bluuebunny/crossref_metadata_2025_split huggingface dataset:
FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data
Authors: Xu Zheng , Zhang Guosheng , Wu Cong , Li Yun , Hu Ming 
Published: May 2016

AbstractMotivation: How chromatin folds in three-dimensional (3D) space is closely related to transcription regulation. As powerful tools to study such 3D chromatin conformation, the recently developed Hi-C technologies enable a genome-wide measurement of pair-wise chromatin interaction. However, methods for the detection of biologically meaningful chromatin interactions, i.e. peak calling, from Hi-C data, are still under development. In our previous work, we have developed a novel hidden Markov random field (HMRF) based Bayesian method, which through explicitly modeling the non-negligible spatial dependency among adjacent pairs of loci manifesting in high resolution Hi-C data, achieves substantially improved robustness and enhanced statistical power in peak calling. Superior to peak callers that ignore spatial dependency both methodologically and in performance, our previous Bayesian framework suffers from heavy computational costs due to intensive computation incurred by modeling the correlated peak status of neighboring loci pairs and the inference of hidden dependency structure.Results: In this work, we have developed FastHiC, a novel approach based on simulated field approximation, which approximates the joint distribution of the hidden peak status by a set of independent random variables, leading to more tractable computation. Performance comparisons in real data analysis showed that FastHiC not only speeds up our original Bayesian method by more than five times, bus also achieves higher peak calling accuracy.Availability and Implementation: FastHiC is freely accessible at: http://www.unc.edu/∼yunmli/FastHiC/Contacts : yunli@med.unc.edu or ming.hu@nyumc.orgSupplementary information: Supplementary data are available at Bioinformatics online.
Subtractive Morphology
Authors: Manova Stela 
Published: May 2016

Subtraction consists in a shortening of a morphological base as in the Russian derivation mikrobiologija ‘microbiology’ → mikrobiolog ‘microbiologist.’ Of course, one can doubt the correctness of the direction of this derivation and claim that the shorter form mikrobiolog serves as a base for mikrobiologija and not vice versa. However, from the literature on word-formation it is well known that the most important diagnostic criterion for being a product of a derivation is semantic dependence; i.e., the definition of the derivative depends on the meaning of its base. In our case, the definition of mikrobiolog depends on mikrobiologija (a microbiologist is not a microscopic biologist but a person specialized in the field of microbiology; microbiology is the study of microscopic organisms). As can be seen from the Russian example, subtraction differs from concatenative affixation, i.e., from affixation by addition of a discrete affix (see the Oxford Bibliographies article “Affixation.” Therefore, in the literature, subtraction is seen as an instance of nonconcatenative morphology and is usually analyzed either as process morphology without morphemes or as addition of defective phonological material. Subtraction has been reported in derivation and inflection and in well-studied and lesser-studied languages. Among the most frequently cited examples of subtraction in textbooks and reference resources are the masculine forms of some French adjectives (e.g., masc. bon /bõ/ ‘good’—fem. bonne /bon/) and the formation of perfective verbs from imperfective ones in the Uto-Aztekan language Tohono O’odham (called “Papago” in some sources) (e.g., singular: imperf. him ‘walk’—perf. hi:, plural: imperf. hihim—perf. hihi). However, it has to be mentioned here that numerous studies on theoretical morphology have provided alternative, nonsubtractive analyses of those French and Tohono O’odham data. Additionally, opinions differ on how much form can be deleted in subtraction. Some linguists claim that subtraction deletes a phoneme, others speak of a mora, and still others assume that subtractive morphology deletes segments of different lengths. Some linguists postulate subtraction only if the shortened material does not coincide with an existing morpheme elsewhere in a language, whereas others show that the deleted material can be equal in form with an existing affix. Opinions also differ on what a proper word-formation process is and which morphological derivations involve subtraction. Unlike most morphology textbooks, some theoretical studies see hypocoristics, blends, and clippings as instances of (more or less regular) word-formation and refer to them as either “subtractive truncation” or “subtractive word-formation.” Thus we come to terminology; in the literature, different labels have been used to refer to subtraction(-like) formations: minus feature, minus formation, disfixation, subtractive morph, (subtractive) truncation, backformation, or just shortening.
Ethnic Inequalities in Rectal Cancer Care in a Universal Access Healthcare System: A Nationwide Register-Based Study
Authors: Elferink Marloes A. G. , Lamkaddem Majda , Dekker Evelien , Tanis Pieter J. , Visser Otto , Essink-Bot Marie-Louise 
Published: May 2016

BACKGROUND:
Ethnic inequalities in colorectal cancer care were reported previously in the United States. Studies specifically reporting on ethnic inequalities in rectal cancer care are limited.

