bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opportunistically recorded acoustic data support Northeast Atlantic mackerel expansion theory
Authors: van der Kooij Jeroen , Fässler Sascha M.M. , Stephens David , Readdy Lisa , Scott Beth E. , Roel Beatriz A. 
Published: March 2016

Abstract
Fisheries independent monitoring of widely distributed pelagic fish species which conduct large seasonal migrations is logistically complex and expensive. One of the commercially most important examples of such a species in the Northeast Atlantic Ocean is mackerel for which up to recently only an international triennial egg survey contributed to the stock assessment. In this study, we explore whether fisheries acoustic data, recorded opportunistically during the English component of the North Sea International Bottom Trawl Survey, can contribute to an improved understanding of mackerel distribution and provide supplementary data to existing dedicated monitoring surveys. Using a previously published multifrequency acoustic mackerel detection algorithm, we extracted the distribution and abundance of schooling mackerel for the whole of the North Sea during August and September between 2007 and 2013. The spatio-temporal coverage of this unique dataset is of particular interest because it includes part of the unsurveyed summer mackerel feeding grounds in the northern North Sea. Recent increases in landings in Icelandic waters during this season suggested that changes have occurred in the mackerel feeding distribution. Thus far it is poorly understood whether these changes are due to a shift, i.e. mackerel moving away from their traditional feeding grounds in the northern North Sea and southern Norwegian Sea, or whether the species' distribution has expanded. We therefore explored whether acoustically derived biomass of schooling mackerel declined in the northern North Sea during the study period, which would suggest a shift in mackerel distribution rather than an expansion. The results of this study show that in the North Sea, schooling mackerel abundance has increased and that its distribution in this area has not changed over this period. Both of these findings provide, to our knowledge, the first evidence in support of the hypothesis that mackerel have expanded their distribution rather than moved away.
Risks and Benefits of Stress Ulcer Prophylaxis for Patients With Severe Sepsis*
Authors: Sasabuchi Yusuke , Matsui Hiroki , Lefor Alan K. , Fushimi Kiyohide , Yasunaga Hideo 
Published: March 2016

Objectives:
The Surviving Sepsis Campaign Guidelines recommend stress ulcer prophylaxis for patients with severe sepsis who have bleeding risks. Although sepsis has been considered as a risk factor for gastrointestinal bleeding, the effect of stress ulcer prophylaxis has not been studied in patients with severe sepsis. Furthermore, stress ulcer prophylaxis may be associated with an increased risk of hospital-acquired pneumonia or Clostridium difficile infection. The aim of this study was to investigate the risks and benefits of stress ulcer prophylaxis for patients with severe sepsis.

Design:
Retrospective cohort study.

Setting:
Five hundred twenty-six acute care hospitals in Japan.

Patients:
A total of 70,862 patients with severe sepsis.

Interventions:
None.

Measurements and Main Results:
One-to-one propensity score matching created 15,651 pairs of patients who received stress ulcer prophylaxis within 2 days of admission and those who did not. Patient characteristics were well balanced between the two groups. No significant differences were seen between the stress ulcer prophylaxis group and the control group with regard to gastrointestinal bleeding requiring endoscopic hemostasis (0.6% vs 0.5%; p = 0.208), 30-day mortality (16.4% vs 16.9%; p = 0.249), and Clostridium difficile infection (1.4% vs 1.3%; p = 0.588). The stress ulcer prophylaxis group had a significantly higher proportion of hospital-acquired pneumonia (3.9% vs 3.3%; p = 0.012) compared with the control group.

Conclusions:
Since the rate of gastrointestinal bleeding requiring endoscopic hemostasis is not different comparing patients with and without stress ulcer prophylaxis, and the increase in hospital-acquired pneumonia is significant, routine stress ulcer prophylaxis for patients with severe sepsis may be unnecessary.
Differential Diagnosis of Immunoglobulin G4-associated Cholangitis From Cholangiocarcinoma
Authors: Du Shunda , Liu Gang , Cheng Xinqi , Li Yue , Wang Qian , Li Ji , Lu Xin , Zheng Yongchang , Xu Haifeng , Chi Tianyi , Zhao Haitao , Xu Yiyao , Sang Xinting , Zhong Shouxian , Mao Yilei 
Published: March 2016

Background and Aim:
Immunoglobulin G4-associated cholangitis (IAC) shares many similar symptoms with cholangiocarcinoma (CCA). However, the treatment and the prognosis are substantially different. This study aimed to identify the important markers for the differential diagnosis of these 2 diseases.

