bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Detection of Necrosis in Breast Cancer with Desorption Electrospray Ionization Mass Spectrometry
Authors: Tata Alessandra , Woolman Michael , Ventura Manuela , Bernards Nicholas , Ganguly Milan , Gribble Adam , Shrestha Bindesh , Bluemke Emma , Ginsberg Howard J. , Vitkin Alex , Zheng Jinzi , Zarrine-Afsar Arash 
Published: October 2016

AbstractIdentification of necrosis in tumors is of prognostic value in treatment planning, as necrosis is associated with aggressive forms of cancer and unfavourable outcomes. To facilitate rapid detection of necrosis with Mass Spectrometry (MS), we report the lipid MS profile of necrotic breast cancer with Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) imaging validated with statistical analysis and correlating pathology. This MS profile is characterized by (1) the presence of the ion of m/z 572.48 [Cer(d34:1) + Cl]− which is a ceramide absent from the viable cancer subregions; (2) the absence of the ion of m/z 391.25 which is present in small abundance only in viable cancer subregions; and (3) a slight increase in the relative intensity of known breast cancer biomarker ions of m/z 281.25 [FA(18:1)-H]− and 303.23 [FA(20:4)-H]−. Necrosis is accompanied by alterations in the tissue optical depolarization rate, allowing tissue polarimetry to guide DESI-MS analysis for rapid MS profiling or targeted MS imaging. This workflow, in combination with the MS profile of necrosis, may permit rapid characterization of necrotic tumors from tissue slices. Further, necrosis-specific biomarker ions are detected in seconds with single MS scans of necrotic tumor tissue smears, which further accelerates the identification workflow by avoiding tissue sectioning and slide preparation.
Effects of light acclimation on shoot morphology, structure, and biomass allocation of two Taxus species in southwestern China
Authors: Liu Wande , Su Jianrong 
Published: October 2016

AbstractAcclimation to changing light conditions plays a crucial role in determining the competitive capability of tree species. There is currently limited information about acclimation to natural light gradient and its effect on shoot structure and biomass in Taxus species. We examined the acclimation of the leaf and shoot axis morphology, structure and biomass allocation of Taxus yunnanensis and T. chinensis var. mairei under three different natural light environments, full daylight, 40–60% full daylight and <10% full daylight. The leaf biomass, nitrogen content per unit area, leaf carbon content per dry mass and leaf dry mass to fresh mass ratio increased with light in both species, demonstrating an enhanced investment of photosynthetic biomass and structural investment under high light. The number of leaves per unit shoot axis length and the leaf dry mass per unit shoot axis length increased with light in both species. However, the light increase did not result in the increase of the total shoot mass. T. yunnanensis produced larger leaves under low light and a higher shoot axis length per unit dry mass under high light, whereas the leaf size and biomass yield of T. chinensis var. mairei were not sensitive to light.
Directional amorphization of boron carbide subjected to laser shock compression
Authors: Zhao Shiteng , Kad Bimal , Remington Bruce A. , LaSalvia Jerry C. , Wehrenberg Christopher E. , Behler Kristopher D. , Meyers Marc A. 
Published: October 2016

Significance
When crystalline solids are stressed quasi-statically, dislocation slip, twinning, and phase transformations are the predominant mechanisms to dissipate the imparted elastic energy. Under shock, high hydrostatic and shear stresses promptly build up at the shock front, favoring fast energy dissipation mechanisms. Amorphization, which may only involve localized atomic arrangements, is therefore an additional potential candidate. Shock-induced amorphization has now been reported in various materials and hence should be incorporated as a deformation/damage mechanism of crystals subjected to high-strain-rate loading.
Recognition of enzymes lacking bound cofactor by protein quality control
Authors: Martínez-Limón Adrián , Alriquet Marion , Lang Wei-Han , Calloni Giulia , Wittig Ilka , Vabulas R. Martin 
Published: October 2016

Significance
Newly synthetized enzymes must fold correctly and associate with cofactors to reach their functional state. Mutations often interfere with the structural and functional maturation and lead to unstable proteins. Here we demonstrate that cofactor deprivation caused by vitamin B2 deficiency results in the destabilization of a significant fraction of flavin-containing enzymes, even if they have wild-type sequences. The accumulation of conditionally unstable proteins would overload cellular protein degradation systems; consequently, these proteins would contribute to amyloidogenesis and protein aggregation disorders. Because nutritional deficits often develop in aging organisms, this study provides an additional, protein stability-based explanation of the connection between vitamin supplies and healthy aging.
MIToS.jl: mutual information tools for protein sequence analysis in the Julia language
Authors: Zea Diego J , Anfossi Diego , Nielsen Morten , Marino-Buslje Cristina 
Published: October 2016

