bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Methodology to Identify a Cohort of Medicare Beneficiaries Residing in Large Assisted Living Facilities Using Administrative Data
Authors: Thomas Kali S. , Dosa David , Gozalo Pedro L. , Grabowski David C. , Nazareno Jennifer , Makineni Rajesh , Mor Vincent 
Published: November 2016

Background:
Assisted living is a popular option for housing and long-term care.

Objective:
To develop and test a methodology to identify Medicare beneficiaries residing in assisted living facilities (ALFs).

Research Design:
We compiled a finder file of 9-digit ZIP codes representing large ALFs (25+ beds) by matching Outcome and Assessment Information Set (OASIS) assessments and Medicare Part B Claims to the Medicare enrollment records and addresses of 11,751 ALFs. Using this finder file, we identified 738,567 beneficiaries residing in validated ALF ZIP codes in 2007–2009. We compared characteristics of this cohort to those of ALF residents in the National Survey of Residential Care Facilities (n=3009), a sample of community-dwelling Medicare beneficiaries (n=33,025,690), and long-stay nursing home residents (n=1,287,572).

Data Sources:
A national list of licensed ALFs, Medicare enrollment records, and administrative health care databases.

Results:
The ALF cohort we identified had good construct validity based on their demographic characteristics, health, and health care utilization when compared with ALF residents in the National Survey of Residential Care Facilities, community-dwelling Medicare beneficiaries, and long-stay nursing home residents.

Conclusions:
Our finder file of 9-digit ZIP codes enables identification of ALF residents using administrative data. This approach will allow researchers to examine questions related to the quality of care, health care utilization, and outcomes of residents in this growing sector of long-term care.
The Relationship Between Index Hospitalizations, Sepsis, and Death or Transition to Hospice Care During 30-Day Hospital Readmissions
Authors: Dietz Brett W. , Jones Tiffanie K. , Small Dylan S. , Gaieski David F. , Mikkelsen Mark E. 
Published: November 2016

Background:
Hospital readmissions are common, expensive, and increasingly used as a metric for assessing quality of care. The relationship between index hospitalizations and specific outcomes among those readmitted remains largely unknown.

Objectives:
Identify risk factors present during the index hospitalization associated with death or transition to hospice care during 30-day readmissions and examine the contribution of infection in readmissions resulting in death.

Research Design:
Retrospective cohort study.

Subjects:
A total of 17,716 30-day readmissions in an academic health system.

Measures:
We used mixed-effects multivariable logistic regression models to identify risk factors associated with the primary outcome, in-hospital death, or transition to hospice during 30-day readmissions.

Results:
Of 17,716 30-day readmissions, 1144 readmissions resulted in death or transition to hospice care (6.5%). Risk factors identified included: age, burden, and type of comorbid conditions, recent hospitalizations, nonelective index admission type, outside hospital transfer, low discharge hemoglobin, low discharge sodium, high discharge red blood cell distribution width, and disposition to a setting other than home. Sepsis (OR=1.33; 95% CI, 1.02–1.72; P=0.03) and shock (OR=1.78; 95% CI, 1.22–2.58; P=0.002) during the index admission were associated with the primary outcome, and in-hospital mortality specifically. In patients who died, infection was the primary cause for readmission in 51.6% of readmissions after sepsis and 28.6% of readmissions after a nonsepsis hospitalization (P=0.009).

Conclusions:
We identified factors, including sepsis and shock during the index hospitalization, associated with death or transition to hospice care during readmission. Infection was frequently implicated as the cause of a readmission that ended in death.
The role of the transcriptional repressor growth factor independent 1 in the formation of myeloid cells
Authors: Fraszczak Jennifer , Möröy Tarik 
Published: November 2016

Purpose of review
Growth factor independent 1 (Gfi1) is a transcriptional repressor that plays multiple roles during myeloid commitment and development. Gfi1-deficient mice lack granulocytes, accumulate aberrant monocytes and show a hyperactivity of macrophages toward bacterial cell wall components. Since these initial findings, numerous additional studies have confirmed the role of Gfi1 in myeloid differentiation from hematopoietic stem cells and multipotent progenitors to bipotential lymphoid/myeloid precursors and myeloid effector cells. This review will summarize the existing knowledge concerning the mechanisms through which Gfi1 exerts these actions and will highlight recent insights into its additional implication in myeloid malignancies.

