bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPR-bind: a simple, custom CRISPR/dCas9-mediated labeling of genomic DNA for mapping in nanochannel arrays
Authors: Zhang Denghong , Chan Saki , Sugerman Kenneth , Lee Joyce , Lam Ernest T. , Bocklandt Sven , Cao Han , Hastie Alex R. 
Published: July 2018

AbstractBionano genome mapping is a robust optical mapping technology used for de novo construction of whole genomes using ultra-long DNA molecules, able to efficiently interrogate genomic structural variation. It is also used for functional analysis such as epigenetic analysis and DNA replication mapping and kinetics. Genomic labeling for genome mapping is currently specified by a single strand nicking restriction enzyme followed by fluorophore incorporation by nick-translation (NLRS), or by a direct label and stain (DLS) chemistry which conjugates a fluorophore directly to an enzyme-defined recognition site. Although these methods are efficient and produce high quality whole genome mapping data, they are limited by the number of available enzymes—and thus the number of recognition sequences—to choose from. The ability to label other sequences can provide higher definition in the data and may be used for countless additional applications. Previously, custom labeling was accomplished via the nick-translation approach using CRISPR-Cas9, leveraging Cas9 mutant D10A which has one of its cleavage sites deactivated, thus effectively converting the CRISPR-Cas9 complex into a nickase with customizable target sequences. Here we have improved upon this approach by using dCas9, a nuclease-deficient double knockout Cas9 with no cutting activity, to directly label DNA with a fluorescent CRISPR-dCas9 complex (CRISPR-bind). Unlike labeling with CRISPR-Cas9 D10A nickase, in which nicking, labeling, and repair by ligation, all occur as separate steps, the new assay has the advantage of labeling DNA in one step, since the CRISPR-dCas9 complex itself is fluorescent and remains bound during imaging. CRISPR-bind can be added directly to a sample that has already been labeled using DLS or NLRS, thus overlaying additional information onto the same molecules. Using the dCas9 protein assembled with custom target crRNA and fluorescently labeled tracrRNA, we demonstrate rapid labeling of repetitive DUF1220 elements. We also combine NLRS-based whole genome mapping with CRISPR-bind labeling targeting Alu loci. This rapid, convenient, non-damaging, and cost-effective technology is a valuable tool for custom labeling of any CRISPR-Cas9 amenable target sequence.
Human hippocampal theta oscillations reflect sequential dependencies during spatial planning
Authors: Kaplan Raphael , Campo Adrià Tauste , Bush Daniel , King John , Principe Alessandro , Koster Raphael , Ley-Nacher Miguel , Rocamora Rodrigo , Friston Karl J. 
Published: July 2018

AbstractMovement-related theta oscillations in rodent hippocampus coordinate ‘forward sweeps’ of location-specific neural activity that could be used to evaluate spatial trajectories online. This raises the possibility that increases in human hippocampal theta power accompany the evaluation of upcoming spatial choices. To test this hypothesis, we measured neural oscillations during a spatial planning task that closely resembles a perceptual decision-making paradigm. In this task, participants searched visually for the shortest path between a start and goal location in novel mazes that contained multiple choice points, and were subsequently asked to make a spatial decision at one of those choice points. We observed ~4-8 Hz hippocampal/medial temporal lobe theta power increases specific to sequential planning that were negatively correlated with subsequent decision speed, where decision speed was inversely correlated with choice accuracy. These results implicate the hippocampal theta rhythm in decision tree search during planning in novel environments.
A credibility-based yield forecasting model for crop reinsurance pricing and weather risk management
Authors: Zhu Wenjun , Porth Lysa , Tan Ken Seng 
Published: July 2018

Purpose
The purpose of this paper is to propose an improved reinsurance pricing framework, which includes a crop yield forecasting model that integrates weather variables and crop production information from different geographically correlated regions using a new credibility estimator, and closed form reinsurance pricing formulas. A yield restatement approach to account for changing crop mix through time is also demonstrated.

Design/methodology/approach
The new crop yield forecasting model is empirically analyzed based on detailed farm-level data from Manitoba, Canada, covering 216 crop varieties from 19,238 farms from 1996 to 2011. As well, corresponding weather data from 30 stations, including daily temperature and precipitation, are considered. Algorithms that combine screening regression, cross-validation and principal component analysis are evaluated for the purpose of achieving efficient dimension reduction and model selection.

