bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weighted minimizer sampling improves long read mapping
Authors: Jain Chirag , Rhie Arang , Zhang Haowen , Chu Claudia , Koren Sergey , Phillippy Adam 
Published: February 2020

AbstractMotivationIn this era of exponential data growth, minimizer sampling has become a standard algorithmic technique for rapid genome sequence comparison. This technique yields a sub-linear representation of sequences, enabling their comparison in reduced space and time. A key property of the minimizer technique is that if two sequences share a substring of a specified length, then they can be guaranteed to have a matching minimizer. However, because thek-mer distribution in eukaryotic genomes is highly uneven, minimizer-based tools (e.g., Minimap2, Mashmap) opt to discard the most frequently occurring minimizers from the genome in order to avoid excessive false positives. By doing so, the underlying guarantee is lost and accuracy is reduced in repetitive genomic regions.ResultsWe introduce a novel weighted-minimizer sampling algorithm. A unique feature of the proposed algorithm is that it performs minimizer sampling while taking into account a weight for eachk-mer; i.e, the higher the weight of ak-mer, the more likely it is to be selected. By down-weighting frequently occurringk-mers, we are able to meet both objectives: (i) avoid excessive false-positive matches, and (ii) maintain the minimizer match guarantee. We tested our algorithm, Winnowmap, using both simulated and real long-read data and compared it to a state-of-the-art long read mapper, Minimap2. Our results demonstrate a reduction in the mapping error-rate from 0.14% to 0.06% in the recently finished human X chromosome (154.3 Mbp), and from 3.6% to 0% within the highly repetitive X centromere (3.1 Mbp). Winnowmap improves mapping accuracy within repeats and achieves these results with sparser sampling, leading to better index compression and competitive runtimes.Contactadam.phillippy@nih.govAvailabilityWinnowmap is built on top of the Minimap2 codebase (Li, 2018) and is available athttps://github.com/marbl/winnowmap.
Citation behavior of Pondicherry University faculty in digital environment: a survey
Authors: Singson Mangkhollen , Sunny Stephy K. , Thiyagarajan S. , Dkhar Valerie 
Published: February 2020

Purpose
The purpose of this paper is to understand the citation behavior of Pondicherry University faculty with a focus on their recent publication experience, indexed in Scopus. The paper endeavors to gain an insight into their pattern of citation of scientific papers and attempts to understand the underlying motive in doing so especially in an era where information resources have transitioned from print to digital.

Design/methodology/approach
The study adopted a judgmental sample consisting of 100 selected faculty members whose recent papers were indexed by Scopus database. A pre-defined questionnaire consisting of demographic profile and 23 items on citation trust and authority statements of citing sources was self-administered to them.

Findings
The findings of the study indicate that the citation behavior of faculty in Pondicherry University is complex and multi-faceted. Although majority of the faculty depicted an inclination toward normative citation behavior (concerned with the intellectual content of the work), there are others who displayed social constructivist (concerned with the social aspects of the work) citation behavior as well. However, in spite of the differences observed in the citation behavior of the faculty, it was observed that they remained traditional while making trust decisions even in the digital era. Finally, findings suggest no statistical significant difference when it comes to variables, such as gender and discipline in the citation behavior of the faculty.

Originality/value
Given the ever-increasing importance of citation in judging the quality of research journals, in ranking institutions and in determining the efficacy of faculty in India, author-based approach of understanding citer motivation definitely carry research value.
Challenge or opportunity of climate financial fragmentation
Authors: Liang Chao , Liu Bai 
Published: February 2020