OBJECTIVE:
This study aimed to explore potential ethnic inequalities in rectal cancer care in the Netherlands.

DESIGN:
This was a nationwide, population-based observational study.

SETTINGS:
The study linked data of the Netherlands Cancer Registry with the Dutch population registry and the Social Statistics Database of Statistics Netherlands. Data were analyzed using stepwise multivariable logistic regression models.

PATIENTS:
All of the patients diagnosed with rectal carcinoma in 2003–2011 in the Netherlands (N = 27,159) were included.

MAIN OUTCOME MEASURES:
We analyzed 2 rectal cancer treatment indicators (preoperative radiotherapy and sphincter-sparing surgery) and 2 indicators of short-term outcome of rectal cancer surgery (anastomotic leakage and 30-day postoperative mortality).

RESULTS:
Patients of Western non-Dutch and non-Western origin with rectal cancer were significantly younger and had a higher tumor stage than ethnic Dutch patients. Considering preoperative radiotherapy, anastomotic leakage, and 30-day postoperative mortality, no ethnic inequalities were detected. After adjustment for age, sex, disease characteristics, and socioeconomic status, Western non-Dutch and non-Western patients were significantly more likely to receive sphincter-sparing surgery than ethnic Dutch patients (OR = 1.27 (95% CI, 1.04–1.55) and OR = 1.57 (95% CI, 1.02–2.42)).

LIMITATIONS:
This study was limited by the relatively low numbers of non-Dutch patients with rectal cancer.

CONCLUSIONS:
Non-Dutch ethnic origin was associated with a higher rate of sphincter-sparing surgery. The absence of ethnic inequalities in preoperative radiotherapy, anastomotic leakage, and 30-day postoperative mortality suggests that ethnic minority patients have similar chances of optimal rectal cancer care outcomes as Dutch patients.
Peritoneal Cytokine Levels Can Predict Anastomotic Leak on the First Postoperative Day.
Authors: Sammour Tarik , Singh Parry P. , Zargar-Shoshtari Kamran , Su’a Bruce , Hill Andrew G. 
Published: May 2016

BACKGROUND:Accumulating evidence suggests that peritoneal cytokine concentrations may predict anastomotic leak after colorectal surgery, but previous studies have been underpowered.OBJECTIVE:We aimed to test this hypothesis by using a larger prospectively collected data set.DESIGN:This study is an analysis of prospectively collected data.SETTINGS:This study was conducted at 3 public hospitals in Auckland, New Zealand.PATIENTS:Patients undergoing colorectal surgery recruited as part of 3 previous randomized controlled trials were included.MAIN OUTCOME MEASURES:Data on peritoneal and plasma levels of interleukin-6, interleukin-8, interleukin-10, and tumor necrosis factor-α on day 1 after colorectal surgery were reanalyzed to evaluate their predictive value for clinically important anastomotic leak. Area under receiver operating characteristic curve analysis was performed.RESULTS:A total of 206 patients with complete cytokine data were included. The overall anastomotic leak rate was 8.3%. Concentration levels of peritoneal interleukin-6 and interleukin-10 on day 1 after colorectal surgery were predictive of anastomotic leak (area under receiver operating characteristic curve, 0.72 and 0.74;p= 0.006 and 0.004). Plasma cytokine levels of interleukin-6 were higher on day 1 after colorectal surgery in patients who had an anastomotic leak, but this was a poor predictor of anastomotic leak. Levels of other peritoneal and plasma cytokines were not predictive.LIMITATIONS:The study was not powered a priori for anastomotic leak prediction. Although the current data do suggest that peritoneal levels of interleukin-6 and interleukin-10 are predictive of leak, the discriminative value in clinical practice remains unclear.CONCLUSIONS:Peritoneal levels of interleukin-6 and interleukin-10 on day 1 after colorectal surgery can predict clinically important anastomotic leak.
RAPID MACULAR HOLE FORMATION, SPONTANEOUS CLOSURE, AND REOPENING AFTER PARS PLANA VITRECTOMY FOR MACULA-SPARING RETINAL DETACHMENT
Authors: Sridhar Jayanth , Townsend Justin H. , Rachitskaya Aleksandra V. 
Published: May 2016