Methods:
Thirty IAC patients and 275 CCA patients were reviewed retrospectively for their clinical symptoms, serological tests, and imaging characteristics. Posttreatment responses were also studied.

Results:
IgG4 had 100% specificity for IAC at a cutoff of 6 times the upper normal limit. IAC patients had a significantly higher incidence of weight loss (P=0.025) and a higher level of weight loss (P=0.008) than CCA patients. The positive rates of biological markers CA199, CA242, and CEA in CCA and IAC were 81.5% versus 42.9%, 45.5% versus 4.5%, and 29.2% versus 7.1%, respectively. Levels of these tumor markers in CCA were significantly higher than in IAC (P<0.05). The thickened wall [17/18 (94.4%) vs. 3/10 (30%), P=0.001] and the occupying lesion on the bile duct [1/18 (5.6%) vs. 8/10 (80%), P<0.001] were found to be significantly different in IAC and CCA, respectively, by endoscopic ultrasonography. Autoimmune pancreatitis was the most frequently observed comorbidity of IAC (25/30). All IAC patients respond positively to steroid treatment.

Conclusions:
Increased tumor markers, 6-fold higher levels of serum IgG4, and other organs’ involvement could be the reference factors for a differential diagnosis of IAC and CCA. Endoscopic ultrasonography might be an effective imaging tool for diagnosis, although clinical signs and symptoms of IAC and CCA are similar. Experimental steroid treatment can be useful in the diagnosis for certain difficult cases.
Identification and Fibrosis Staging of Hepatitis C Patients Using the Electronic Medical Record System
Authors: Anand Vijay , Hyun Christian , Khan Qasim M. , Hall Curtis , Hessefort Norbert , Sonnenberg Amnon , Fimmel Claus J. 
Published: March 2016

Background and Aims:
The aim of this study was to noninvasively assess the severity of chronic hepatitis C virus (HCV) in large patient populations. It would be helpful if fibrosis scores could be calculated solely on the basis of data contained in the patients’ electronic medical records (EMR). We performed a pilot study to identify all HCV-infected patients in a large health care system, and predict their fibrosis stage on the basis of demographic and laboratory data using common data from their EMR.

Materials and Methods:
HCV-infected patients were identified using the EMR. The liver biopsies of 191 HCV patients were graded using the Ishak and Metavir scoring systems. Demographic and laboratory data were extracted from the EMR and used to calculate the aminotransferase to platelet ratio index, Fib-4, Fibrosis Index, Forns, Göteborg University Cirrhosis Index, Lok Index, and Vira-HepC.

Results:
In total, 869 HCV-infected patients were identified from a population of over 1 million. In the subgroup of patients with liver biopsies, all 7 algorithms were significantly correlated with the fibrosis stage. The degree of correlation was moderate, with correlation coefficients ranging from 0.22 to 0.60. For the detection of advanced fibrosis (Metavir 3 or 4), the areas under the receiver operating characteristic curve ranged from 0.71 to 0.84, with no significant differences between the individual scores. Sensitivities, specificities, and positive and negative predictive values were within the previously reported range. All scores tended to perform better for higher fibrosis stages.

Conclusions:
Our study demonstrates that HCV-infected patients can be identified and their fibrosis staged using commonly available EMR-based algorithms.
Outcomes of Seropositive Patients With Marsh 1 Histology in Clinical Practice
Authors: Singh Prashant , Lauwers Gregory Y. , Garber John J. 
Published: March 2016

Goals:
We retrospectively studied all seropositive Marsh 1 patients seen at 2 tertiary care hospitals in the last 15 years to determine their clinical, serological, and histologic outcomes.

Background:
Patients with positive celiac serologies and Marsh 1 histology represent an understudied subgroup of patients, and it is unclear whether they should be advised to adopt a gluten-free diet (GFD).

Study:
Subjects were identified based on positive celiac serologies and Marsh 1 histology while on a full-gluten diet. Clinical presentation and baseline laboratory data were noted. Clinical course, repeat serologies, and histology were determined.

Results:
Of 620 patients with positive celiac serologies and abnormal duodenal histology, we identified 36 (5.8%) with positive tissue transglutaminase and/or antiendomysial antibodies and Marsh 1 lesions who had adequate follow-up. Abdominal pain was the commonest (47.2%) presenting symptom. Twenty-eight patients were advised to adopt GFD, whereas 8 were not. Among patients treated with GFD, 88.9% improved symptomatically and 95% normalized serology. In contrast, among patients who continued to consume gluten, 85.7% remained symptomatic and 80% had persistently positive serologies. Among the 8 patients on normal diet, 5 underwent repeat biopsy, and 4 of them had the same or worse histology, with 3 patients progressing to Marsh 3c. Among the 28 patients on GFD, 5 underwent repeat biopsy and all improved to normal histology.