Findings
The results show that the new yield forecasting model provides significant improvements over the classical regression model, both in terms of in-sample and out-of-sample forecasting abilities.

Research limitations/implications
The empirical analysis is limited to data from the province of Manitoba, Canada, and other regions may show different results.

Practical implications
This research is useful from a risk management perspective for insurers and reinsurers, and the framework may also be used to develop improved weather risk management strategies to help manage adverse weather events.

Originality/value
This is the first paper to integrate a credibility estimator for crop yield forecasting, and develop a closed form reinsurance pricing formula.
Two Novel Methods for Enhancing Postmortem Fingerprint Recovery from Mummified Remains
Authors: Morgan Lee O. , Johnson Marty , Cornelison Jered , Isaac Carolyn , deJong Joyce , Prahlow Joseph A. 
Published: July 2018

AbstractPostmortem fingerprint collection is a routine part of many forensic death investigations. Although the production of postmortem prints is usually straight forward, several obstacles and scenarios can make the collection difficult. A common challenge occurs when finger pads are mummified. Several current techniques allow for softening and rehydration of mummified finger pads; however, despite the employment of such techniques, the production of adequate postmortem fingerprints can remain elusive. The authors present two techniques that can improve the chances of obtaining suitable fingerprints from mummified remains. The “baby powder method” involves applying a cornstarch‐based powder, such as baby powder, onto the darkened and mummified finger pads, to allow better visualization of the fingerprint detail. The “transillumination method” involves carefully dissecting away the tissues underlying the finger pad, followed by placement of a bright light source underneath the finger pad, such that the finger ridge pattern is illuminated.
Female mice exhibit both sexual and social partner preferences for vocalizing males
Authors: NOMOTO Kensaku , IKUMI Mayu , OTSUKA Monami , ASABA Akari , KATO Masahiro , KOSHIDA Nobuyoshi , MOGI Kazutaka , KIKUSUI Takefumi 
Published: July 2018

AbstractAcoustic signals are widely used as courtship signals in the animal kingdom. It has long been known that male mice emit ultrasonic vocalizations (USVs) in the presence of female mice or in response to female secretions. This observation led to the hypothesis that male USVs play a role in courtship behavior. Although previous studies showed that female mice have a social partner preference for vocalizing males, it is not known if they exhibit a sexual partner preference when given a choice. To address this issue, we examined the copulatory behaviors of female mice with either devocalized males (with or without the playback of the USVs) or sham‐operated males in 2 different behavioral paradigms: the no‐choice paradigm in the home cage of a male mouse (without choice of mating partners) or the mate‐choice paradigm in a 3‐chambered apparatus (with choice of mating partners). In the no‐choice paradigm, female mice exhibited comparable sexual receptivity with sham‐operated and devocalized males. In addition, we found that female mice showed more approach behavior towards devocalized males when male USVs were played back. In the mate‐choice paradigm, female mice visited more frequently and stayed longer with sham‐operated than devocalized males. Furthermore, we showed that female mice received more intromissions from sham‐operated males than devocalized males. In summary, our results suggested that, although female mice can copulate equally with both devocalized and vocalizing males when given no choice of mating partner, female mice exhibit both sexual and social partner preferences for vocalizing males in the mate‐choice paradigm.
Seed value influences cache pilfering rates by desert rodents
Authors: VANDER WALL Stephen B. , DIMITRI Lindsay A. , LONGLAND William S. , WHITE Joseph D. M. 
Published: July 2018

