bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lenalidomide-Associated Secondary B-Lymphoblastic Leukemia/Lymphoma—A Unique Entity
Authors: Germans Sharon Koorse , Kulak Ozlem , Koduru Prasad , Oliver Dwight , Gagan Jeffery , Patel Prapti , Anderson Larry D , Fuda Franklin S , Chen Weina , Jaso Jesse Manuel 
Published: June 2020

Abstract

Objectives
Autologous stem cell transplant with lenalidomide maintenance therapy has greatly improved the relapse-free and overall survival rates of patients with multiple myeloma but also has been associated with an increased risk of secondary B-lymphoblastic leukemia/lymphoma (B-ALL).

Methods
We report a comprehensive review of the clinicopathologic features of 2 patients with multiple myeloma who developed secondary B-ALL during lenalidomide maintenance.

Results
Our observations showed that the disease may initially present with subtle clinical, morphologic, and flow-cytometric findings. The flow cytometry findings in such cases may initially mimic an expansion of hematogones with minimal immunophenotypic variation. Both patients achieved complete remission of secondary B-ALL after standard chemotherapy; however, one patient continues to have minimal residual disease, and the other experienced relapse. Next-generation sequencing of the relapse specimen showed numerous, complex abnormalities, suggesting clonal evolution.

Conclusions
Our findings suggest the need for increased awareness and further study of this unique form of secondary B-ALL.
Causal Effects of Air Pollution on Mortality Rate in Massachusetts
Authors: Wei Yaguang , Wang Yan , Wu Xiao , Di Qian , Shi Liuhua , Koutrakis Petros , Zanobetti Antonella , Dominici Francesca , Schwartz Joel D 
Published: June 2020

Abstract
Air pollution epidemiology studies have primarily investigated long- and short-term exposures separately, have used multiplicative models, and have been associational studies. Implementing a generalized propensity score adjustment approach with 3.8 billion person-days of follow-up, we simultaneously assessed causal associations of long-term (1-year moving average) and short-term (2-day moving average) exposure to particulate matter with an aerodynamic diameter less than or equal to 2.5 μm (PM2.5), ozone, and nitrogen dioxide with all-cause mortality on an additive scale among Medicare beneficiaries in Massachusetts (2000–2012). We found that long- and short-term PM2.5, ozone, and nitrogen dioxide exposures were all associated with increased mortality risk. Specifically, per 10 million person-days, each 1-μg/m3 increase in long- and short-term PM2.5 exposure was associated with 35.4 (95% confidence interval (CI): 33.4, 37.6) and 3.04 (95% CI: 2.17, 3.94) excess deaths, respectively; each 1–part per billion (ppb) increase in long- and short-term ozone exposure was associated with 2.35 (95% CI: 1.08, 3.61) and 2.41 (95% CI: 1.81, 2.91) excess deaths, respectively; and each 1-ppb increase in long- and short-term nitrogen dioxide exposure was associated with 3.24 (95% CI: 2.75, 3.77) and 5.60 (95% CI: 5.24, 5.98) excess deaths, respectively. Mortality associated with long-term PM2.5 and ozone exposure increased substantially at low levels. The findings suggested that air pollution was causally associated with mortality, even at levels below national standards.
No acclimation: instantaneous responses to temperature maintain homeostatic photosynthetic rates under experimental warming across a precipitation gradient in Ulmus americana
Authors: Smith Nicholas G , McNellis Risa , Dukes Jeffrey S 
Published: June 2020

