bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of Descemet Membrane Endothelial Keratoplasty in Eyes With a Previous Descemet Stripping Automated Endothelial Keratoplasty Graft
Authors: Sorkin Nir , Showail Mahmood , Einan-Lifshitz Adi , Boutin Tanguy , Borovik Armand , Kreimei Mohammad , Rosenblatt Amir , Chan Clara C. , Rootman David S. 
Published: March 2018

Purpose:
To analyze the outcomes of Descemet membrane endothelial keratoplasty (DMEK) in eyes with previous Descemet stripping automated endothelial keratoplasty (DSAEK).

Methods:
This retrospective interventional case series included 26 eyes (26 patients) that underwent DMEK to replace a previous DSAEK graft with at least 6 months of follow-up. The outcome measures were indications for surgery, best spectacle-corrected visual acuity (BSCVA), endothelial cell density, rebubbling rate, rejection, and failure.

Results:
Patient age was 71.9 ± 12.6 years. The average follow-up time after DMEK was 15.1 ± 10.6 months. Indications for DMEK were DSAEK graft failure (69%) and a DSAEK suboptimal visual outcome (31%). BSCVA of the entire cohort (n = 26) improved from 1.33 ± 0.78 logMAR preoperatively to 1.04 ± 0.78 and 1.06 ± 0.89 logMAR at 6 months postoperatively and at the last follow-up, respectively (P = 0.019 and P = 0.033). BSCVA among eyes without visual comorbidities (n = 13) improved from 0.84 ± 0.50 logMAR preoperatively to 0.55 ± 0.47 and 0.51 ± 0.49 logMAR at 6 months postoperatively and at final follow-up, respectively (P = 0.023 for both). Of these eyes, 84.6% had improvement in BSCVA at 6 months postoperatively and at last follow-up. In the subgroup of 8 eyes with DMEK for suboptimal visual outcomes after DSAEK, BSCVA improved from 0.81 ± 0.44 to 0.52 ± 0.35 logMAR at final follow-up (P = 0.024). When excluding eyes with visual comorbidities, BSCVA of this subgroup (n = 5) improved from 0.54 ± 0.32 to 0.36 ± 0.25 logMAR at final follow-up (P = 0.038). BSCVA of this subgroup at 6 months postoperatively was not significantly different from preoperative BSCVA, when including visual comorbidities (n = 8, 0.75 ± 0.60 logMAR, P = 0.79) and when excluding visual comorbidities (n = 5, 0.40 ± 0.28 logMAR, P = 0.621). Endothelial cell density decreased from 2753 ± 307 cells/mm2 to 1659 ± 655 cells/mm2 6 months after surgery (39.7% loss, P = 0.005). Three eyes (11.5%) required rebubbling, and 5 eyes (19.2%) had secondary graft failure at 2 to 20 months.

Conclusions:
DMEK is effective for replacing previous DSAEK not only for graft failure but also for suboptimal visual outcomes.
Orbital Radiotherapy Combined With Corticosteroid Treatment for Thyroid Eye Disease-Compressive Optic Neuropathy
Authors: Gold Katherine G. , Scofield Stacy , Isaacson Steven R. , Stewart Michael W. , Kazim Michael 
Published: March 2018

Purpose:
To evaluate the effectiveness of orbital radiotherapy (ORT) in the treatment of thyroid eye disease (TED)–compressive optic neuropathy.

Methods:
A retrospective review of patients with corticosteroid-responsive compressive optic neuropathy due to TED treated with ORT. Study was conducted in compliance with Health Insurance Portability and Accountability Act. One hundred four patients (163 orbits) with a mean age of 61.7 years met inclusion criteria. Seventy-four percent (77/104) were female, and 32.7% (34/104) were current or previous smokers. A total absorbed dose of 2000 cGy fractionated in 10 treatment doses over the course of 2 weeks was administered to the retroocular tissues according to a standard protocol. The primary end point was failure of ORT, defined as persistent optic neuropathy following completion of radiotherapy that mandated urgent orbital decompression surgery.