Conclusions:
Most patients with positive celiac serology and Marsh 1 lesions benefit from GFD and, if not treated, a majority will continue to be symptomatic and remain at risk of progressing to villous atrophy.
Liver Failure in Early Infancy
Authors: Bitar Rana , Thwaites Rosemary , Davison Suzanne , Rajwal Sanjay , McClean Patricia 
Published: March 2016

ABSTRACTObjective:Acute liver failure (ALF) in early infancy is rare and challenging to recognize and manage. We aim to describe the presentation and outcome of infants with ALF according to their final aetiology to elucidate features to facilitate early recognition leading to prompt diagnosis and management.Methods:All infants presenting within 120 days from birth with liver failure were included in a retrospective review over a 19‐year period. The aetiology, clinical features, presenting investigations, and outcome were collected.Results:Seventy‐eight young infants presented with ALF. The aetiology was established in 94% and included metabolic disease (36%), hypoxic‐ischaemic (HI) insult (19%), infection (17%), neonatal haemochromatosis (9%), and infiltrative disease (9%). Infections, infiltrative disease, and acute HI insult usually resulted in higher transaminases and international normalized ratio, whereas neonatal haemochromatosis and tyrosinaemia were characterized by lower or near normal transaminases. Overall jaundice was not visible in 24% of infants at presentation. Forty‐five (58%) infants were alive at discharge from hospital. Survival at 1 year was 53% and survival with native liver 50%. Later deaths occurred in infants with mitochondrial disease. Six infants received a liver transplant and 4 subsequently died from their underlying disease.Conclusion:ALF should be considered in any young infant with a coagulopathy as transaminases and/or bilirubin levels can be near normal at presentation. Better intensive care and the judicious use of liver transplantation may have contributed to the improved outcomes for this group compared with previous decades.
Transient Ocular Wavefront Data in Type 1 Diabetes Mellitus
Authors: Blendowske Ralf , Kalb Max 
Published: March 2016

ABSTRACT

Purpose
We report transient ocular wavefront and blood glucose data for one patient with acute type 1 diabetes mellitus after the treatment with insulin has been initiated.

Case Report
The wavefront data for both eyes of a 34-year-old male patient were examined by a Hartmann-Shack wavefront sensor. Refraction data and higher-order aberrations were recorded during 130 days for eyes in natural conditions, without cycloplegia. At the beginning, we sampled data every 3 to 4 days and enlarged the intervals, when values settled. In total, we report 20 measurements and 1 baseline entry. Blood glucose levels were recorded at least six times a day during the complete period. For the equivalent sphere, we recorded a bilateral hyperopic shift of 5 D from −2.75 DS to +2.25 DS, followed by a reverse myopic shift of the same amount. The equivalent sphere peaked about 15 to 18 days after the treatment with insulin had begun. Cylinder values kept remarkably stable. Higher-order aberrations are dominated by the spherical aberration. The Zernike coefficient c
12 for both eyes changed substantially from OD 0.036 μm and OS 0.062 μm to OD 0.24 μm and OS 0.22 μm (5 mm pupil diameter) following the time pattern of the equivalent sphere. About 60 days after they had reached their peak, all refraction values and higher-order aberrations stabilized at their baseline levels. The baseline was defined by records taken 4 years before the treatment with insulin was commenced.

Conclusions
Wavefront aberrometry gives quantitative insights in the transient alteration and recovering of the eye’s optics whilst the therapy of acute type 1 diabetes mellitus is being initiated. The data of this case support the assumption that variations in the crystalline lens, most probably the modification of its refractive gradient index, as a cause for the transient behavior. An explanation is still missing.
Pharmacologic Management of Pressure-Induced Stromal Keratopathy after LASIK
Authors: Unlu Metin , Hondur Ahmet M. , Korkmaz Safak , Kumova Deniz , Yuksel Erdem 
Published: March 2016

ABSTRACT

Purpose
To emphasize the importance of anticipation of pressure-induced stromal keratopathy (PISK) in eyes with a previous history of LASIK.

