bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary Gastric Choriocarcinoma Presenting as a Pregnancy of Unknown Location
Authors: Larish Alyssa , Kumar Amanika , Kerr Sarah , Langstraat Carrie 
Published: January 2017

BACKGROUND:
Pregnancy of unknown location presents a diagnostic challenge, in rare occasions leading to the diagnosis of malignancy. We describe a case of β-hCG-secreting nongestational primary gastric choriocarcinoma presenting as a pregnancy of unknown location.

CASE:
A 37-year-old woman, gravida 4 para 3013, presented with several days of vaginal bleeding and rising β-hCG level without ultrasound localization of pregnancy. The diagnosis of pregnancy of unknown location was made and methotrexate administered at a β-hCG level of 7,779 milli-international units/mL. A 40% decrease in β-hCG level was noted between days 4 and 7. One week later, an inappropriate β-hCG level rise to 10,937 milli-international units/mL was noted, prompting a second dose of methotrexate and computed tomography imaging, leading to the discovery of gastric and liver lesions. Pathology from gastric biopsies revealed nongestational choriocarcinoma. The patient was treated with chemotherapy, with death from cardiac arrest 7 months after diagnosis.

CONCLUSION:
Malignancies that can secrete β-hCG include gestational trophoblastic disease, gonadal and extragonadal germ cell tumors, and malignancies with choriocarcinoma differentiation. Although ectopic pregnancy compromises approximately 2% of first-trimester pregnancy, gestational trophoblastic neoplasia and gestational choriocarcinoma can be seen in 1 of 1,500 and 1 of 20,000 pregnancies, respectively. When β-hCG levels do not fall appropriately in women undergoing medical management for pregnancy of unknown location, ectopic β-hCG secretion by a malignancy must be considered.
Neurodevelopmental Outcomes After Assisted Reproductive Technologies
Authors: Balayla Jacques , Sheehy Odile , Fraser William D. , Séguin Jean R. , Trasler Jacquetta , Monnier Patricia , MacLeod Andrea A. , Simard Marie-Noëlle , Muckle Gina , Bérard Anick ,   on Behalf of the 3D-Study Research Group From the Integrated Research Network in Perinatology of Quebec and Eastern Ontario
Published: January 2017

OBJECTIVE:
To compare children's cognitive, motor, and language development at 2 years of age after assisted reproductive technologies (ARTs) relative to natural conception.

METHODS:
The 3D-Study (2010–2012) is a prospective cohort study, which sought to improve the understanding among perinatal events, obstetric outcomes, and child development. A total of 2,366 pregnant women were recruited, of whom 278 conceived with ART: ovarian stimulation, intrauterine sperm insemination, in vitro fertilization, intracytoplasmic sperm injection, or in vitro maturation. Natural conception was defined as the unassisted establishment of pregnancy. Cognitive, motor, and language neurodevelopmental outcomes were compared between ART and natural conception groups at 24 months using the Bayley Scales of Infant and Toddler Development, 3rd edition, and the MacArthur-Bates Communicative Development Inventories. Adjusted linear regression models evaluated the effect of ART on neurodevelopmental outcomes using natural conception as a reference.

RESULTS:
A total of 175 children in the ART group (62.9%) and 1,345 children in the natural conception group (64.4%) underwent neurodevelopmental assessment at 24 months postpartum. After adjusting for relevant confounders, children born after ART showed no difference in Bayley scales' cognitive scores (B1 [standard error]=−1.60 [0.9], 95% confidence interval [CI] −3.36 to 0.16), composite motor scores (B1 [standard error]=−1.33 [1.0], 95% CI −3.29 to 0.63), or MacArthur-Bates language scores (B1 [standard error]=−0.28 [2.1], 95% CI −4.39 to 3.83). No difference was observed when independent ART techniques were compared nor when comparing in vivo (ovarian stimulation or intrauterine insemination) or in vitro (in vitro fertilization, intracytoplasmic sperm injection, or in vitro maturation) techniques (P>.05).