AbstractPast research has shown that plants possess the capacity to alter their instantaneous response of photosynthesis to temperature in response to a longer-term change in temperature (i.e. acclimate). This acclimation is typically the result of processes that influence net photosynthesis (Anet), including leaf biochemical processes such as the maximum rate of Rubisco carboxylation (Vcmax) and the maximum rate of photosynthetic electron transport (Jmax), stomatal conductance (gs) and dark respiration (Rd). However, these processes are rarely examined in the field or in concert with other environmental factors, such as precipitation amount. Here, we use a fully factorial warming (active heating up to +4 °C; mean = +3.1 °C) by precipitation (−50 % ambient to 150 % ambient) manipulation experiment in an old-field ecosystem in the north-eastern USA to examine the degree to which Ulmus americana saplings acclimate through biochemical and stomatal adjustments. We found that rates of Anet at ambient CO2 levels of 400 µmol mol−1 (A400) did not differ across climate treatments or with leaf temperatures from 20 to 30 °C. Canopy temperatures rarely reached above 30 °C in any treatment, suggesting that seasonal carbon assimilation was relatively homeostatic across all treatments. Assessments of the component processes of A400 revealed that decreases in gs with leaf temperature from 20 to 30 °C were balanced by increases in Vcmax, resulting in stable A400 rates despite concurrent increases in Rd. Photosynthesis was not affected by precipitation treatments, likely because the relatively dry year led to small treatment effects on soil moisture. As temperature acclimation is likely to come at a cost to the plant via resource reallocation, it may not benefit plants to acclimate to warming in cases where warming would not otherwise reduce assimilation. These results suggest that photosynthetic temperature acclimation to future warming will be context-specific and that it is important to consider assimilatory benefit when assessing acclimation responses.
IBDkin: fast estimation of kinship coefficients from identity by descent segments
Authors: Zhou Ying , Browning Sharon R , Browning Brian L 
Published: June 2020

Abstract

Motivation
Estimation of pairwise kinship coefficients in large datasets is computationally challenging because the number of related individuals increases quadratically with sample size.

Results
We present IBDkin, a software package written in C for estimating kinship coefficients from identity by descent (IBD) segments. We use IBDkin to estimate kinship coefficients for 7.95 billion pairs of individuals in the UK Biobank who share at least one detected IBD segment with length ≥ 4 cM.

Availability and implementation
https://github.com/YingZhou001/IBDkin.

Supplementary information
Supplementary data are available at Bioinformatics online.
Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference
Authors: Aubin-Frankowski Pierre-Cyril , Vert Jean-Philippe 
Published: June 2020

Abstract

Motivation
Single-cell RNA sequencing (scRNA-seq) offers new possibilities to infer gene regulatory network (GRNs) for biological processes involving a notion of time, such as cell differentiation or cell cycles. It also raises many challenges due to the destructive measurements inherent to the technology.

Results
In this work, we propose a new method named GRISLI for de novo GRN inference from scRNA-seq data. GRISLI infers a velocity vector field in the space of scRNA-seq data from profiles of individual cells, and models the dynamics of cell trajectories with a linear ordinary differential equation to reconstruct the underlying GRN with a sparse regression procedure. We show on real data that GRISLI outperforms a recently proposed state-of-the-art method for GRN reconstruction from scRNA-seq data.

Availability and implementation
The MATLAB code of GRISLI is available at: https://github.com/PCAubin/GRISLI.

Supplementary information
Supplementary data are available at Bioinformatics online.
A rapid and low-cost method for genomic DNA extraction from the cyanobacterium Synechocystis
Authors: Harrison Dale J A , Thompson Elinor P 
Published: June 2020

Abstract
A two-step method is reported for preparation of genomic DNA from the model cyanobacterium Synechocystis that can be performed with minimal equipment and reagents in about an hour. High yields of genetic material can be obtained (200–450 ng/μl) with reasonable purity. A further ethanol precipitation step can be included but is not necessary if template is simply required for polymerase chain reaction (PCR) or digestion. This new protocol is helpful for amplification of genes of interest in early-stage research projects and for low throughput screening of transformants. It is more reliable than colony PCR of Synechocystis cultures, and less involved and cheaper than existing clean-DNA preparation methods. It represents an unusually simple and reliable extraction protocol for the growing body of research making use of this cyanobacterium.
A Māori specific RFC1 pathogenic repeat configuration in CANVAS, likely due to a founder allele
Authors: Beecroft Sarah J , Cortese Andrea , Sullivan Roisin , Yau Wai Yan , Dyer Zoe , Wu Teddy Y , Mulroy Eoin , Pelosi Luciana , Rodrigues Miriam , Taylor Rachael , Mossman Stuart , Leadbetter Ruth , Cleland James , Anderson Tim , Ravenscroft Gianina , Laing Nigel G , Houlden Henry , Reilly Mary M , Roxburgh Richard H 
Published: June 2020