Case Report
A 40-year-old man developed LASIK-related pressure-induced stromal keratopathy after uneventful phacoemulsification (Phaco) and intraocular lens (IOL) implantation in his left eye. With immediate discontinuation of the steroid drops and initiation of antiglaucoma medication, his visual acuity, interface edema, and haze improved rapidly. One year later, during Phaco with IOL implantation in his other eye, with anticipation of a similar LASIK-related pressure-induced stromal keratopathy, a very brief course of soft steroid therapy was given together with antiglaucoma medication. Intraocular pressure elevation was avoided, and no interface edema or haze was observed.

Conclusions
This case illustrates that the risk for LASIK-related pressure-induced stromal keratopathy may be reduced with appropriate precautions.
Melanoma Extirpation with Immediate Reconstruction: The Oncologic Safety and Cost Savings of Single-Stage Treatment
Authors: Karanetz Irena , Stanley Sharon , Knobel Denis , Smith Benjamin D. , Bastidas Nicholas , Beg Mansoor , Kasabian Armen K. , Tanna Neil 
Published: March 2016

Background:
The timing of reconstruction following melanoma extirpation remains controversial, with some advocating definitive reconstruction only when the results of permanent pathologic evaluation are available. The authors evaluated oncologic safety and cost benefit of single-stage neoplasm extirpation with immediate reconstruction.

Methods:
The authors reviewed all patients treated with biopsy-proven melanoma followed by immediate reconstruction during a 3-year period (January of 2011 to December of 2013). Patient demographic data, preoperative biopsies, operative details, and postoperative pathology reports were evaluated. Cost analysis was performed using hospital charges for single-stage surgery versus theoretical two-stage surgery.

Results:
During the study period, 534 consecutive patients were treated with wide excision and immediate reconstruction, including primary closure in 285 patients (55 percent), local tissue rearrangement in 155 patients (30 percent), and skin grafting in 78 patients (15 percent). The mean patient age was 67 years (range, 19 to 98 years), and the median follow-up time was 1.2 years. Shave biopsy was the most common diagnostic modality, resulting in tumor depth underestimation in 30 patients (6.0 percent). Nine patients (2.7 percent) had positive margins on permanent pathologic evaluation. The only variables associated with positive margins were desmoplastic melanoma (p = 0.004) and tumor location on the cheek (p = 0.0001). The mean hospital charge for immediate reconstruction was $22,528 compared with the theoretical mean charge of $35,641 for delayed reconstruction, leading to mean savings of 38.5 percent (SD, 7.9 percent).

Conclusion:
This large series demonstrates that immediate reconstruction can be safely performed in melanoma patients with an acceptable rate of residual tumor requiring reoperation and significant health care cost savings.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Fracture Prediction With Modified-FRAX in Older HIV-Infected and Uninfected Men
Authors: Yin Michael T. , Shiau Stephanie , Rimland David , Gibert Cynthia L. , Bedimo Roger J. , Rodriguez-Barradas Maria C. , Harwood Katherine , Aschheim Josh , Justice Amy C. , Womack Julie A. 
Published: March 2016

Background:
FRAX is a validated, computer-based clinical fracture risk calculator that estimates the 10-year risk of major osteoporotic (clinical spine, forearm, hip, or shoulder) fracture, and hip fracture alone. It is widely used for decision making in fracture prevention, but it may underestimate the risk in HIV-infected individuals. Some experts recommend considering HIV as a cause of secondary osteoporosis when calculating FRAX in HIV-infected individuals.

Methods:
From the Veterans Aging Cohort Study Virtual Cohort, we included 24,451 HIV-infected and uninfected men aged 50–70 years with complete data in the year 2000 to approximate all but 2 factors (ie, history of secondary osteoporosis and parental hip fracture) for modified-FRAX calculation without bone density and 10-year observational data for incident fragility fracture. The accuracy of the modified-FRAX calculation was compared by the observed/estimated (O/E) ratios of fracture by HIV status.

Results:
The accuracy of modified-FRAX was less for HIV-infected [O/E = 1.62, 95% confidence interval (CI) 1.45 to 1.81] than uninfected men (O/E = 1.29, 95% CI: 1.19 to 1.40), but improved when HIV was included as a cause of secondary osteoporosis (O/E = 1.20, 95% CI: 1.08 to 1.34). However, only 3%–6% of men with incident fractures were correctly identified by the modified-FRAX using accepted FRAX thresholds for pharmacologic therapy.