Abstract

Motivation
MIToS is an environment for mutual information analysis and a framework for protein multiple sequence alignments (MSAs) and protein structures (PDB) management in Julia language. It integrates sequence and structural information through SIFTS, making Pfam MSAs analysis straightforward. MIToS streamlines the implementation of any measure calculated from residue contingency tables and its optimization and testing in terms of protein contact prediction. As an example, we implemented and tested a BLOSUM62-based pseudo-count strategy in mutual information analysis.

Availability and Implementation
The software is totally implemented in Julia and supported for Linux, OS X and Windows. It’s freely available on GitHub under MIT license: http://mitos.leloir.org.ar.

Supplementary information
Supplementary data are available at Bioinformatics online.
Aseptically Processed Placental Membrane Improves Healing of Diabetic Foot Ulcerations: Prospective, Randomized Clinical Trial
Authors: DiDomenico Lawrence A. , Orgill Dennis P. , Galiano Robert D. , Serena Thomas E. , Carter Marissa J. , Kaufman Jarrod P. , Young Nathan J. , Zelen Charles M. 
Published: October 2016

Background:
Allogeneic grafts derived from amnion/chorion are known to be efficacious in healing chronic diabetic foot ulcerations (DFUs). The goal of this study was to compare aseptically processed dehydrated human amnion and chorion allograft (dHACA) versus standard of care (SOC) in facilitating wound closure in nonhealing DFUs.

Methods:
Patients with DFUs treated with SOC (off-loading, appropriate debridement, and moist wound care) after a 2-week screening period were randomized to either SOC or wound-size-specific dHACA (AmnioBand, Musculoskeletal Transplant Foundation, Edison, N.J.) applied weekly for up to 12 weeks plus SOC. Primary endpoint was the percentage of wounds healed at 6 weeks between groups.

Results:
At 6 weeks, 70% (14/20) of the dHACA-treated DFUs healed compared with 15% (3/20) treated with SOC alone. Furthermore, at 12 weeks, 85% (17/20) of the DFUs in the dHACA group healed compared with 25% (5/20) in the SOC group, with a corresponding mean time to heal of 36 and 70 days, respectively. At 12 weeks, the mean number of grafts used per healed wound for the dHACA group was 3.8 (median 3.0), and mean cost of the tissue to heal a DFU was $1400. The mean wastage at 12 weeks was 40%. One adverse event and 1 serious adverse event occurred in the dHACA group; neither was graft related. Three adverse events and 1 serious adverse event occurred in the SOC group.

Conclusion:
Aseptically processed dHACA heals diabetic foot wounds significantly faster than SOC at 6 and 12 weeks with minimal graft wastage.
Cochleariform Process Abutment on TBCT in Early Congenital Cholesteatoma
Authors: Lee Chang Ho , Kim So Young , Kim Hyoung-Mi , Kim Young Ju , Kim Ji Yoon , Kim Mi Kyung 
Published: October 2016

Objectives:
To study the influence of the cochleariform process abutment (CPA) of early congenital cholesteatomas (CC) (ECCs) on surgical outcomes.

Study Design:
Retrospective case review.

Setting:
University hospital otology referral clinic.

Patients:
Two hundred consecutive pediatric ECC patients.

Interventions:
The patients were classified into three groups based on the temporal bone computed tomography (TBCT) findings of ECC: A) the absence of CPA, B) the presence of CPA, and C) the presence of CPA and extension posterior to the malleus handle.

Main Outcome Measures:
Residual CC according to each of the TBCT and surgical stages during 34.9 ± 20.1 months of follow-up.

Results:
Group A was significantly associated with effortless delivery without matrix tearing (77%) even with simple myringotomy. Only 17% of group B experienced this outcome, and troublesome matrix tearing occurred in significantly more patients (p < 0.0001). Residual CCs were present in 17.5% of group B if matrix tears occurred, which was comparable to group C (22.0%) and significantly greater than group A (4.4%, p = 0.03). Normal hearing was preserved in 97.5% of the ECC patients both when the ECCs did not recur and when they recurred without CPA. However, residual ECCs with positive CPAs in five children (2.5%) required ossicle removal, and subsequent hearing loss.

