lobes, a sinuous channel system and its abandoned meander loops, and sediment wave features in overbank areas. Delineated channel morphologies and transport directions varied both laterally and vertically and were possibly dependent upon the disposition of the pre‐thrusting paleo‐seafloor. Terminal splay lobes are fragmented and coincident with the locations of topographic lows, which are possibly related to the initial configurations of the oceanic basement below. Predicted porosity and resistivity distributions have morphologies that correlate well with the mapping provided by the spectral decomposition scheme. The property distributions indicate that reservoir prone systems in the Field and possibly within the outer fold and thrust belt are composed primarily of channel systems, both linear and sinuous, and their associated splay lobes. The channel systems appear vertically stacked, and this situation possibly increases the potential success rate for exploration wells in the region. Beyond channel limits, redistributive bottom currents varying rapidly in speed and direction apparently encouraged the dispersal of sand‐rich sediments to form sediment waves.Despite the limited well control, the methodology significantly aided our interpretation. It proved effective at revealing the distribution of reservoir prone facies within the Field and provided insight into the dominant factors that controlled deposition within the Field.