CONCLUSION:
Children born after ART had similar cognitive, motor, and language development as children born after natural conception at 2 years of age. These findings may be useful in the clinical counseling of patients undergoing ART.
Relationship Between Alternative Resuscitation Strategies, Host Response and Injury Biomarkers, and Outcome in Septic Shock: Analysis of the Protocol-Based Care for Early Septic Shock Study
Authors: Kellum John A. , Pike Francis , Yealy Donald M. , Huang David T. , Shapiro Nathan I. , Angus Derek C. 
Published: January 2017

Objectives:
The Protocol-based Care for Early Septic Shock trial found no differences across alternative resuscitation strategies in all-cause mortality. A separate aim was to determine whether differences in resuscitation strategies affected trajectories of biomarkers of key pathways associated with downstream clinical outcomes of sepsis and whether there were differences in survival across treatment arms for patients with different baseline biomarker profiles.

Design:
Secondary analysis of a large randomized clinical trial.

Setting:
Thirty-one U.S. hospitals.

Patients:
Six hundred twenty-eight patients with septic shock.

Interventions:
Two resuscitation protocols versus usual care.

Measurements and Main Results:
We measured a panel of biomarkers representing four pathophysiologic domains: “inflammation” (tumor necrosis factor, interleukin-6, and -10); “coagulation” (D-dimers, thrombin-antithrombin complex); “oxidative stress” (urine isoprostane); and “tissue hypoxia” (lactate) at 0, 6, 24, and 72 hours after treatment. We analyzed whether alternative resuscitation strategies affected biomarker trajectories over 72 hours and whether effects on 90-day hospital mortality varied by baseline (time 0) biomarker profiles—both using regression models with interaction terms for treatment arms. For all baseline biomarkers, higher concentrations were associated with increased risk of death by 90 days. However, there was no significant effect of treatment assignment on subsequent biomarker trajectories. We did find evidence for heterogeneity of treatment effect of protocol-based care on mortality for patients with different baseline [interleukin-6] and [interleukin-6] × [interleukin-10] profiles, whereas patients with the lowest quartiles fared better with protocol-based care (odds ratios, 0.32 [0.13–075]; p = 0.01 and 0.32 [0.14–0.73]; p = 0.01, respectively).

Conclusions:
In patients with septic shock, alterations in inflammation, coagulation, oxidative stress, and tissue hypoxia are common and associated with adverse outcomes but are not influenced by protocol-based resuscitation compared with usual care. However, contrary to expectation, protocol-based resuscitation appeared to be superior in patients with lower concentrations of inflammatory biomarkers. The mechanisms responsible for this effect are unclear.
Mapping Regional Differences of Local Pressure-Volume Curves With Electrical Impedance Tomography
Authors: Beda Alessandro , Carvalho Alysson R. , Carvalho Nadja C. , Hammermüller Sören , Amato Marcelo B. P. , Muders Thomas , Gittel Claudia , Noreikat Katharina , Wrigge Hermann , Reske Andreas W. 
Published: January 2017

Objectives:
Lung-protective mechanical ventilation aims to prevent alveolar collapse and overdistension, but reliable bedside methods to quantify them are lacking. We propose a quantitative descriptor of the shape of local pressure-volume curves derived from electrical impedance tomography, for computing maps that highlight the presence and location of regions of presumed tidal recruitment (i.e., elastance decrease during inflation, pressure-volume curve with upward curvature) or overdistension (i.e., elastance increase during inflation, downward curvature).

Design:
Secondary analysis of experimental cohort study.

Setting:
University research facility.

Subjects:
Twelve mechanically ventilated pigs.

Interventions:
After induction of acute respiratory distress syndrome by hydrochloric acid instillation, animals underwent a decremental positive end-expiratory pressure titration (steps of 2 cm H2O starting from ≥ 26 cm H2O).

Measurements and Main Results:
Electrical impedance tomography-derived maps were computed at each positive end-expiratory pressure-titration step, and whole-lung CT taken every second steps. Airway flow and pressure were recorded to compute driving pressure and elastance. Significant correlations between electrical impedance tomography-derived maps and positive end-expiratory pressure indicate that, expectedly, tidal recruitment increases in dependent regions with decreasing positive end-expiratory pressure (p < 0.001) and suggest that overdistension increases both at high and low positive end-expiratory pressures in nondependent regions (p < 0.027), supporting the idea of two different scenarios of overdistension occurrence. Significant correlations with CT measurements were observed: electrical impedance tomography-derived tidal recruitment with poorly aerated regions (r = 0.43; p < 0.001); electrical impedance tomography-derived overdistension with nonaerated regions at lower positive end-expiratory pressures and with hyperaerated regions at higher positive end-expiratory pressures (r ≥ 0.72; p < 0.003). Even for positive end-expiratory pressure levels minimizing global elastance and driving pressure, electrical impedance tomography-derived maps showed nonnegligible regions of presumed overdistension and tidal recruitment.