Conclusions:
CPA is directly related to intraoperative matrix tear or increased recidivism, that CPA should be the landmark to distinguish stage II ECC from stage I. Surgeons should evaluate CPA on preoperative TBCTs of ECC patients, and restrict myringotomy approach to CPA negative ECC.
Usefulness of the Saccharin Test for Assessment of Eustachian Tube Function in Patients With Chronic Otitis Media With Perforation
Authors: Ikehata Miki , Ohta Shigeto , Mishiro Yasuo , Katsura Hirokazu , Miuchi Shinya , Tsuzuki Kenzo , Sakagami Masafumi 
Published: October 2016

Objective:
The eustachian tube (ET) has two important functions, ventilation and clearance of the middle ear. We evaluated the ET ventilator function by the sonotubometry and the inflation-deflation test that are widely used today, and the ET clearance function by the saccharin test. Results of both tests were compared with surgical outcomes, and assessed which test was more closely related to the surgical outcomes.

Study Design:
Prospective case series.

Setting:
A single university hospital.

Patients and Intervention:
One hundred four ears of 95 patients with chronic otitis media with perforation underwent type I tympanoplasty.

Main Outcomes and Measures:
Based on sonotubometry and the inflation–deflation test, the patients were divided into normal, stenosis, and patulous types. Based on the saccharin test, they were divided into a normal function group and a partial/gross dysfunction group. Surgical outcomes about the hearing results and the condition of the eardrum were assessed 1 year postoperatively. Preoperative evaluation of ET function was compared with the surgical outcome.

Results:
Sonotubometry and inflation-deflation tests showed there was no significant difference among the groups about the hearing improvement and the surgical success rate. The saccharin test showed that the rate of the hearing improvement was significantly lower in the gross dysfunction group and that the success rate of Type I tympanoplasty was significantly higher in the normal group than in the dysfunction group.

Conclusion:
There is a relationship between the saccharin test results and surgical outcomes.
Can Probiotics Reduce Diarrhea and Infant Mortality in Africa?
Authors: Del Piano Mario , Coggiola Francesco , Pane Marco , Amoruso Angela , Nicola Stefania , Mogna Luca 
Published: October 2016

Background:
Diarrhea accounts for 9% of the mortality among children under 5 years of age worldwide, and it is significantly associated with malnutrition. Each year, diarrhea kills around 760,000 children under 5 years of age and most of these are in sub-Saharan Africa.
In Uganda, the infant mortality rate of 58 per 1000 is unacceptably high, and the major contributors include malnutrition, diarrhea, pneumonia, malaria, prematurity, sepsis, and newborn illnesses.
There is an urgent need for intervention to prevent and control diarrheal diseases.

Study Design:
Our open-label, randomized controlled study has the primary endpoint of reducing diarrhea and infectious diseases (number of episodes/severity) and the secondary endpoint of decreasing infant mortality. The trial is currently conducted in Luzira, a suburb of Kampala, the capital of Uganda, and in Gulu and Lira, in the north of Uganda.
The study is projected to enroll 4000 babies (control=2000 and treatment=2000) who will be followed till 1 year of life. As controls, 2000 babies of the same community are planned to be considered.
The probiotic product selected for the trial is composed of 3 designated microorganisms, namely Bifidobacterium breve BR03 (DSM 16604), B. breve B632 (DSM 24706), and Lactobacillus delbrueckii subsp. delbrueckii LDD01 (DSM 22106). The concentration of the 3 bacteria is 108 viable cells/strain/daily dose (5 drops).

Perspectives:
For a total sample of 4000 babies, the study has an 80% power at a 5% significance level.
The Possible Innovative Use of Bifidobacterium longum W11 in Association With Rifaximin
Authors: Graziano Teresa , Amoruso Angela , Nicola Stefania , Deidda Francesca , Allesina Serena , Pane Marco , Piffanelli Pietro , Strozzi Francesco , Mogna Luca , Del Piano Mario 
Published: October 2016

Goals:
The aim of the study was to unequivocally demonstrate the nontransmissibility of the genes mediating the resistance of the strain Bifidobacterium longum W11 (LMG P-21586) to rifaximin.