Results:
Ninety-eight of 104 (94%) patients or 152 of 163 (93.3%) orbits did not require orbital decompression surgery during the acute phase. Patients who responded successfully to ORT had similar improvements in visual acuity, color vision, Humphrey threshold visual field testing, and afferent pupillary defects compared with patients who failed ORT and underwent urgent decompression surgery. Only 36.7% of successfully treated patients ultimately underwent elective surgery, including orbital decompression, strabismus, or eyelid surgery, during the inactive phase of TED.

Conclusions:
The data from this study, the largest retrospective review reported to date, supports the use of ORT in eyes with corticosteroid-responsive TED–compressive optic neuropathy. ORT may favorably alter the natural history of active-phase TED by preventing recurrent compressive optic neuropathy after withdrawal of corticosteroids.
Clinical presentation, assessment, and management of inducible laryngeal obstruction
Authors: Haines Jemma , Hull James H. , Fowler Stephen J. 
Published: March 2018

Purpose of review
Many aspects of inducible laryngeal obstruction (ILO) are still poorly understood. However, in recent years there have been advances made and an international consensus has achieved a standardized taxonomy. This review will synthesize recent research; specifically, relating to clinical presentation, assessment, and therapeutic interventions.

Recent findings
The evidence base is growing but still limited for ILO and mostly comprises retrospective reviews, case studies, and anecdotal reports. The proposed relationship between ILO and other manifestations of laryngeal dysfunction via laryngeal hypersensitivity and hyperresponsiveness warrants further investigation. Progress has been made with guidelines published on laryngoscopy reporting procedures and validated symptom questionnaires produced for clinical use, although diagnostic algorithms are yet to be established. Emerging conservative and surgical interventions show promise, although as yet there are no randomized controlled trials investigating treatment efficacy.

Summary
The field is in an embryonic state and key research priorities, acknowledged in the current literature, need to be addressed to positively impact patient care.
Anal Malignant Melanoma Manifesting Hepatic Metastases Shown on FDG PET/CT
Authors: Zou Sijuan , Cheng Zhaoting , Song Shuang , Kuang Dong , Zhu Xiaohua 
Published: March 2018

Abstract
Multiple hepatic metastases are uncommon as initial presentation of primary anal malignant melanoma. We report FDG PET/CT findings of pathology-proven hepatic metastases from anal malignant melanoma of unknown origin in a 43-year-old woman whose initial presentation was worsening abdominal pain.
We need to talk about reliability: Making better use of test-retest studies for study design and interpretation
Authors: Matheson Granville J. 
Published: March 2018

ABSTRACTPositron emission tomography (PET), along with many other fields of clinical research, is both timeconsuming and expensive, and recruitable patients can be scarce. These constraints limit the possibility of large-sample experimental designs, and often lead to statistically underpowered studies. This problem is exacerbated by the use of outcome measures whose accuracy is sometimes insufficient to answer the scientific questions posed. Reliability is usually assessed in validation studies using healthy participants, however these results are often not easily applicable to clinical studies examining different populations. I present a new method and tools for using summary statistics from previously published test-retest studies to approximate the reliability of outcomes in new samples. In this way, the feasibility of a new study can be assessed during planning stages, and before collecting any new data. An R package called relfeas also accompanies this article for performing these calculations. In summary, these methods and tools will allow researchers to avoid performing costly studies which are, by virtue of their design, unlikely to yield informative conclusions.
Knomics-Biota - a system for exploratory analysis of human gut microbiota data
Authors: Popenko Anna , Tyakht Alexander , Vasilyev Anatoly , Altukhov Ilya , Efimova Daria , Odintsova Vera , Klimenko Natalya , Loshkarev Robert , Pashkova Maria , Elizarova Anna , Voroshilova Viktoriya , Slavskii Sergei , Pekov Yury , Filipova Ekaterina , Shashkova Tatyana , Levin Evgenii , Alexeev Dmitry 
Published: March 2018

AbstractSummaryMetagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for exploration of experimental data are of high interest to researchers. Knomics-Biota is a Web-based resource for exploratory analysis of human gut metagenomes. Users can generate analytical reports that correspond to common experimental schemes (like case-control study or paired comparison). Statistical analysis and visualizations of microbiota composition are provided in association with the external factors and in the context of thousands of publicly available datasets.Availability and ImplementationThe Web-service is available at https://biota.knomics.ru.Contactanna.popenko@knomics.ru or a.tyakht@gmail.com.Supplementary informationSupplementary figures are available at Bioinformatics online.
Latent-Based Imputation of Laboratory Measures from Electronic Health Records: Case for Complex Diseases
Authors: Abedi V. , Shivakumar M.K. , Lu P. , Hontecillas R. , Leber A. , Ahuja M. , Ulloa A.E. , Shellenberger M.J. , Bassaganya-Riera J. 
Published: March 2018