Conclusions:
Modified-FRAX underestimated the fracture rates more in older HIV-infected than in otherwise similar uninfected men. The accuracy improved when HIV was included as a cause of secondary osteoporosis, but it still performed poorly for case finding. Further studies are necessary to determine how to use FRAX or define an HIV-specific index to risk stratify for screening and treatment in older HIV-infected individuals.
FOXP3+Helios+ Regulatory T Cells, Immune Activation, and Advancing Disease in HIV-Infected Children
Authors: Khaitan Alka , Kravietz Adam , Mwamzuka Mussa , Marshed Fatma , Ilmet Tiina , Said Swalehe , Ahmed Aabid , Borkowsky William , Unutmaz Derya 
Published: March 2016

Abstract:
Regulatory T cells (Tregs) are functionally suppressive CD4 T cells, critical for establishing peripheral tolerance and controlling inflammatory responses. Previous reports of Tregs during chronic HIV disease have conflicting results with higher or lower levels compared with controls. Identifying true Tregs with suppressive activity proves challenging during HIV infection, as traditional Treg markers, CD25 and FOXP3, may transiently upregulate expression as a result of immune activation (IA). Helios is an Ikaros family transcription factor that marks natural Tregs with suppressive activity and does not upregulate expression after activation. Coexpression of FOXP3 and Helios has been suggested as a highly specific marker of “bona fide” Tregs. We evaluated Treg subsets by FOXP3 coexpressed with either CD25 or Helios and their association with HIV disease progression in perinatally infected HIV-positive children. Identifying Tregs by FOXP3 coexpression with Helios rather than CD25 revealed markedly higher Treg frequencies, particularly in HIV+ children. Regardless of antiretroviral therapy, HIV-infected children had a selective expansion of memory FOXP3+Helios+ Tregs. The rise in memory Tregs correlated with declining HIV clinical status, indicated by falling CD4 percentages and CD4:CD8 ratios and increasing HIV plasma viremia and IA. In addition, untreated HIV+ children exhibited an imbalance between the levels of Tregs and activated T cells. Finally, memory Tregs expressed IA markers CD38 and Ki67 and exhaustion marker, PD-1, that tightly correlated with a similar phenotype in memory CD4 T cells. Overall, HIV-infected children had significant disruptions of memory Tregs that associated with advancing HIV disease.
Magnetic Resonance Elastography of the Liver
Authors: Wagner Mathilde , Besa Cecilia , Bou Ayache Jad , Yasar Temel Kaya , Bane Octavia , Fung Maggie , Ehman Richard L. , Taouli Bachir 
Published: March 2016

Objective
The aim of this study was to compare 2-dimensional (2D) gradient recalled echo (GRE) and 2D spin echo echoplanar imaging (SE-EPI) magnetic resonance elastography (MRE) sequences of the liver in terms of image quality and quantitative liver stiffness (LS) measurement.

Materials and Methods
This prospective study involved 50 consecutive subjects (male/female, 33/17; mean age, 58 years) who underwent liver magnetic resonance imaging at 3.0 T including 2 MRE sequences, 2D GRE, and 2D SE-EPI (acquisition time 56 vs 16 seconds, respectively). Image quality scores were assessed by 2 independent observers based on wave propagation and organ coverage on the confidence map (range, 0–15). A third observer measured LS on stiffness maps (in kilopascal). Mean LS values, regions of interest size (based on confidence map), and image quality scores between SE-EPI and GRE-MRE were compared using paired nonparametric Wilcoxon test. Reproducibility of LS values between the 2 sequences was assessed using intraclass coefficient correlation, coefficient of variation, and Bland-Altman limits of agreement. T2* effect on image quality was assessed using partial Spearman correlation.

Results
There were 4 cases of failure with GRE-MRE and none with SE-EPI-MRE. Image quality scores and region of interest size were significantly higher using SE-EPI-MRE versus GRE-MRE (P < 0.0001 for both measurements and observers). Liver stiffness measurements were not significantly different between the 2 sequences (3.75 ± 1.87 kPa vs 3.55 ± 1.51 kPa, P = 0.062), were significantly correlated (intraclass coefficient correlation, 0.909), and had excellent reproducibility (coefficient of variation, 10.2%; bias, 0.023; Bland-Altman limits of agreement, −1.19; 1.66 kPa). Image quality scores using GRE-MRE were significantly correlated with T2* while there was no correlation for SE-EPI-MRE.

Conclusions
Our data suggest that SE-EPI-MRE may be a better alternative to GRE-MRE. The diagnostic performance of SE-EPI-MRE for detection of liver fibrosis needs to be assessed in a future study.