Recent findings
Gfi1 has more recently been implicated in myeloid malignancies, in particular in myelodysplasia, myeloproliferative neoplasms and in acute myeloid leukemia, a fatal disease, which is essentially treated today the same way as 30 years ago.

Summary
Recent findings on the role of Gfi1 in myeloid malignancies together with the knowledge base built over many years on this molecule may help us to find new ways to predict the progression of acute myeloid leukemia and to design more efficient epigenetic drugs to treat this disease.
Platelets in neutrophil recruitment to sites of inflammation
Authors: Pitchford Simon , Pan Dingxin , Welch Heidi C.E. 
Published: November 2016

Purpose of review
This review describes the essential roles of platelets in neutrophil recruitment from the bloodstream into inflamed and infected tissues, with a focus on recent findings.

Recent findings
Platelets are required for the recruitment of neutrophils to sites of inflammation and infection. They fulfil this role largely by enabling contacts of circulating neutrophils with the inflamed blood vessel wall prior to extravasation. Platelets promote both early stages of neutrophil recruitment (tethering, rolling, arrest, firm adhesion) and – as recent work has demonstrated – later stages (intravascular crawling and diapedesis). Recent studies have also begun to identify platelet-signaling pathways that can elicit the underlying interactions between platelets, neutrophils and vascular endothelial cells without stimulating concomitant platelet aggregation and thrombus formation. These pathways include Rho-guanine-nucleotide binding proteins and Rho-guanine-nucleotide exchange factors.

Summary
Recent findings have contributed to our burgeoning understanding of the platelet-dependent mechanisms that control neutrophil recruitment to sites of inflammation and have opened up new avenues of research aimed at increasing our knowledge of these mechanisms further. These insights might lead to the development of novel anti-inflammatory drugs that will be useful in a wide range of inflammatory diseases without causing immunodeficiency.
Consequences of extracellular trap formation in sepsis
Authors: O’Brien Xian M. , Biron Bethany M. , Reichner Jonathan S. 
Published: November 2016

Purpose of review
This review will focus on in-vivo findings derived from animal models of sepsis regarding the trapping role of neutrophil extracellular traps (NETs) which is difficult to assess ex vivo. The NETotic response of neutrophils at sites of sterile injury or autoimmune disease is destructive as no antimicrobial advantage to the host is realized and dampening NETosis is largely beneficial. In early stages of local infection or in sepsis, the trapping function of NETs may help abscess formation and limit microbial dissemination.

Recent findings
The trapping function of NETs limits bacterial dissemination keeping an abscess from becoming bacteremic or confining tissue infection to local sites. Once containment is lost and disease has progressed, the best therapeutic approach suggested by animal studies to date is to inhibit protein arginine deiminase 4 and prevent NETosis rather than attempting to neutralize caustic NET components. Prognostic value may best be realized by taking cell free DNA, citrulllinated histones, neutrophil function and counts of immature granulocytes into consideration rather than rely on any one measure alone.

Summary
The trapping function of NETs may supercede the value of antimicrobial function in the early phases of sepsis such that degradation of the DNA backbone is contraindicated.
Immune Dysfunction After Completion of Childhood Leukemia Therapy
Authors: Perkins Joanna L. , Harris Anne , Pozos Tamara C. 
Published: November 2016

Background:
Children with leukemia suffer immune dysfunction from their malignancy and chemotherapy. The immune system components most affected, the degree to which immune suppression occurs, and the duration of immunodeficiency are incompletely characterized. This study measures immunologic parameters following completion of therapy.

Methods:
This is a prospective, single institution cohort study. Eligible children with acute myelogenous or acute lymphoblastic leukemia diagnosed between 1 and 21 years of age were enrolled at therapy completion. Immune parameters were assessed at the end of therapy and 6 months later: complete blood counts, immunoglobulin levels, quantitative lymphocyte subsets, mitogen-induced lymphocyte proliferation, natural killer cell function, and vaccine titers.