Background/Purpose:
To report a single case of macular hole (MH) opening, spontaneous closure, and reopening in the 3-month period after pars plana vitrectomy for rhegmatogenous retinal detachment (RRD).

Methods:
Case report.

Results:
A 59-year-old man with a macula-sparing RRD underwent uncomplicated pars plana vitrectomy with gas tamponade. The patient developed a FTMH 2 months postoperatively. The hole was noted to spontaneously close 3 months postoperatively, but then reopened 4 months postoperatively and required repeat pars plana vitrectomy and inner limiting membrane peel for definitive closure. The rapidity with which the MH developed after pars plana vitrectomy for macula-sparing RRD and its dynamic behavior have not been previously reported.

Conclusion:
Full-thickness macular holes may rarely develop rapidly, spontaneous close, and reopen after pars plana vitrectomy for RRD, even in macula-sparing cases.
Mechanisms and Genetic Susceptibility of Chemotherapy-Induced Cardiotoxicity in Patients With Breast Cancer
Authors: Mihalcea Diana J. , Florescu Maria , Vinereanu Dragos 
Published: May 2016

Background:
Cardiotoxicity remains an important adverse reaction of chemotherapy used in the treatment of breast cancer, leading to increased morbidity and mortality.

Data Sources:
Anthracyclines, taxanes, and trastuzumab are the most commonly used cytotoxic drugs for the treatment of breast cancer. Cardiotoxicity may vary from asymptomatic forms to irreducible heart failure and death.

Areas of Uncertainty:
Susceptibility for the occurrence of chemotherapy-induced cardiotoxicity and treatment resistance is multifactorial, with interindividual variability, determined by the interaction between genetic and phenotypic factors. Implementation of pharmacogenomic findings into clinical practice might be useful, to predict cardiotoxicity and to allow appropriate therapeutic measures.

Results and Conclusions:
This review will summarize the cellular mechanisms of chemotherapy-induced cardiotoxicity in breast cancer patients and will discuss the role of the genetic susceptibility for cardiac dysfunction.
Brief Report: Geographical Variation in Prevalence of Cryptococcal Antigenemia Among HIV-Infected, Treatment-Naive Patients in Nigeria: A Multicenter Cross-Sectional Study
Authors: Ezeanolue Echezona E. , Nwizu Chidi , Greene Gregory S. , Amusu Olatilewa , Chukwuka Chinwe , Ndembi Nicaise , Smith Rachel M. , Chiller Tom , Pharr Jennifer , Kozel Thomas R. 
Published: May 2016

Objective:
Worldwide, HIV-associated cryptococcal meningitis affects approximately 1 million persons and causes 600,000 deaths each year mostly in sub-Saharan Africa. Limited data exist on cryptococcal meningitis and antigenemia in Nigeria, and most studies are geographically restricted. We determined the prevalence of cryptococcal antigenemia (CrAg) among HIV-infected, treatment-naive individuals in Nigeria.

Design/Methods:
This was a retrospective, cross-sectional study across 4 geographic regions in Nigeria. We performed CrAg testing using a lateral flow immunoassay on archived whole-blood samples collected from HIV-infected participants at US President's Emergency Plan for AIDS Relief (PEPFAR)-supported sites selected to represent the major geographical and ethnic diversity in Nigeria. Eligible samples were collected from consenting patients (>15 years) naive to antiretroviral therapy with CD4+ count less than 200 cells per cubic millimeter and were stored in an −80°C freezer.