AbstractImputation is a key step in Electronic Health Records-mining as it can significantly affect the conclusions derived from the downstream analysis. There are three main categories that explain the missingness in clinical settings–incompleteness, inconsistency, and inaccuracy–and these can capture a variety of situations: the patient did not seek treatment, the health care provider did not enter the information, etc. We used EHR data from patients diagnosed with Inflammatory Bowel Disease from Geisinger Health System to design a novel imputation that focuses on a complex phenotype. Our approach is based on latent-based analysis integrated with clustering to group patients based on their comorbidities before imputation. IBD is a chronic illness of unclear etiology and without a complete cure. We have taken advantage of the complexity of IBD to pre-process the EHR data of 10,498 IBD patients and show that imputation can be improved using shared latent comorbidities. The R code and sample simulated input data will be available at a future time.
Genome-wide association study meta-analysis of the Alcohol Use Disorder Identification Test (AUDIT) in two population-based cohorts (N=141,932)
Authors: Sanchez-Roige Sandra , Palmer Abraham A. , Fontanillas Pierre , Elson Sarah L. ,   The 23andMe Research Team,   Substance Use Disorder Working Group of the Psychiatric Genomics Consortium, Adams Mark J. , Howard David M. , Edenberg Howard J. , Davies Gail , Crist Richard C. , Deary Ian J. , McIntosh Andrew M. , Clarke Toni-Kim 
Published: March 2018

AbstractAlcohol use disorders (AUD) are common conditions that have enormous social and economic consequences. We obtained quantitative measures using the Alcohol Use Disorder Identification Test (AUDIT) from two population-based cohorts of European ancestry: UK Biobank (UKB; N=121,604) and 23andMe (N=20,328) and performed a genome-wide association study (GWAS) meta-analysis. We also performed GWAS for AUDIT items 1-3, which focus on consumption (AUDIT-C), and for items 4-10, which focus on the problematic consequences of drinking (AUDIT-P). The GWAS meta-analysis of AUDIT total score identified 10 associated risk loci. Novel associations localized to genes including JCAD and SLC39A13; we also replicated previously identified signals in the genes ADH1B, ADH1C, KLB, and GCKR. The dimensions of AUDIT showed positive genetic correlations with alcohol consumption (rg=0.76-0.92) and Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) alcohol dependence (rg=0.33-0.63). AUDIT-P and AUDIT-C showed significantly different patterns of association across a number of traits, including psychiatric disorders. AUDIT-P was positively genetically correlated with schizophrenia (rg=0.22, p=3.0×10−10), major depressive disorder (rg=0.26, p=5.6×10−3), and attention-deficit/hyperactivity disorder (ADHD; rg=0.23, p=1.1×10−5), whereas AUDIT-C was negatively genetically correlated with major depressive disorder (rg=−0.24, p=3.7×10−3) and ADHD (rg=−0.10, p=1.8×10−2). We also used the AUDIT data in the UKB to identify thresholds for dichotomizing AUDIT total score that optimize genetic correlations with DSM-IV alcohol dependence. Coding individuals with AUDIT total score of ≤4 as controls and ≥12 as cases produced a high genetic correlation with DSM-IV alcohol dependence (rg=0.82, p=3.2×10−6) while retaining most subjects. We conclude that AUDIT scores ascertained in population-based cohorts can be used to explore the genetic basis of both alcohol consumption and AUD.
Inflammatory bowel disease microbiotas alter gut CD4 T-cell homeostasis and drive colitis in mice
Authors: Britton Graham J. , Contijoch Eduardo J. , Mogno Ilaria , Vennaro Olivia H. , Llewellyn Sean R. , Ng Ruby , Li Zhihua , Mortha Arthur , Merad Miriam , Das Anuk , Gevers Dirk , McGovern Dermot P.B. , Singh Namita , Braun Jonathan , Jacobs Jonathan P. , Clemente Jose C. , Grinspan Ari , Sands Bruce E. , Colombel Jean-Frederic , Dubinsky Marla C. , Faith Jeremiah J. 
Published: March 2018