AbstractSome rodents gather and store seeds. How many seeds they gather and how they treat those seeds is largely determined by seed traits such as mass, nutrient content, hardness of the seed coat, presence of secondary compounds, and germination schedule. Through their consumption and dispersal of seeds, rodents act as agents of natural selection on seed traits, and those traits influence how rodents forage. Many seeds that are scatter‐hoarded by rodents are pilfered, or stolen, by other rodents, and seed traits also likely influence pilfering rates and seed fates of pilfered seeds. To clarify coevolutionary relationships between rodents and the plants that they disperse, one needs to understand the role of seed traits in rodent foraging decisions. We compared how the seeds of 4 species of plants that are dispersed by scatter‐hoarding animals and that differ in value (singleleaf piñon pine, Pinus monophylla; desert peach, Prunus andersonii; antelope bitterbrush, Purshia tridentata; Utah juniper, Juniperus osteosperma) were pilfered and recached by rodents. One hundred artificial caches of the 4 seed species (25 per species) were prepared, and removal by rodents was monitored. Rodents pilfered high‐value seeds more rapidly than the other seeds. Desert peach seeds, which contain toxic secondary compounds, were more frequently recached. Relatively low value seeds like Utah juniper and antelope bitterbrush were pilfered more slowly and were sometimes left at cache sites, and seeds of the latter species were transported shorter distances to new cache sites. The background density of seeds also appeared to influence the relative value of seeds.
The Associations Between Oral Complex Carbohydrate Sensitivity, BMI, Liking, and Consumption of Complex Carbohydrate Based Foods
Authors: Low Julia Y.Q. , Lacy Kathleen E. , McBride Robert L. , Keast Russell S.J. 
Published: July 2018

AbstractRecent work suggests that humans may perceive complex carbohydrates and that their sensitivity to simple carbohydrates (i.e., glucose and sucrose) is independent from tasting complex carbohydrates. The aim of this study was to confirm whether humans could sense complex carbohydrates from a range of concentration levels; and if their oral sensitivity to complex carbohydrate relates to their BMI, liking, and consumption of complex carbohydrate‐based foods using a large sample group of adults. Participants’ (n = 92 females, age 23.7 ± 0.5 yr [range, 19 to 47 yr]) oral sensitivity towards complex carbohydrate (maltodextrin) and sweet taste function (glucose) was assessed by measuring detection threshold and suprathreshold intensity perception (gLMS). Participants were asked to complete an online version of a Food Frequency Questionnaire and a Likes and Dislikes Questionnaire. Hedonic ratings for complex carbohydrate and sweet solutions, as well as for a range of complex carbohydrate and sweet prototypical foods, were also measured. Consistent with previous findings, there was large interindividual variation in detection and intensity measures for maltodextrin and glucose. No significant associations were found between oral complex carbohydrate sensitivity, Body Mass Index (BMI), and frequency of consumption of complex carbohydrate‐based foods measured. Similarly, no differences were observed between liking of complex carbohydrates, BMI, and food intake. All in, these results from a large sample group further support the proposition that complex carbohydrates are not invisible to the human palate, and can be sensed in the oral cavity even at low concentration levels.
New RANZCR clinical radiology written report guidelines
Authors: Pool Felicity Jane , Siemienowicz Miranda Lynette 
Published: July 2018

SummaryThe Royal Australian and New Zealand College of Radiologists (RANZCR) Radiology Written Report Guideline was first issued in 2011. A survey‐based consultation of clinical radiology members of the college in 2015 found that the vast majority of 235 respondents supported all components of the guideline. Since the original guideline was developed, considerable new research has been published about radiology reporting, particularly regarding structured/template reports. In 2016/17 a RANZCR working group used the consultation results, stakeholder feedback and recent research to develop revised guidelines. This article outlines the consultation survey results and guideline revision process as well as some of the supporting evidence from the literature.
Accumulation of NO2‐cobalamin in nutrient‐stressed ammonia‐oxidizing archaea and in the oxygen deficient zone of the eastern tropical North Pacific
Authors: Heal Katherine R. , Qin Wei , Amin Shady A. , Devol Allan H. , Moffett James W. , Armbrust E. Virginia , Stahl David A. , Ingalls Anitra E. 
Published: July 2018

SummaryCobalamin (vitamin B12) is a precious resource in natural systems that is produced by select prokaryotes and required by a broad range of organisms. In this way, the production of cobalamin reinforces numerous microbial interdependencies. Here we report the accumulation of an unusual form of cobalamin, nitrocobalamin (NO2‐cobalamin), in a marine oxygen deficient zone (ODZ), isolates of ammonia‐oxidizing archaea (AOA), and an anaerobic ammonium‐oxidizing (anammox) bacteria enriched bioreactor. Low oxygen waters were enriched in NO2‐cobalamin, and AOA isolates experiencing ammonia or copper stress produced more NO2‐cobalamin, though there is wide strain‐to‐strain and batch‐to‐batch variability. NO2‐cobalamin has no known biochemical role. We hypothesize that AOA and anammox bacteria are a source of marine NO2‐cobalamin in the environment via a reactive nitrogen intermediate. These findings suggest connections between cobalamin forms and nitrogen transformations, physiological stress and ocean deoxygenation.
ddPCR applied on archived Continuous Plankton Recorder samples reveals long‐term occurrence of class 1 integrons and a sulphonamide resistance gene in marine plankton communities
Authors: Di Cesare Andrea , Petrin Sara , Fontaneto Diego , Losasso Carmen , Eckert Ester M. , Tassistro Giovanni , Borello Alessio , Ricci Antonia , Wilson William H. , Pruzzo Carla , Vezzulli Luigi 
Published: July 2018