Results:
Twenty patients were evaluated; 13 (65%) were female, 15 had acute lymphoblastic leukemia (75%). Mean age at diagnosis was 7.9 years. At end of therapy, all patients had some degree of immune dysfunction. At 6 months posttherapy, persistent abnormalities included: leukopenia (25%), neutropenia (15%), lymphopenia (5%), hypogammaglobulinemia (25%), one or more subtherapeutic vaccine titers (100%), abnormal lymphocyte subset levels (20%), decreased (15%), or absent (10%) natural killer cell function and abnormal lymphocyte proliferative responses (25%).

Conclusions:
All patients had multiple abnormalities at end of therapy, and all patients had some degree of persistent immune dysfunction at 6 months after completion of therapy. Clinical implications of these laboratory abnormalities are currently unknown; longer term evaluations are ongoing. We demonstrate that survivors of childhood cancer have lasting quantitative and functional immunologic defects and may remain at risk for infectious complications after completion of therapy.
Seasonal Effect on Ocular Sun Exposure and Conjunctival UV Autofluorescence
Authors: Haworth Kristina M. , Chandler Heather L. 
Published: November 2016

ABSTRACT

Purpose
To evaluate feasibility and repeatability of measures for ocular sun exposure and conjunctival ultraviolet autofluorescence (UVAF), and to test for relationships between the outcomes.

Methods
Fifty volunteers were seen for two visits 14 ± 2 days apart. Ocular sun exposure was estimated over a 2-week time period using questionnaires that quantified time outdoors and ocular protection habits. Conjunctival UVAF was imaged using a Nikon D7000 camera system equipped with appropriate flash and filter system; image analysis was done using ImageJ software. Repeatability estimates were made using Bland-Altman plots with mean differences and 95% limits of agreement calculated. Non-normally distributed data was transformed by either log10 or square root methods. Linear regression was conducted to evaluate relationships between measures.

Results
Mean (±SD) values for ocular sun exposure and conjunctival UVAF were 8.86 (±11.97) hours and 9.15 (±9.47) mm2, respectively. Repeatability was found to be acceptable for both ocular sun exposure and conjunctival UVAF. Univariate linear regression showed outdoor occupation to be a predictor of higher ocular sun exposure; outdoor occupation and winter season of collection both predicted higher total UVAF. Furthermore, increased portion of day spent outdoors while working was associated with increased total conjunctival UVAF.

Conclusions
We demonstrate feasibility and repeatability of estimating ocular sun exposure using a previously unreported method and for conjunctival UVAF in a group of subjects residing in Ohio. Seasonal temperature variation may have influenced time outdoors and ultimately calculation of ocular sun exposure. As winter season of collection and outdoor occupation both predicted higher total UVAF, our data suggests that ocular sun exposure is associated with conjunctival UVAF and, possibly, that UVAF remains for at least several months after sun exposure.
When Protocols Become Fairy Tales and Gods Remain Buried Under
Authors: Acharya Jenash , Shrestha Rijen , Shrestha Pramod Kumar , Kanchan Tanuj , Krishan Kewal 
Published: November 2016

Abstract
More than a year has passed since the mega quake hit Nepal. Although a lot is written about the lacunae in disaster preparedness, lessons learnt, and public health concerns after the aftermath, nothing much has been written about the fate of the deceased. Although saving takes priority after a disaster, the management of dead bodies also requires immediate attention because the process of identification becomes more difficult and expensive as time passes. This article shares the firsthand experiences of forensic experts at ground zero during the quake that may be useful to forensic experts responsible for handling such situations worldwide.
Impact of Functional Deficits in Instrumental Activities of Daily Living in Mild Cognitive Impairment
Authors: Devanand Davangere P. , Liu Xinhua , Brown Patrick J. 
Published: November 2016

Background:
The utility of functional deficits in patients with mild cognitive impairment is not established.