Background:
Most antibiotic treatments can induce unfavorable side effects such as antibiotic-associated diarrhea, which is largely attributable to the disruption of the intestinal microbiota. The parallel intake of probiotic bacteria might reduce these events, even if with generally very poor results. In this regard, the use of antibiotic-resistant beneficial bacteria could represent a worthy strategy.

Study:
Rifaximin was tested in parallel with rifampicin, rifapentine, and rifabutin, all rifamycin derivates, using 5 different concentrations. Susceptibility tests were performed by the disc diffusion method of Kirby-Bauer, and inhibition zones were measured after incubation at 37°C. B. longum BL03 was used as comparison. The B. longum W11 genome was sequenced on Illumina MiSeq with a 250 PE reads module. After mapping the reads with the reference bacterial genome, the alignment data were processed using FreeBayes software.

Results:

B. longum BL03 was inhibited by all antibiotics even at the lowest concentration. In contrast, the W11 strain was inhibited by rifampicin, rifabutin, and rifaximin only at the highest concentration (512 μg/mL). The genomic analysis showed a mutation into the chromosomal DNA. No transposable elements were found, and the genetic locus was not flanked by close mobile genetic elements.

Conclusions:

B. longum W11 could be used in combined therapy with rifaximin, thus opening new focused frontiers in the probiotic era while preserving the necessary safety of use for consumers.
In Vitro Activity of Lactobacillus fermentum LF5 Against Different Candida Species and Gardnerella vaginalis
Authors: Deidda Francesca , Amoruso Angela , Allesina Serena , Pane Marco , Graziano Teresa , Del Piano Mario , Mogna Luca 
Published: October 2016

Goals:
This study was undertaken to demonstrate the ability of Lactobacillus fermentum LF5 (DSM 32277) to inhibit in vitro different Candida species and Gardnerella vaginalis to weigh its potential effectiveness even in mixed vaginal infections.

Background:
A wide female population is suffering from various vulvovaginal infections. These diseases are often associated with a decrease in the concentration of Lactobacilli in the vagina. Mixed vaginal infections represent >20% of women with vulvovaginal infection.

Study:
LF5 strain was cocultured in De Man, Rogosa and Sharpe with Candida according to a 1:100 ratio in favor of the yeast. Each culture was sampled after 24 hours of incubation for the selective enumeration of the yeasts performed on yeast extract glucose chloramphenicol agar medium.
The growth of Gardnerella alone (positive control) and in the presence of different concentrations of neutralized supernatants of L. fermentum LF5 ranging from 5% to 20% was quantified by means of optical density at 600 nm (OD600).

Results:

L. fermentum LF5 demonstrated the ability to inhibit significantly the growth of the 5 species of Candida by at least 4 logarithms.
Furthermore, L. fermentum LF5 showed a significant activity after both 24 and 48 hours (46% and 82% with 20% of neutralized supernatant, respectively). A significant dose-dependent growth inhibition was recorded in particular after 48 hours of incubation, even achieving a 80% inhibition of G. vaginalis growth.

Conclusions:
The biotherapeutic LF5 could be the only documented strain effective in mixed forms. For this purpose, a human clinical trial is in progress.
Bipolar Disorder With Psychotic Features and Ocular Toxoplasmosis
Authors: Del Grande Claudia , Contini Carlo , Schiavi Elisa , Rutigliano Grazia , Maritati Martina , Seraceni Silva , Pinto Barbara , Dell’Osso Liliana , Bruschi Fabrizio 
Published: October 2016

Abstract
Recent evidence suggests the involvement of Toxoplasma gondii infection in the emergence of psychotic and affective disorders. In this report, we describe the case of a young Brazilian woman affected by recurrent ocular toxoplasmosis and presenting with a manic episode with psychotic features in the context of a diagnosis of Bipolar Disorder (BD), type I. We observed a relationship between ocular manifestations and the clinical course of bipolar illness, confirmed by molecular analyses (nested-PCR), as well as by the high level of T. gondii specific IgG. This case report is the first showing the presence of circulating parasite DNA at the time of occurrence of psychiatric symptoms, thus providing further support for a possible role of the parasite in the pathogenesis of some cases of BD.
Assessing Binary Diagnoses of Bio-behavioral Disorders
Authors: Cicchetti Domenic V. , Klin Ami , Volkmar Fred R. 
Published: October 2016