Abstract
Cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS) is a recently recognized neurodegenerative disease with onset in mid- to late adulthood. The genetic basis for a large proportion of Caucasian patients was recently shown to be the biallelic expansion of a pentanucleotide (AAGGG)n repeat in RFC1. Here, we describe the first instance of CANVAS genetic testing in New Zealand Māori and Cook Island Māori individuals. We show a novel, possibly population-specific CANVAS configuration (AAAGG)10-25(AAGGG)exp, which was the cause of CANVAS in all patients. There were no apparent phenotypic differences compared with European CANVAS patients. Presence of a common disease haplotype among this cohort suggests this novel repeat expansion configuration is a founder effect in this population, which may indicate that CANVAS will be especially prevalent in this group. Haplotype dating estimated the most recent common ancestor at ∼1430 ce. We also show the same core haplotype as previously described, supporting a single origin of the CANVAS mutation.
Tumor protein expression of the DNA repair gene BRCA1 and lethal prostate cancer
Authors: Stopsack Konrad H , Gerke Travis , Zareba Piotr , Pettersson Andreas , Chowdhury Dipanjan , Ebot Ericka M , Flavin Richard , Finn Stephen , Kantoff Philip W , Stampfer Meir J , Loda Massimo , Fiorentino Michelangelo , Mucci Lorelei A 
Published: June 2020

Abstract
DNA repair genes are commonly altered in metastatic prostate cancer, but BRCA1 mutations are rare. Preliminary studies suggest that higher tumor expression of the BRCA1 protein may be associated with worse prognosis. We undertook a prospective study among men with prostate cancer in the Health Professionals Follow-up Study and evaluated BRCA1 via immunohistochemical staining on tissue microarrays. BRCA1 was expressed in 60 of 589 tumors. Prevalence of BRCA1 positivity was 43% in the 14 men with metastases at diagnosis compared with 9% in non-metastatic tumors [difference, 33 percentage points; 95% confidence interval (CI), 7–59]. BRCA1-positive tumors had 2.16-fold higher Ki-67 proliferative indices (95% CI, 1.18–3.95), higher tumor aneuploidy as predicted from whole-transcriptome profiling, and higher Gleason scores. Among the 575 patients with non-metastatic disease at diagnosis, we evaluated the association between BRCA1 expression and development of lethal disease (metastasis or cancer-specific death, 69 events) during long-term follow-up (median, 18.3 years). A potential weak association of BRCA1 positivity with lethal disease (hazard ratio, 1.61; 95% CI, 0.82–3.15) was attenuated when adjusting for age, Gleason score and clinical stage (hazard ratio, 1.11; 95% CI, 0.54–2.29). In summary, BRCA1 protein expression is a feature of more proliferative and more aneuploid prostate tumors and is more common in metastatic disease. While not well suited as a prognostic biomarker in primary prostate cancer, BRCA1 protein expression may be most relevant in advanced disease.
Automatic Encoding of a View-Centered Background Image in the Macaque Temporal Lobe
Authors: Chen He , Naya Yuji 
Published: June 2020