Conclusions:
Electrical impedance tomography-derived maps of pressure-volume curve shapes allow to detect regions in which elastance changes during inflation. This could promote individualized mechanical ventilation by minimizing the probability of local tidal recruitment and/or overdistension. Electrical impedance tomography-derived maps might become clinically feasible and relevant, being simpler than currently available alternative approaches.
Short article: Mortality and differential diagnoses of villous atrophy without coeliac antibodies
Authors: Schiepatti Annalisa , Biagi Federico , Fraternale Giacomo , Vattiato Claudia , Balduzzi Davide , Agazzi Simona , Alpini Claudia , Klersy Catherine , Corazza Gino R. 
Published: January 2017

Objective
Villous atrophy (VA) of the small bowel is mainly related to coeliac disease (CD), whose diagnosis is made on the basis of positive endomysial/tissue transglutaminase antibodies while on a gluten-containing diet in the vast majority of patients. However, VA can also occur in other conditions whose epidemiology is little known. Our aim was to study the epidemiology and clinical features of these rare enteropathies.

Patients and methods
Clinical and laboratory data of all the patients with VA directly diagnosed in our centre in the last 15 years were collected and statistically analysed.

Results
Between September 1999 and June 2015, 274 patients were diagnosed with VA. A total of 260 patients were also positive to coeliac antibodies; the other 14 had VA, but no IgA endomysial antibodies: five had common variable immunodeficiency, three had dermatitis herpetiformis, two had IgA deficiency associated with CD, one had abdominal lymphoma, one had unclassified sprue, one had olmesartan-associated enteropathy and one had seronegative CD. Mortality was 6.0 deaths per 100 person years (95% confidence interval: 2.2–16) in patients with VA but negative coeliac antibodies, whereas only 0.2 deaths per 100 person years (95% confidence interval: 0.1–0.6) occurred in coeliac patients.

Conclusion
Patients with VA and negative endomysial antibodies are rare. However, these forms of VA identify specific causes that can be diagnosed. These patients are affected by a very high mortality.
Clinical Characteristics of Herpes Simplex Virus Urethritis Compared With Chlamydial Urethritis Among Men
Authors: Ong Jason J. , Morton Anna N. , Henzell Helen R. , Berzins Karen , Druce Julian , Fairley Christopher K. , Bradshaw Catriona S. , Read Tim RH , Hocking Jane S. , Chen Marcus Y. 
Published: January 2017

Background
The aim of this study was to ascertain the clinical characteristics associated with herpes simplex virus (HSV) urethritis in men and to compare those with chlamydial urethritis.

Methods
We compared clinical and laboratory data from men diagnosed with polymerase chain reaction confirmed HSV urethritis with those of men with chlamydial urethritis presenting to Melbourne Sexual Health Centre between 2000 and 2015.

Results
Eighty HSV urethritis cases were identified: 55 (68%, 95% confidence interval, 58–78) were by HSV-1 and 25 (32%, 95% confidence interval, 22–42) by HSV-2. Compared with chlamydial urethritis, men with HSV urethritis were significantly more likely to report severe dysuria (20% vs 0%, P < 0.01) or constitutional symptoms (15% vs 0%, P < 0.01). Men with HSV urethritis were significantly more likely to have meatitis (62% vs 23%, P < 0.01), genital ulceration (37% vs 0%, P < 0.01), or inguinal lymphadenopathy (30% vs 0%, P < 0.01) but less likely to have urethral discharge (32% vs 69%, P < 0.01). There was no significant difference in the proportion of men who had raised (≥5) polymorphonuclear leukocytes per high-powered field between the two groups (P = 0.46).