Materials and Methods:
In 3886 individuals with mild cognitive impairment evaluated and followed at 34 National Alzheimer Coordinating Center sites, informant-reported Pfeffer Functional Activities Questionnaire (FAQ) items associated with progression to dementia were derived in a training set (n=1943) and tested in the validation set (n=1943).

Results:
In the training set, the optimal combination comprised 6 FAQ items (FAQ6): difficulties with finances (2 items), remembering events/appointments, playing games of skill, current events, and travel. In the validation set, hazard ratio for dementia increased from 2.00 for 1 FAQ6 deficit to 5.56 for 6 FAQ6 deficits. In patients 50 to 67 years old with high Mini Mental State Exam scores, dementia risk rose from 12.06% for no FAQ6 deficits to 56.75% for 6 functional deficits. Likelihood of progression to dementia reached 80% to 89% in older age groups with low Mini Mental State Exam and severe FAQ6 deficits.

Conclusions:
Specific functional deficits increased dementia risk and, with age and global cognition, constituted a validated clinical algorithm to estimate dementia risk. Clinicians can use this clinically important algorithm to personalize decision-making about further investigation and identify high-risk patients for early treatment or inclusion in clinical trials.
Recruiting US Chinese Elders Into Clinical Research for Dementia
Authors: Li Clara , Neugroschl Judith , Umpierre Mari , Martin Jane , Huang QiYing , Zeng Xiaoyi , Cai Dongming , Sano Mary 
Published: November 2016

Purpose:
This study described and evaluated the rapid recruitment of elderly Chinese into clinical research at the Mount Sinai Alzheimer’s Disease Research Center (MSADRC).

Design and Methods:
Methods of publicizing the study included lectures to local senior centers/churches and publications in local Chinese newspapers. The amount of time and success of these methods were evaluated. A “go to them” model of evaluation was used to enable participants to complete the study visit at locations where they were comfortable.

Results:
From January to December 2015, we recruited 98 participants aged 65 years or older who primarily speak Mandarin/Cantonese and reside in New York. The mean age and years of education was 73.93±6.34 and 12.79±4.58, respectively. The majority of participants were female (65.3%) and primarily Mandarin speaking (53.1%). Of all enrollees, 54.1% were recruited from community lectures, 29.6% through newspapers, 10.2% through word of mouth, and 6.1% from our clinical services. About 40.8% of participants underwent evaluations at the MSADRC, 44.9% at local senior centers/churches, and 14.3% at home.

Implications:
Given that the majority of our participants had low English proficiency, the use of bilingual recruiters probably allowed us to overcome the language barrier, facilitating recruitment. Our “go to them” model of evaluation is another important factor contributing to our successful recruitment.
Periodic Discharges: Insight From Magnetoencephalography
Authors: Shvarts Vladimir , Zoltay Gabor , Bowyer Susan M. , Zillgitt Andrew , Moran John E. , Mason Karen , Tepley Norman , Burdette David 
Published: November 2016

Purpose:
This study used magnetoencephalography (MEG) dipole localization and coherence measurement to evaluate the magnetic fields associated with periodic discharges. The primary goal of the study was to evaluate whether MEG could consistently localize quasiperiodic discharges that were observed on the EEG portion of the recording. The secondary objective was to evaluate whether coherence measurements would correlate with topographic maxima of epileptiform activity.

Methods:
A total of 13 inpatients, whose electrographic records demonstrated lateralized periodic discharges (LPDs), were recruited from Henry Ford Hospital neurology and intensive care units. Nine patients were found clinically to be in status epilepticus before the EEG determination of LPDs. Spontaneous cortical brain activity was recorded with 148-channel MEG for 10 minutes. Data were sampled at 508 Hz and DC-100 Hz and filtered from 1 Hz to 40 Hz. Interictal events were imaged with single equivalent current dipole localization. Magnetoencephalography coherence source imaging analysis was performed and compared with the cortical topography of LPD patterns and with the focal lesions seen on the MRI (9 patients) or computed tomography (5 patients) imaging modalities.