SummaryAntibiotic resistance is a rising threat for human health. Although in clinical settings and terrestrial environments the rise of antibiotic resistant bacteria is well documented, their dissemination and spread in the marine environment, covering almost two‐thirds of the Earth's surface, is still poorly understood. In this study, the presence and abundance of sulphonamide resistance gene (sul2) and class 1 integron‐integrase gene (intI1), used as markers for the occurrence and spread of antibiotic resistance genes since the beginning of the antibiotic era, were investigated. Twenty‐nine archived formalin‐fixed samples, collected by the Continuous Plankton Recorder (CPR) survey in the Atlantic Ocean and North Sea from 1970 to 2011, were analysed using Droplet Digital PCR (ddPCR) applied for the first time on CPR samples. The two marker genes were present in a large fraction of the samples (48% for sul2 and 76% for intI1). In contrast, results from Real‐Time PCR performed on the same samples greatly underestimate their occurrence (21% for sul2 and 52% for intI1). Overall, besides providing successful use of ddPCR for the molecular analysis of CPR samples, this study reveals long‐term occurrence and spread of sul2 gene and class 1 integrons in the plankton‐associated bacterial communities in the ocean.
Alcohol dependence and very high risk level of alcohol consumption: a life‐threatening and debilitating disease
Authors: Rehm Jürgen , Guiraud Julien , Poulnais Roch , Shield Kevin D. 
Published: July 2018

AbstractWomen and men with alcohol dependence and very high risk drinking level (VHRDL; defined as drinking >60 or 100 g of ethanol per day, respectively) experience severe health consequences; however, data on the number of these individuals and their health risks are limited. This study estimated (1) the prevalence of VHRDL in 13 European Union (EU) countries among people 15–65 years of age, (2) the risk of disease and injury occurrence associated with VHRDL, (3) the proportion of deaths in nine EU countries attributable to VHRDL and (4) the life expectancy of people in France with VHRDL. Prevalence estimates of VHRDL were based on data obtained from clinical trials and the Global Information System on Alcohol and Health. The risk of disease and injury occurrence was estimated using microsimulations. Population‐attributable fractions (PAFs) were estimated using a Levin‐based methodology. The estimated prevalence of VHRDL in the 13 EU countries examined was 0.74–0.85 percent, with a disease and injury occurrence risk of 13.5 per 100 people with VHRDL per year. For the nine EU countries examined, VHRDL caused 53.6 percent of all liver cirrhosis, 43.8 percent of all pancreatitis and 41.1 percent of oral cavity and pharyngeal cancers (all other PAFs were below 30 percent). Applying these PAFs to French mortality data resulted in a life expectancy of 47–61 years for people with VHRDL—21–35 years less than the general population. These results indicate that the health burdens of VHRDL are potentially large, and interventions targeting VHRDL should be considered when formulating public health policies.
Comparison of three measurement models of discounting among individuals with methamphetamine use disorder
Authors: Yoon Jin H. , Weaver Matthew T. , De La Garza Richard , Suchting Robert , Nerumalla Chandra S. , Omar Yasmine , Brown Gregory S. , Haliwa Ilana , Newton Thomas F. 
Published: July 2018