Abstract
Cohen's (Educ Psychol Meth. 1960;23:37–40) kappa statistic has been criticized recently for providing low chance-corrected coefficients (<0.40) despite high levels of examiner agreement (e.g., ≥85%). The AC1 statistic (Series. 2002;2:1–9; BMC Med Res Methodol. 2013;13:61), the alpha statistic (J Clin Epidemiol. 1996;49:775–782), the B statistic (BMC Med Res Methodol. 2013;13:97), and the delta statistic (Commun Statist Theory Meth. 2008;37:760–772) were developed to “correct” this “problem.” Each of these statistics produces inaccurate results because they either derive from levels of chance agreement that are incorrect (Gwet's AC1 statistic) or fail to correct for chance levels of agreement (the alpha, B, and delta approaches). Implications for diagnoses of psychiatric disorders are critically discussed. The importance of kappa is demonstrated in a number of clinical scenarios.
Simulated Keratometry Repeatability in Subjects with and without Down Syndrome
Authors: Ravikumar Ayeswarya , Marsack Jason D. , Benoit Julia S. , Anderson Heather A. 
Published: October 2016

ABSTRACTPurposeTo assess the repeatability of simulated keratometry measures obtained with Zeiss Atlas topography for subjects with and without Down syndrome (DS).MethodsCorneal topography was attempted on 140 subjects with DS and 138 controls (aged 7–59 years). Subjects who had at least three measures in each eye were included in analysis (DS: n = 140 eyes (70 subjects) and controls: n = 264 eyes (132 subjects)). For each measurement, the steep corneal power (K), corneal astigmatism, flat K orientation, power vector representation of astigmatism (J0, J45), and astigmatic dioptric difference were determined for each measurement (collectively termed keratometry values here).For flat K orientation comparisons, only eyes with >0.50 DC of astigmatism were included (DS: n = 131 eyes (68 subjects) and control: n = 217 eyes (119 subjects)). Repeatability was assessed using (1) group mean variability (average standard deviation (SD) across subjects), (2) coefficient of repeatability (COR), (3) coefficient of variation (COV), and (4) intraclass correlation coefficient (ICC).ResultsThe keratometry values showed good repeatability as evidenced by low group mean variability for DS versus control eyes (≤0.26D vs. ≤0.09D for all dioptric values; 4.51° vs. 3.16° for flat K orientation); however, the group mean variability was significantly higher in DS eyes than control eyes for all parameters (p ≤ 0.03). On average, group mean variability was 2.5 times greater in the DS eyes compared to control eyes across the keratometry values. Other metrics of repeatability also indicated good repeatability for both populations for each keratometry value, although repeatability was always better in the control eyes.ConclusionsDS eyes showed more variability (on average: 2.5×) compared to controls for all keratometry values. Although differences were statistically significant, on average 91% of DS eyes had variability ≤0.50D for steep K and astigmatism, and 75% of DS eyes had variability ≤5 degrees for flat K orientation.
Modeling Corneal Oxygen with Scleral Gas Permeable Lens Wear
Authors: Compañ Vicente , Aguilella-Arzo Marcel , Edrington Timothy B. , Weissman Barry A. 
Published: October 2016

ABSTRACTPurposeThe main goal of this current work is to use an updated calculation paradigm, and updated boundary conditions, to provide theoretical guidelines to assist the clinician whose goal is to improve his or her scleral gas permeable (GP) contact lens wearing patients’ anterior corneal oxygen supply.MethodsOur model uses a variable value of corneal oxygen consumption developed through Monod equations that disallows negative oxygen tensions within the stroma to predict oxygen tension at the anterior corneal surface of scleral GP contact lens wearing eyes, and to describe oxygen tension and flux profiles, for various boundary conditions, through the lens, tears, and cornea. We use several updated tissue and boundary parameters in our model. Tear exchange with GP scleral lenses is considered nonexistent in this model.ResultsThe majority of current scleral GP contact lenses should produce some levels of corneal hypoxia under open eye conditions. Only lenses producing the thinnest of tear vaults should result in anterior corneal surface oxygen tensions greater than a presumed critical oxygen tension of 100 mmHg. We also find that corneal oxygen tension and flux are each more sensitive to modification in tear vault than to changes in lens oxygen permeability, within the ranges of current clinical manipulation.ConclusionsOur study suggests that clinicians would be prudent to prescribe scleral GP lenses manufactured from higher oxygen permeability materials and especially to fit without excessive corneal clearance.