PurposeThis study aims to investigate the environmental effects of climate financial fragmentation in the form of emerging multilateral institutions.Design/methodology/approachAmong the countries that have economic relations with China, those involved in climate finance cooperation are taken as the experimental group, and those not involved in other areas are taken as a control group. Using system generalized method of moments regression, the difference-in-differences method is used to test the environmental effects of climate finance cooperation of emerging multilateral institutions. In this way, this study explores the financial and trade mechanisms of cooperation among emerging multilateral institutions.FindingsThe results of this empirical study show that the cooperation of emerging multilateral institutions has a positive impact on the environment. Research results further reveal the financial and trade mechanisms of climate finance cooperation projects. When the invested countries are more likely to obtain international capital, environmental effects will be greater. However, trade intimacy could inhibit the improved environmental effects.Originality/valueThis research is one of the few studies to test the environmental effects of climate financial fragmentation empirically. This study provides a better understanding of the multilateral cooperation of emerging economic entities and China’s climate finance policy, thus providing evidence for the collaborative governance of global climate finance.
Scale up predictive models for early detection of at-risk students: a feasibility study
Authors: Cui Ying , Chen Fu , Shiri Ali 
Published: February 2020

Purpose
This study aims to investigate the feasibility of developing general predictive models for using the learning management system (LMS) data to predict student performances in various courses. The authors focused on examining three practical but important questions: are there a common set of student activity variables that predict student performance in different courses? Which machine-learning classifiers tend to perform consistently well across different courses? Can the authors develop a general model for use in multiple courses to predict student performance based on LMS data?

Design/methodology/approach
Three mandatory undergraduate courses with large class sizes were selected from three different faculties at a large Western Canadian University, namely, faculties of science, engineering and education. Course-specific models for these three courses were built and compared using data from two semesters, one for model building and the other for generalizability testing.

Findings
The investigation has led the authors to conclude that it is not desirable to develop a general model in predicting course failure across variable courses. However, for the science course, the predictive model, which was built on data from one semester, was able to identify about 70% of students who failed the course and 70% of students who passed the course in another semester with only LMS data extracted from the first four weeks.

Originality/value
The results of this study are promising as they show the usability of LMS for early prediction of student course failure, which has the potential to provide students with timely feedback and support in higher education institutions.
Evaluating the use of data-based offender profiling by researchers, practitioners and investigative journalists to address unresolved serial homicides
Authors: Yaksic Enzo 
Published: February 2020

PurposeThe purpose of this article is to improve the use of evidence-based practice and research utilization in the offender profiling process. The use of offender profiling has been met with increasing resistance given its exaggerated accuracy. The “Investigative Journalist/Expert Field Micro Task Force” model, a collaborative method that incorporates offender profiling and is designed to address unresolved serial homicides, is introduced and evaluated alongside recommendations on attaining adherence.Design/methodology/approachThe model was field tested in 17 instances. The measures used by the Federal Bureau of Investigation to gauge the usefulness of their case consultations, whether their input helped catch the offender, offer new leads, move the case forward, provide new avenues or give new ideas, were used to evaluate the model.FindingsThe model established likely patterns of serial murder activity among strangulations of women in Chicago, Cleveland, and Panama and resulted in convictions of suspects in Louisiana and Kansas City. This model is valuable when used to parse modern-day offenders from those who committed unresolved homicides as the latter display different behaviors that can make investigations difficult endeavors. Results from the field tests mirror those from the literature in that profiling alone did not result in the capture of serial killers. Instead, profiling was used in conjunction with other efforts and mainly as a means to keep the investigation moving forward.Originality/valueUnresolved homicides are at a point of crisis and represent a significant but largely unaddressed societal problem. The success of this model may compel law enforcement to restore faith in offender profiling.
An Entrepreneurial Management System for established companies
Authors: Osiyevskyy Oleksiy , Radnejad Amir Bahman , MahdaviMazdeh Hossein 
Published: February 2020

Purpose
The article introduces the Entrepreneurial Management System (EMS), which delineates a strategic process within an organizational context that is aimed at encouraging and supporting the pursuit of opportunities that have the potential to create value through innovative strategic actions. It is designed to stimulate entrepreneurial thinking and corporate venturing at all levels.

Design/methodology/approach
The authors offer an approach to organization-wide continuous innovation that incorporates proven concepts from existing research with lessons learned from the authors’ research analysis and consulting experience in helping large and medium companies across different industries and markets to establish effective entrepreneurial management.