Results:
A total of 2752 stored blood samples were retrospectively screened for CrAg. Most of the samples were from participants aged 30–44 years (57.6%), and 1570 (57.1%) were from women. The prevalence of CrAg positivity in specimens with CD4 <200 cells per cubic millimeter was 2.3% (95% confidence interval: 1.8% to 3.0%) and varied significantly across the 4 regions (P < 0.001). At 4.4% (3.2% to 5.9%), the South East contained the highest prevalence.

Conclusions:
The significant regional variation in CrAg prevalence found in Nigeria should be taken into consideration as plans are made to integrate routine screening into clinical care for HIV-infected patients.
Competitive service quality benchmarking in airline industry using AHP
Authors: Singh Alok Kumar 
Published: May 2016

Purpose
– The purpose of this paper is to measure competitive service quality (SQ) performances of domestic full service airlines in India by providing a framework based on analytic hierarchy process (AHP), in order to benchmark their SQ thus, enhancing competitiveness and gaining competitive advantage.

Design/methodology/approach
– The present study has used the AHP methodology to benchmark the SQ of airlines in India. Subsequently, competitive SQ gap analysis is performed to evaluate and compare strength and weakness of focal firm (Airline “B”) against its competitors.

Findings
– In this research work, total of 23 SQ attributes and five dimensions have been identified based on extensive literature review, focus group brainstorming and experts opinion from the Indian airline industry. The study reveals that air travelers rate assurance as the most important criteria and safety as the most important sub criteria followed by on time performance, performing the services right, the first time and remedial process for delayed or missing baggage. Furthermore, based on AHP methodology, the result shows that Airline “A” has emerged as a market leader and is considered as a benchmark airline.

Practical implications
– This framework will help airline management and policy makers to identify area of service improvements and identify SQ gaps with respect to the benchmark airline. This will help in formulating suitable competitive strategies for SQ improvements, thus gaining competitive advantage.

Originality/value
– In this research work, AHP-based SQ framework have been applied in Indian domestic aviation industry for competitive SQ benchmarking which is a novel contribution, thus widening the existing knowledge base in aviation SQ literature.
Performance measurement in airport settings: a systematic literature review
Authors: Bezerra George C. L. , Gomes Carlos F. 
Published: May 2016

Purpose– The purpose of this paper is to provide a comprehensive overview of the literature related to performance measurement (PM) in airport settings. Two research questions were addressed: how the literature has evolved during the last 45 years; and which performance dimensions have been emphasized during this period.Design/methodology/approach– For the purpose of this study, 380 documents, published between 1970 and 2015 were systematically analyzed. The literature reviewed comprises academic peer-reviewed articles, and studies published by other relevant sources, including professional-related literature.Findings– The literature reviewed points to three stages relating to the evolution of the PM in airport settings during the period analyzed. Although with a significant lag, this evolution seems to have followed the broad literature on PM. Moreover, a relationship between these stages and the changes occurring at the airport industry was found. Several aspects of airport multidimensional performance are identified and discussed.Research limitations/implications– Based on the findings of this study, it is concluded that a more comprehensive approach to airport PM is needed. In this context, a research agenda is suggested.Practical implications– The findings of this study have relevant practical implications for the airport industry. In this context, a framework representing a comprehensive approach to airport performance dimensions with impact on external stakeholders is presented. This framework can be a relevant contribution for researchers and practitioners which are looking for a more comprehensive and multidimensional approach to airport PM.Originality/value– To the best of the authors’ knowledge, this study appears to be the first to examine the literature related to airport PM according to such a comprehensive approach. A framework of the performance dimensions related to the airport business is provided.
Aversion of information ambiguity and momentum effect in China’s stock market
Authors: Xu Yuandong 
Published: May 2016

Purpose
– The empirical studies have indicated that the information uncertainty is one of the reasons leading to the momentum effect in the stock market. Based on this conclusion, the concept of “information uncertainty” is deepened into the concept hierarchy of “information ambiguity,” the purpose of this paper is to explain the momentum effect in the China’s stock market from information ambiguity.

Design/methodology/approach
– Based on the information ambiguity, the paper puts forward two hypotheses, portfolio analysis and cross-sectional regression analysis method were used to empirically test these hypothesis based on the weekly data.

Findings
– The empirical results support the two hypotheses.