Conclusions
The clinical presentation of HSV urethritis in men may differ from those of chlamydial urethritis and guide testing for HSV in men presenting with non-gonococcal urethritis.
How Reliable Is Microscopy and Culture for the Diagnosis of Gonorrhea? An 11-Year Experience from INDIA
Authors: Bhargava Aradhana , Bala Manju , Singh Vikram , Joshi Naveen Chandra , Kakran Monika , Puri Poonam , Khunger Niti , Ramesh Venkatesh , Saxena Ashok Kumar 
Published: January 2017

Abstract
Positivity of microscopy and culture was greater (P < 0.0001) in men with urethral discharge syndrome (65.8%) than in women with vaginal/cervical discharge (0.5%), indicating that basic diagnostic tests may not be cost-effective for diagnosis of vaginal/cervical discharge syndrome. Microscopy when compared with culture showed sensitivity, specificity, positive predictive value and negative predictive value of 95.4%, 77.6%, 84.6%, and 95.3%, in men, whereas in women, it was 77.8%, 99.9%, 92.1%, and 99.9%, respectively.
Lens Opacity and Hydrogen Sulfide in a New Zealand Geothermal Area
Authors: Bates Michael N. , Bailey Ian L. , DiMartino Robert B. , Pope Karl , Crane Julian , Garrett Nick 
Published: January 2017

ABSTRACT

Purpose
Hydrogen sulfide (H2S) is a highly toxic gas with well-established, acute irritation effects on the eye. The population of Rotorua, New Zealand, sited on an active geothermal field, has some of the highest ambient H2S exposures in the world. Evidence from ecological studies in Rotorua has suggested that H2S is associated with cataract. The purpose of the present study was, using more detailed exposure characterization, clinical examinations, and anterior eye photography, to more directly investigate this previously reported association.

Methods
Enrolled were 1637 adults, ages 18 to 65, from a comprehensive Rotorua primary care medical register. Patients underwent a comprehensive ophthalmic examination, including pupillary dilation and lens photography to capture evidence of any nuclear opacity, nuclear color, and cortical and posterior subcapsular opacity. Photographs were scored for all four outcomes on the LOCS III scale with decimalized interpolation between the exemplars. H2S exposure for up to the last 30 years was estimated based on networks of passive samplers set out across Rotorua and knowledge of residential, workplace, and school locations over the 30 years. Data analysis using linear and logistic regression examined associations between the degree of opacification and nuclear color or cataract (defined as a LOCS III score ≥2.0) in relation to H2S exposure.

Results
No associations were found between estimated H2S exposures and any of the four ophthalmic outcome measures.

Conclusions
Overall, results were generally reassuring. They provided no evidence that H2S exposure at the levels found in Rotorua is associated with cataract. The previously found association between cataract and H2S exposure in the Rotorua population seems likely to be attributable to the limitations of the ecological study design. These results cannot rule out the possibility of an association with cataract at higher levels of H2S exposure.
An Exploratory Study to Assess Individual and Structural Level Barriers Associated With Poor Retention and Re-engagement in Care Among Persons Living With HIV/AIDS
Authors: Colasanti Jonathan , Stahl Natalie , Farber Eugene W. , del Rio Carlos , Armstrong Wendy S. 
Published: January 2017

Background:
Retention in care is the most challenging step along the HIV care continuum. Many patients who engage in care and achieve viral suppression have care interruptions, characterized by moving in and out of care (“churn”). Poor retention has clinical consequences and contributes to new HIV transmissions, but how to predict or prevent it remains elusive. This study sought to understand the relationship between individual- and structural-level barriers, and poor retention for persons living with HIV/AIDS in Atlanta, GA.

Methods:
We administered a survey, through interviews, with HIV-infected patients continuously retained in care for 6 years (“continuously retained,” n = 32) and patients with recent gaps in care (“unretained” n = 27). We assessed individual-level protective factors for successful engagement (self-efficacy, resilience, perceived social support, and disclosure), risk factors for poor engagement (substance use, mental illness, and stigma), and structural/systemic-level barriers (financial and housing instability, transportation, food insecurity, communication barriers, and incarceration history). Chi-square and Mann–Whitney U tests were used to compare the 2 populations.

Results:
Both continuously retained and unretained populations had high rates of prior viral suppression but few unretained patients were virologically suppressed upon return to care (11%). Younger age, crack cocaine use, food insecurity, financial instability, housing instability, and phone number changes in the past year were significantly more likely to be present in the unretained population.