Findings
Given the spectre of constant disruption from new technologies or business models, management teams will be judged on how they proactively respond to these challenges by turning them into value-creating opportunities.

Practical implications
Multidisciplinary teams allow employees to become familiar with other domains and see possible solutions, share their problems and ideas and vet their insights with the input of colleagues.

Originality/value
An Entrepreneurial Management System allows a firm to "internalize" the marketplace’s evolutionary processes so that a company can generate, develop and implement ideas that will have value for customers. It should be a clear decision for all of today’s business leaders and investors to have an implementation plan to ensure continuous innovation.
Manipulation of sensory characteristics and volatile compounds in strawberry fruit through the use of isolated wavelengths of light
Authors: Campbell Sean M. , Sims Charles A. , Bartoshuk Linda M. , Colquhoun Thomas A. , Schwieterman Michael L. , Folta Kevin M. 
Published: February 2020

AbstractConsumers consistently note that there is room for improvement in the flavor of commercial strawberries. Fruit flavor and aroma are affected by both genetics and environment. This work tests the hypothesis that sensory quality may be manipulated using postharvest light treatments. Individual detached fruits representing two different cultivars received a 24‐hr treatment of 100 µmol m−2 s−1 blue LED light while the control was kept in complete darkness. Following treatment, samples were analyzed for flavor volatiles, sugars, acids, firmness, and sensory differences in human trials. Fruits were rated for overall liking, texture, sweetness, sourness, and overall strawberry flavor intensity (OSFI) on the sensory and hedonic versions of the global intensity scale (GIS). A positive treatment effect was observed for “Strawberry Festival” fruit for the overall liking rating. A triangle test revealed a significant treatment effect, as light‐treated fruit tested higher in many flavor volatiles including those known to contribute to sweetness in strawberries. Levels of several volatiles were consistently higher in the treated fruit across all four harvests: acetic acid hexyl ester, butanoic acid octyl ester, methyl isovalerate, and pentanoic acid ethyl ester. The results show that postharvest light treatment can be used to modulate sensory quality of fruit, perhaps offering a means to complement genetic efforts in fruit flavor and aroma improvement.Practical ApplicationThe results indicate that it may be possible to increase the sensory quality of strawberry fruits using an inexpensive and noninvasive light treatment. Light may be applied during transport or storage to improve fruit quality. This concept could also be extended into other realms of storage, such as residential and commercial refrigeration, further increasing the quality impact of the approach.
Variability and effectiveness of comparator group interventions in smoking cessation trials: a systematic review and meta‐analysis
Authors: Black Nicola , Eisma Maarten C. , Viechtbauer Wolfgang , Johnston Marie , West Robert , Hartmann‐Boyce Jamie , Michie Susan , de Bruin Marijn 
Published: February 2020

AbstractAimsTo examine variability and effectiveness of interventions provided to comparator (control) groups in smoking cessation trials.MethodsSystematic review with meta‐analysis of randomized controlled trials (RCTs) of behavioral interventions for smoking cessation, with or without stop‐smoking medication. We searched the Cochrane Tobacco Addiction Group Specialized Register for RCTs with objective outcomes measured at ≥ 6 months. Study authors were contacted to obtain comprehensive descriptions of their comparator interventions. Meta‐regression analyses examined the relationships of smoking cessation rates with stop‐smoking medication and behavior change techniques.ResultsOne hundred and four of 142 eligible comparator groups (n = 23 706) had complete data and were included in analyses. There was considerable variability in the number of behavior change techniques delivered [mean = 15.97, standard deviation (SD) = 13.54, range = 0–45] and the provision of smoking cessation medication (43% of groups received medication) throughout and within categories of comparator groups (e.g. usual care, brief advice). Higher smoking cessation rates were predicted by provision of medication [B = 0.334, 95% confidence interval (CI) = 0.030–0.638, P = 0.031] and number of behavior change techniques included (B = 0.020, 95% CI = 0.008–0.032, P < 0.001). Modelled cessation rates in comparator groups that received the most intensive support were 15 percentage points higher than those that received the least (23 versus 8%).ConclusionsInterventions delivered to comparator groups in smoking cessation randomized controlled trials vary considerably in content, and cessation rates are strongly predicted by stop‐smoking medication and number of behavior change techniques delivered.
A randomized controlled trial of a Group psychological intervention to increase locus of control for alcohol consumption among Alcohol‐Misusing Short‐term (male) Prisoners (GASP)
Authors: Taylor Pamela J. , Playle Rebecca , Robling Michael , Bezeczky Zoe , John‐Evans Hannah , Dimitropoulou Polyxeni , McNamara Rachel , Moriarty Yvonne , Summers Zelda , Bagshaw Ruth 
Published: February 2020