Results:
The morphology of periodic waveforms was similar between EEG and MEG portions of the study. In patients with substrate positivity on imaging studies, coherence analysis revealed a tendency for LPDs to arise from the interface between the lesion and the surrounding, uncompromised cortex rather than from the lesion itself. In nonlesional patients with recent status epilepticus, the localization of maximal coherence was in the temporal lobes.

Conclusions:
This study demonstrated that MEG is able to detect and localize LPDs arising from damaged and adjacent cortex. The MEG coherence source imaging measurements also suggest the presence of epileptogenic networks perilesionally in cases with focal lesions on imaging. In patients without acute anatomic abnormality, the MEG coherence identified the epileptogenic networks in temporal lobe structures. Magnetoencephalography coherence source imaging may provide physicians with markers for differentiating between LPDs arising from acute injury currents versus LPDs arising from prolonged status epilepticus.
Secure Wavelet Matrix: Alphabet-Friendly Privacy-Preserving String Search
Authors: Sudo Hiroki , Jimbo Masanobu , Nuida Koji , Shimizu Kana 
Published: November 2016

AbstractMotivationPrivacy-preserving substring matching is an important task for sensitive biological/biomedical sequence database searches. It enables a user to obtain only a substring match while his/her query is concealed to a server. The previous approach for this task is based on a linear-time algorithm in terms of alphabet size |Σ|. Therefore, a more efficient method is needed to deal with strings with large alphabet size such as a protein sequence, time-series data, and a clinical document.ResultsWe present a novel algorithm that can search a string in logarithmic time of |Σ|. In our algorithm, named secure wavelet matrix (sWM), we use an additively homomorphic encryption to build an efficient data structure called a wavelet matrix. In an experiment using a simulated string of length 10,000 whose alphabet size ranges from 4 to 1024, the run time of the sWM was an order of magnitude faster than that of the previous method. We also tested the sWM on all sequences of one protein family in Pfam (9,826 residues in total) and clinical texts written in a natural language (77,712 letters in total). By using a laptop computer for the user and a desktop PC for the server, we found that its run time was ≈ 2.5 s (user) and ≈ 6.7 s (server) for the protein sequences and ≈ 10 s (user) and ≈ 60 s (server) for the clinical texts.Availabilityhttps://github.com/cBioLab/sWM
Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes
Authors: Osato Naoki 
Published: November 2016

AbstractBackgroundTranscriptional target genes show functional enrichment of genes. However, how many and how significantly transcriptional target genes include functional enrichments are still unclear. To address these issues, I predicted human transcriptional target genes using open chromatin regions, ChIP-seq data and DNA binding sequences of transcription factors in databases, and examined functional enrichment and gene expression level of putative transcriptional target genes.ResultsGene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone, independent of transcriptional target genes. To compare the number of functional enrichments of putative transcriptional target genes between cells or search conditions, I normalized the number of functional enrichment by calculating its ratios in the total number of transcriptional target genes. With this analysis, native putative transcriptional target genes showed the largest normalized number of functional enrichments, compared with target genes including 5 – 60% of randomly selected genes. The normalized number of functional enrichments was changed according to the criteria of enhancer-promoter interactions such as distance from transcriptional start sites and orientation of CTCF-binding sites. Forward-reverse orientation of CTCF-binding sites showed significantly higher normalized number of functional enrichments than the other orientations. Journal papers showed that the top five frequent functional enrichments were related to the cellular functions in the three cell types. The median expression level of transcriptional target genes changed according to the criteria of enhancer-promoter assignments (i.e. interactions) and was correlated with the changes of the normalized number of functional enrichments of transcriptional target genes.ConclusionsHuman putative transcriptional target genes showed significant functional enrichments. Functional enrichments were related to the cellular functions. The normalized number of functional enrichments of human putative transcriptional target genes changed according to the criteria of enhancer-promoter assignments and correlated with the median expression level of the target genes. These analyses and characters of human putative transcriptional target genes would be useful to examine the criteria of enhancer-promoter assignments and to predict the novel mechanisms and factors such as DNA binding proteins and DNA sequences of enhancer-promoter interactions.