Originality/value
– Finally, the paper discusses the importance from ambiguity to understand financial anomalies, such as momentum effect.
Ward rounds, participants, roles and perceptions: literature review
Authors: Walton Victoria , Hogden Anne , Johnson Julie , Greenfield David 
Published: May 2016

Purpose
– The purpose of this paper is to classify and describe the purpose of ward rounds, who attends each round and their role, and participants’ perception of each other’s role during the respective ward rounds.

Design/methodology/approach
– A literature review of face-to-face ward rounds in medical wards was conducted. Peer reviewed journals and government publications published between 2000 and 2014 were searched. Articles were classified according to the type of round described in the study. Purposes were identified using keywords in the description of why the round was carried out. Descriptions of tasks and interactions with team members defined participant roles.

Findings
– Eight round classifications were identified. The most common were the generalised ward; multidisciplinary; and consultant rounds. Multidisciplinary rounds were the most collaborative round. Medical officers were the most likely discipline to attend any round. There was limited reference to allied health clinicians and patient involvement on rounds. Perceptions attendees held of each other reiterated the need to continue to investigate teamwork.

Practical implications
– A collaborative approach to care planning can occur by ensuring clinicians and patients are aware of different ward round processes and their role in them.

Originality/value
– Analysis fulfils a gap in the literature by identifying and analysing the different ward rounds being undertaken in acute medical wards. It identifies the complexities in the long established routine hospital processes of the ward round.
Time dependent patient no-show predictive modelling development
Authors: Huang Yu-Li , Hanauer David A. 
Published: May 2016

Purpose
– The purpose of this paper is to develop evident-based predictive no-show models considering patients’ each past appointment status, a time-dependent component, as an independent predictor to improve predictability.

Design/methodology/approach
– A ten-year retrospective data set was extracted from a pediatric clinic. It consisted of 7,291 distinct patients who had at least two visits along with their appointment characteristics, patient demographics, and insurance information. Logistic regression was adopted to develop no-show models using two-thirds of the data for training and the remaining data for validation. The no-show threshold was then determined based on minimizing the misclassification of show/no-show assignments. There were a total of 26 predictive model developed based on the number of available past appointments. Simulation was employed to test the effective of each model on costs of patient wait time, physician idle time, and overtime.

Findings
– The results demonstrated the misclassification rate and the area under the curve of the receiver operating characteristic gradually improved as more appointment history was included until around the 20th predictive model. The overbooking method with no-show predictive models suggested incorporating up to the 16th model and outperformed other overbooking methods by as much as 9.4 per cent in the cost per patient while allowing two additional patients in a clinic day.

Research limitations/implications
– The challenge now is to actually implement the no-show predictive model systematically to further demonstrate its robustness and simplicity in various scheduling systems.

Originality/value
– This paper provides examples of how to build the no-show predictive models with time-dependent components to improve the overbooking policy. Accurately identifying scheduled patients’ show/no-show status allows clinics to proactively schedule patients to reduce the negative impact of patient no-shows.
Recommendations for health information technology implementation in rural hospitals
Authors: Huang Yuan-Han , Gramopadhye Anand K. 
Published: May 2016

Purpose
– The purpose of this paper is to investigate violations against work standards associated with using a new health information technology (HIT) system. Relevant recommendations for implementing HIT in rural hospitals are provided and discussed to achieve meaningful use.

Design/methodology/approach
– An observational study is conducted to map medication administration process while using a HIT system in a rural hospital. Follow-up focus groups are held to determine and verify potential adverse factors related to using the HIT system while passing drugs to patients.

Findings
– A detailed task analysis demonstrated several violations, such as only relying on the barcode scanning system to match up with patient and drugs could potentially result in the medical staff forgetting to provide drug information verbally before administering drugs. There was also a lack of regulated and clear work procedure in using the new HIT system. In addition, the computer system controls and displays could not be adjusted so as to satisfy the users’ expectations. Nurses prepared medications and documentation in an environment that was prone to interruptions.

Originality/value
– Recommendations for implementing a HIT system in rural healthcare facilities can be categorized into five areas: people, tasks, tools, environment, and organization. Detailed remedial measures are provided for achieving continuous process improvements at resource-limited healthcare facilities in rural areas.