AbstractBackground and aimReducing alcohol misuse by male prisoners is an important global issue. Control of drinking behaviour could be a useful target for intervention in this population, and locus of control could be a causal factor in this. We aimed to assess the effect of a clinical psychologist‐facilitated group intervention on male prisoners’ locus of control of drinking behaviour.DesignA two‐arm, single‐site, open, randomized controlled trial.SettingA category B local training prison in South Wales, housing about 770 mainly sentenced men.ParticipantsPrisoners serving less than 2 years who met inclusion criteria for pre‐imprisonment alcohol misuse, alone or with drug misuse. A total of 119 were allocated to the intervention arm and 119 to the control arm; 104 and 87, respectively, completed the post‐randomization baseline interview and 68 and 60 completed a second interview approximately 4 weeks later, respectively, after intervention or treatment as usual (TAU) alone.InterventionNine clinical psychologist‐facilitated groups in the prison over 3 weeks. Range of participants per session was one to seven, with three to five most usual.MeasuresThe primary outcome was locus of control of behaviour (LCB); secondary outcomes included mental state generally (comprehensive psychiatric rating scale/CPRS) and specifically (Beck Depression Inventory/BDI). An integral process evaluation was conducted.FindingsLCB scores decreased during the study, but without significant intervention effect [−1.7, 95% confidence interval (CI) = –5.1 to 1.6, P = 0.329]. Change among completers in the control group was from a mean score of 37.4 [standard deviation (SD) = 10.0] to 33.7[SD = 11.7] and in the intervention group from 37.4 (SD = 11.6) to 31.9 (SD = 11.8). Secondary outcomes, including change in mental state, did not differ between arms, but 686 (64%) sessions were lost, most because of ‘prison issues’.ConclusionsA clinical psychologist‐facilitated group intervention did not have a statistically significant effect on sense of control of drinking behaviour among men with pre‐imprisonment alcohol misuse serving less than 2 years in a South Wales prison. The study proved coterminous, however, with 40% prison staff cuts which seem likely to have contributed to the high loss of group sessions and possibly overwhelmed any treatment effect. Intervention completion failures, previously cited as harmful, had no effect here, so the trial should be repeated when the prison climate improves.
Using an electronic self‐completion tool to identify patients at increased risk of melanoma in Australian primary care
Authors: Habgood Emily , Walter Fiona M. , O’Hare Erin , McIntosh Jennifer , McCormack Chris , Emery Jon D. 
Published: February 2020