AbstractTo examine the functional contribution of Inflammatory Bowel Disease (IBD) microbes to immune homeostasis and colitis, we colonized unchallenged and colitis-susceptible germ-free mice with over twenty human intestinal microbiotas from healthy and IBD donors. Compared to healthy microbiotas, IBD microbiotas led to expanded RORγt+Th17 cells and reduced RORγt+Treg in the gut of unchallenged gnotobiotic mice and increased disease severity in colitis-susceptible mice. The proportions of RORγt+Th17 and RORγt+Treg induced by each microbiota were highly predictive of the human disease status and strongly correlated with disease severity in colitis-susceptible mice colonized with the same human microbiotas. The transmittable functional potential of IBD microbes suggests a mechanism for a microbial contribution to IBD pathogenesis and a potential route for its treatment and prevention.
A Russian validation study of the Coma Recovery Scale-Revised (CRS-R)
Authors: Mochalova Elizaveta G. , Legostaeva Liudmila A. , Zimin Alexey A. , Sergeev Dmitry V. , Domashenko Maxim A. , Samorukov Vladislav Y. , Yusupova Dzhamilya G. , Ryabinkina Julia V. , Suponeva Natalia A. , Piradov Michael A. , Bodien Yelena. G. , Giacino Joseph T. 
Published: March 2018

AbstractIntroduction: The aim of the present study was to validate a Russian adaptation of the Coma Recovery Scale–Revised (CRS-R).Subjects and methods: We evaluated 58 patients diagnosed with chronic disorders of consciousness (>4 weeks post-injury, DOC) of various etiology and two patients in a locked-in state at different time points in their post-comatose recovery. We tested sensitivity for changes over 1 week, reliability, as well as criterion validity and diagnostic sensitivity of the Russian adaptation of the CRS-R in comparison with the Russian adaptations of Full Outline of UnResponsiveness Score (FOUR), and Glasgow Coma Scale (GCS).Results: We obtained good sensitivity for changes in neurological status over one week (p<0.0001) and good test-retest reliability (r=1, p<0.0001) of the CRS-R. Inter-rater reliability for the CRS-R total score (κ=0.99, p<0.001) and subscale scores was good. We showed high internal consistency (α=0.87 and 0.89 for the first and second visit respectively). We also showed good criterion validity between two other standardized behavioral scales (moderate correlation with GCS, r=0.597 and high correlation with FOUR Score, r=0.900). CRS-R also demonstrated a significantly higher sensitivity in differential diagnosis of DOC, as compared to GCS, and FOUR Score (p<0.001).Conclusion: The results show that the Russian version of the CRS-R is a valid and sensitive tool for the evaluation of severely brain damaged patients with chronic DOC which can be used for differential diagnosis and for the assessment of dynamic recovery.
Endogenous protection from ischemic brain injury by preconditioned monocytes
Authors: Garcia-Bonilla Lidia , Brea David , Benakis Corinne , Lane Diane , Murphy Michelle , Moore Jamie , Racchumi Gianfranco , Jiang Xinran , Iadecola Costantino , Anrather Josef 
Published: March 2018