Conclusions:
Our findings suggest the need for targeted risk assessment tools to predict the highest-risk patients for poor retention whereby public health interventions can be directed to those individuals.
Polymer dynamics of Alp7A reveals two ‘critical’ concentrations that govern dynamically unstable actin-like proteins
Authors: Petek Natalie A. , Derman Alan I. , Royal Jason A. , Pogliano Joe , Mullins R. Dyche 
Published: January 2017

ABSTRACT:Dynamically unstable polymers capture and move cellular cargos in both bacteria and eukaryotes, but the regulation of their assembly remains poorly understood. Here we describe polymerization of Alp7A, a bacterial Actin-Like Protein (ALP) that segregates the low copy-number plasmid pLS20 inBacillus subtilis.Purified Alp7A forms dynamically unstable polymers with two critical points: an intrinsic critical concentration (0.6 μM), observed when ATP hydrolysis is blocked, and a dynamic critical concentration (10.3 μM), observed when ATP hydrolysis occurs. From biochemical and kinetic analysis, the intrinsic critical concentration reflects a balance between filament elongation and shortening, while the dynamic critical concentration reflects a balance between filament nucleation and catastrophic disassembly. Although Alp7A does not form stable polymers at physiological concentrations, rapid nucleation by an accessory factor, Alp7R, decreases the dynamic critical concentration into the physiological range. Intrinsic and dynamic critical concentrations are fundamental parameters that can be used to describe the behavior of all dynamically unstable polymers.
A quantitative description of the mouse piriform cortex
Authors: Srinivasan Shyam , Stevens Charles F 
Published: January 2017

AbstractIn this report, we provide a quantitative description for 2 aspects of the mouse piriform cortex. First, we give volumetric estimates of regions within the anterior and posterior piriform cortex. Second, we estimate the neuronal densities in each of these regions. From these two estimates, we calculate that the mouse piriform contains around half a million neurons equally distributed over the anterior and posterior piriform cortex. Quantitative descriptions such as these are important because they make it possible to construct realistic models and provide a constraint that theories of the olfactory circuit must fulfil. We show how quantitative descriptions can be useful for modelling by using our data to refine and improve earlier models of piriform cortex activity.
HLA class I binding prediction via convolutional neural networks
Authors: Vang Yeeleng S. , Xie Xiaohui 
Published: January 2017

AbstractMany biological processes are governed by protein-ligand interactions. One such example is the recognition of self and non-self cells by the immune system. This immune response process is regulated by the major histocompatibility complex (MHC) protein which is encoded by the human leukocyte antigen (HLA) complex. Understanding the binding potential between MHC and peptides can lead to the design of more potent, peptide-based vaccines and immunotherapies for infectious autoimmune diseases.We apply machine learning techniques from the natural language processing (NLP) domain to address the task of MHC-peptide binding prediction. More specifically, we introduce a new distributed representation of amino acids, name HLA-Vec, that can be used for a variety of downstream proteomic machine learning tasks. We then propose a deep convolutional neural network architecture, name HLA-CNN, for the task of HLA class I-peptide binding prediction. Experimental results show combining the new distributed representation with our HLA-CNN architecture acheives state-of-the-art results in the majority of the latest two Immune Epitope Database (IEDB) weekly automated benchmark datasets. We further apply our model to predict binding on the human genome and identify 15 genes with potential for self binding. Codes are available athttps://github.com/uci-cbcl/HLA-bind.
Two sides of the same coin: monetary incentives concurrently improve and bias confidence judgments
Authors: Lebreton Maël , Langdon Shari , Slieker Matthijs J. , Nooitgedacht Jip S. , Goudriaan Anna E. , Denys Damiaan , Holst Ruth J. van , Luigjes Judy 
Published: January 2017

AbstractDecisions are accompanied by a feeling of confidence, i.e., a belief about the decision being correct. Confidence accuracy is critical, notably in high-stakes situations such as medical or financial decisionmaking. Here, we investigated how incentive motivation influences confidence accuracy by combining a perceptual task with a confidence incentivization mechanism. Importantly, by varying the magnitude and valence (gains or losses) of monetary incentives, we orthogonalized their motivational and affective components. Corroborating theories of rational decision-making and motivation, our results first reveal that the motivational value of incentives improves aspects of confidence accuracy. However, in line with a value-confidence interaction hypothesis we further show that the affective value of incentives concurrently biases confidence reports, thus degrading confidence accuracy. Finally, we demonstrate that the motivational and affective effects of incentives differentially impact how confidence builds on perceptual evidence. Altogether, these findings may provide new hints about confidence miscalibration in healthy or pathological contexts.