AbstractBackground/ObjectivesSome international guidelines recommend a risk‐based approach to screening for melanoma, but few suggest how to account for multiple risk factors or how to implement risk‐based screening in practice. This study investigated the acceptability and feasibility of identifying patients at increased risk of melanoma in Australian general practice using a self‐completed risk assessment tool. Stratification of risk was based on the validated Williams melanoma risk prediction model.MethodsPatients and companions aged 18 or older in Australian general practices were approached in the waiting room and invited to enter information about their melanoma risk factors into the tool using an iPad. Acceptability was measured by the proportion of people willing to participate from those invited and feasibility by the number of people able to complete the tool unaided. Risk of developing melanoma was stratified into four risk categories using the Williams model.Results1535 (90.4%) participants were recruited from two general practices. Only 200 participants (13%) needed assistance to complete the tool. The mean risk score for participants was 15.2 (±SD 9.8). The Williams model estimated between 5% and 19% of the sample were at increased risk accounting for an estimated 30% to 60% of future incident melanomas.ConclusionsA risk‐stratified tool using the Williams model was acceptable and feasible for patients to self‐complete in general practice clinics. This could be an effective way to identify people in primary care for implementing risk‐based targeted melanoma screening and prevention.
The optic nerve head vasoreactive response to systemic hyperoxia and visual field defect progression in open‐angle glaucoma, a pilot study
Authors: Kiyota Naoki , Shiga Yukihiro , Yasuda Masayuki , Aizawa Naoko , Omodaka Kazuko , Tsuda Satoru , Pak Kyongsun , Kunikata Hiroshi , Nakazawa Toru 
Published: February 2020

AbstractPurposeTo investigate the effect of optic nerve head (ONH) tissue vasoreactivity on glaucoma visual field defect progression.MethodsThis prospective, longitudinal study comprised 28 eyes of 16 patients with open‐angle glaucoma. Baseline data were obtained from oxygen inhalation testing, including laser speckle flowgraphy measurements of tissue‐area mean blur rate (MT), which represents ONH tissue blood flow, and the mean percentage change in MT (MT‐change). Follow‐up data were collected for at least 2 years, including at least 5 reliable visual field tests. The average total deviation (TD) was calculated in each sector of the Garway‐Heath map; in this study, superior, central and inferior TD corresponded to inferior, temporal and superior MT or MT‐change, respectively. MT and MT‐change in three sectors per eye were included as explanatory variables in a multivariable linear mixed‐effects model, with TD slope set as the response variable.ResultsAt baseline, lower MT and higher diastolic blood pressure were associated with lower MT‐change (p < 0.05). Additionally, MT‐change significantly contributed to TD slope in the corresponding sectors (β = 0.41, p = 0.01).ConclusionsWeaker ONH tissue vasoreactivity to systemic hyperoxia, assessed with laser speckle flowgraphy, was associated with lower baseline ONH tissue blood flow, higher diastolic blood pressure and rapid visual field defect progression. Laser speckle flowgraphy variables during oxygen provocation testing may represent potentially useful predictive biomarkers of glaucoma progression.
Predictors of having a dentist among older adults in Iowa
Authors: Marchini Leonardo , Reynolds Julie C. , Caplan Daniel J. , Sasser Shan , Russell Carlene 
Published: February 2020

AbstractObjectivesOral health plays an important role in the general well‐being of older adults, yet older adults experience unique barriers to dental care. In the United States, almost two‐thirds of older adults are dentally uninsured – a reflection of the exclusion of dental benefits from Medicare. The aim of this study was to investigate potential predictors of having a dentist among older adults receiving services funded through the Iowa Department on Aging (IDA).MethodsThis was a cross‐sectional analysis on a convenience sample (n = 2692) of adults age 65+ who completed a required survey to determine eligibility to receive services from the IDA. Data from questionnaires completed between March and December 2017 were used to generate multivariable logistic regression models that identified predictors of having a dentist. The dependent variable, having a dentist, was gathered by self‐report in the survey. Explanatory variables eligible for inclusion in the models included demographic and geographic factors, indicators of access to dental care, and factors related to activities of daily living.ResultsFewer than half (46.2%) of the respondents reported having a dentist. In the final regression model, individuals with dental insurance were more than twice as likely to have a dentist than those without insurance. Conversely, individuals with a tooth/mouth problem and who need help with housekeeping and with transportation were significantly less likely to have a dentist than their counterparts.ConclusionsThese results align with known insurance‐related barriers and identify certain activities of daily living that might influence older adults' ability to access care. The finding that individuals with oral health problems were less likely to have a dentist underscores the need to reduce barriers to care for this population.