AbstractExposure to low dose lipopolysaccharide prior to cerebral ischemia is neuroprotective in stroke models, a phenomenon termed preconditioning. While it is well established that lipopolysaccharide-preconditioning induces central and peripheral immune responses, the cellular mechanisms modulating ischemic injury remain unclear. Here, we investigated the role of immune cells in the brain protection afforded by preconditioning and we tested whether monocytes may be reprogrammed byex vivolipopolysaccharide exposure thus modulating the inflammatory injury after cerebral ischemia in male mice. We found that systemic injection of low-dose lipopolysaccharide induces a distinct subclass of CD115+Ly6Chimonocytes that protect the brain after transient middle cerebral artery occlusion in mice. Remarkably, adoptive transfer of monocytes isolated from preconditioned mice into naïve mice 7 hours after transient middle cerebral artery occlusion reduced brain injury. Gene expression and functional studies showed that IL-10, iNOS and CCR2 in monocytes are essential for the neuroprotection. This protective activity was elicited even if mouse or human monocytes were exposedex vivoto lipopolysaccharide and then injected into male mice after stroke. Cell tracking studies showed that protective monocytes are mobilized from the spleen and reach brain and meninges, wherein they suppressed post-ischemic inflammation and neutrophils influx into the brain parenchyma. Our findings unveil a previously unrecognized subpopulation of splenic monocytes capable to protect the brain with an extended therapeutic window, and provide the rationale for cell therapies based on the delivery of autologous or allogeneic protective monocytes into patients with ischemic stroke.Significance StatementInflammation is a key component of the pathophysiology of the brain in stroke, a leading cause of death and disability with limited therapeutic options. Here, we investigate endogenous mechanisms of protection against cerebral ischemia. Using LPS preconditioning as an approach to induce ischemic tolerance in mice, we found the generation of neuroprotective monocytes within the spleen from where they traffic to the brain and meninges suppressing post-ischemic inflammation. Importantly, systemic LPS preconditioning can be mimicked by adoptive transfer ofin vitro-preconditioned mouse or human monocytes at translational relevant time points after stroke. This model of neuroprotection may facilitate clinical efforts to increase the efficacy of bone marrow mononuclear cell treatments in acute neurological diseases such as cerebral ischemia.
Near-Infrared Spectroscopy for metabolite quantification and species identification
Authors: Aw WC , Ballard JWO 
Published: March 2018

AbstractThe aim of the study was to investigate the accuracy of near-infrared spectroscopy (NIRS) in determining triglyceride level and species of wild caught Drosophila. NIRS is a remote sensing method that uses the near-infrared region of the electromagnetic spectrum. It detects the absorption of light by molecular bonds and can be used with live insects. We employ the chemometric approach to combine spectra and reference data from a known sample to produce a multivariate calibration model. Once the calibration model was developed, we used an independent set to validate the accuracy of the calibration model. The optimized calibration model for triglyceride quantification yielded an accuracy of 73%. Simultaneously, we used NIRS to discriminate two species of Drosophila. Flies from independent sets were correctly classified into D. melanogaster and D. simulans with accuracy higher than 80%. Finally, we show that the biological interpretations derived from reference data and the NIRS predictions do not differ. These results suggest that NIRS has the potential to be used as a high throughput screening method to assess a live individual insect’s triglyceride level and taxonomic status.
Comparison of different methods for average anatomical templates creation: do we really gain anything from a diffeomorphic framework?
Authors: Fonov Vladimir S. , Collins D. Louis 
Published: March 2018

AbstractIn the field of computation anatomy, the diffeomorphic framework is widely used to perform analysis of human brain anatomy in both healthy and diseased populations. While useful for analysis, the framework imposes certain implementation constraints that do not necessarily result in improved accuracy of inter-subject co-registration in case of average anatomical template (AAT) construction – a common technique used in large population studies. In this work, we evaluated several state-of-the-art non-diffeomorphic and diffeomorphic non-linear registration frameworks in terms of their ability to build AATs. While all methods generated well behaved transforms, we found that the diffeomorphic framework does not automatically guarantee an increase of accuracy in average anatomical template construction.
Focal optogenetic suppression in macaque area MT biases direction discrimination and choice confidence, but only transiently
Authors: Fetsch Christopher R. , Odean Naomi N. , Jeurissen Danique , El-Shamayleh Yasmine , Horwitz Gregory D. , Shadlen Michael N. 
Published: March 2018

AbstractInsights from causal manipulations of brain activity depend on targeting the spatial and temporal scale most relevant for behavior. Using a sensitive perceptual decision task in monkeys, we examined the effects of randomly-interleaved, rapid, reversible inactivation on a spatial scale previously achieved only with electrical microstimulation. Inactivating neurons in area MT with consistent direction tuning produced systematic effects on choice and confidence. Behavioral effects were attenuated over the course of each session, suggesting compensatory adjustments in the downstream readout of MT over tens of minutes. Compensation also occurred on a sub-second time scale: behavior was largely unaffected on trials with visual stimuli (and concurrent suppression) longer than ∼350ms. These trends were similar for choice and confidence, consistent with the idea of a common mechanism underlying both measures. The findings demonstrate the utility of hyperpolarizing opsins for linking neural population activity at fine spatial and temporal scales to cognitive functions in primates.