Background and ObjectivesDelay discounting is associated with numerous clinically significant aspects of substance use disorders (SUDs). Recent studies have demonstrated that different models for assessing discounting may result in disparate conclusions. The current study compared two discounting tasks: money now versus money later (M‐M) and methamphetamine now versus money later (MA‐M) among non‐treatment seeking individuals (N = 59) with methamphetamine use disorder (MAUD). Results from each task were assessed using three different models for assessing delay discounting.MethodsDiscounting data were fit to three models of discounting, log k using Mazur's hyperbolic formula, area under the curve (AUC), and an alternative AUC model in which the delay values have been log transformed (AUClog).ResultsFor both discounting tasks, the distribution of model‐related outcomes were normally distributed when using log k and AUClog, but skewed for AUC. Discounting in the MA‐M task was significantly greater compared to the M‐M task when using log k and AUClog but not AUC.ConclusionTo our knowledge, the current study is the first to report significantly greater discounting in a MA‐M relative to M‐M discounting task among individuals with MAUD, an outcome consistent with other psychomotor stimulants and drugs of abuse.Scientific SignificanceThe differential results observed across the three discounting models reaffirm potential issues with AUC noted in recent studies and highlight that researchers must be cautious when deciding on their final model of discounting. (Am J Addict 2018;27:425–432)
Comparative effectiveness of management options for patients with small renal masses: a prospective cohort study
Authors: Alam Ridwan , Patel Hiten D. , Osumah Tijani , Srivastava Arnav , Gorin Michael A. , Johnson Michael H. , Trock Bruce J. , Chang Peter , Wagner Andrew A. , McKiernan James M. , Allaf Mohamad E. , Pierorazio Phillip M. 
Published: July 2018

ObjectivesTo explore the comparative effectiveness of partial nephrectomy (PN), radical nephrectomy (RN), ablative therapies (ablation) and active surveillance (AS) for small renal masses (SRMs; tumour diameter ≤4.0 cm) in the domains of survival, renal function and quality of life (QoL) using the prospectively maintained Delayed Intervention and Surveillance for Small Renal Masses (DISSRM) Registry.Patients and MethodsEstimated glomerular filtration rate (eGFR) was calculated from creatinine values to determine renal function. QoL was measured using the Short Form 12 (SF‐12) questionnaire. The Kaplan–Meier method and Cox proportional hazards regression were used for survival analysis. The mixed‐effects model was used for renal function and QoL analysis.ResultsOf 638 patients, 231 (36.2%) chose PN, 41 (6.4%) RN, 27 (4.2%) ablation and 339 (53.1%) AS. Cancer‐specific survival at 7 years was 98.8% in PN patients and 100% in all other groups. Overall survival (OS) at 7 years was 87.9%, 90.2%, 83.5% and 66.1% in PN, RN, ablation and AS patients, respectively. The OS rate was significantly worse in the AS group than other groups and likely attributable to older age and increased comorbidities. The eGFR was lowest in RN patients but comparable in all other groups. QoL was lowest in AS patients due to lower physical health scores, but mental health scores were similar in all groups.ConclusionsWith excellent oncological outcomes in all groups, nephron‐sparing approaches, like PN and ablation, are preferred over RN when intervention is indicated for SRMs. AS is a reasonable option for select patients, given the comparable oncological and mental health outcomes.
Exploring the heterogeneity of MS lesions using positron emission tomography: a reappraisal of their contribution to disability
Authors: Stankoff Bruno , Poirion Emilie , Tonietto Matteo , Bodini Benedetta 
Published: July 2018

AbstractThe biological mechanisms driving disability worsening in multiple sclerosis (MS) are only partly understood. Monitoring changes in lesion load on MRI has a limited predictive value on the progression of clinical disability, and there is an essential need for novel imaging markers specific for the main candidate mechanisms underlying neurodegeneration which include failing myelin repair, innate immune cell activation and gray matter neuronal damage. Positron Emission Tomography (PET) is an imaging technology based on the injection of radiotracers directed against specific molecular targets, which has recently allowed the selective quantification in‐vivo of the key biological mechanisms relevant to MS pathophysiology. Pilot PET studies performed in patients with all forms of MS allowed to revisit the contribution of MS lesions to disability worsening and showed that the evolution of lesions toward chronic activation, together with their remyelination profile were relevant predictors of disability worsening. PET offers the opportunity to bridge a critical gap between neuropathology and in‐vivo imaging. This technique provides an original approach to disentangle some of the most relevant pathological components driving MS progression, to follow‐up their temporal evolution, to investigate their clinical relevance and to evaluate novel therapeutics aimed to prevent disease progression.