Abstract
Perceptual processing along the ventral visual pathway to the hippocampus (HPC) is hypothesized to be substantiated by signal transformation from retinotopic space to relational space, which represents interrelations among constituent visual elements. However, our visual perception necessarily reflects the first person’s perspective based on the retinotopic space. To investigate this two-facedness of visual perception, we compared neural activities in the temporal lobe (anterior inferotemporal cortex, perirhinal and parahippocampal cortices, and HPC) between when monkeys gazed on an object and when they fixated on the screen center with an object in their peripheral vision. We found that in addition to the spatially invariant object signal, the temporal lobe areas automatically represent a large-scale background image, which specify the subject’s viewing location. These results suggest that a combination of two distinct visual signals on relational space and retinotopic space may provide the first person’s perspective serving for perception and presumably subsequent episodic memory.
Powassan Virus Infection Likely Acquired Through Blood Transfusion Presenting as Encephalitis in a Kidney Transplant Recipient
Authors: Taylor Lindsay , Condon Taryn , Destrampe Eric M , Brown Jennifer A , McGavic Jeanette , Gould Carolyn V , Chambers Trudy V , Kosoy Olga I , Burkhalter Kristen L , Annambhotla Pallavi , Basavaraju Sridhar V , Groves Jamel , Osborn Rebecca A , Weiss John , Stramer Susan L , Misch Elizabeth A 
Published: June 2020

Abstract
A kidney transplant patient without known tick exposure developed encephalitis 3 weeks after transplantation. During the transplant hospitalization, the patient had received a blood transfusion from an asymptomatic donor later discovered to have been infected with Powassan virus. Here, we describe a probable instance of transfusion-transmitted Powassan virus infection.
Crisis Communication and Public Perception of COVID-19 Risk in the Era of Social Media
Authors: Malecki Kristen M C , Keating Julie A , Safdar Nasia 
Published: June 2020

Abstract
A number of important principles in effective risk communication established in the late 20th century can provide important scientific insight into patient response to the risks posed by coronavirus disease 2019 (COVID-19). Early risk communication scholars found acceptability of risk was shaped by 2 key components: hazard and outrage. The number of people who are exposed, infected, and fall ill can be considered the hazard. How the public and patients and respond to messages regarding risk mitigation relates to outrage. Social and cultural factors, immediacy, uncertainty, familiarity, personal control, scientific uncertainty, and trust in institutions and media all shape perception and response to risk mesaging. Outrage factors influence the ever-changing public understanding of COVID-19 risk. In concert, hazard and outrage along with cultural and economic context shape adherence to, and overall acceptance of, personal mitigation strategies including wearing facemasks and social distancing among the general public. The spread of misinformation on social media also provides both challenges and opportunities for clinicians. Social media offers an opportunity for experts to quickly convey true information about hazards, but offers others the opportunity to counter this with the spread of misinformation and exacerbate outrage. We propose strategies for infectious diseases clinicians to apply risk communication principles and frameworks to improve patient care and public message development in response to COVID-19.
Coronavirus Disease 2019 and Antimicrobial Resistance: Parallel and Interacting Health Emergencies
Authors: Nieuwlaat Robby , Mbuagbaw Lawrence , Mertz Dominik , Burrows Lori L , Bowdish Dawn M E , Moja Lorenzo , Wright Gerard D , Schünemann Holger J 
Published: June 2020

Abstract
The coronavirus disease 2019 (COVID-19) pandemic and antimicrobial resistance (AMR) are parallel and interacting health emergencies that provide the opportunity for mutual learning. As their measures and consequences are comparable, the COVID-19 pandemic helps to illustrate the potential long-term impact of AMR, which is less acute but not less crucial. They may also impact each other as there is a push to use existing antimicrobials to treat critically ill COVID-19 patients in the absence of specific treatments. Attempts to manage the spread of COVID-19 may also lead to a slowdown in AMR. Understanding how COVID-19 affects AMR trends and what we can expect if these trends remain the same or worsen will help us to plan the next steps for tackling AMR. Researchers should start collecting data to measure the impact of current COVID-19 policies and programs on AMR.
Pseudomonas aeruginosa Strain-sharing in Early Infection Among Children With Cystic Fibrosis
Authors: Stapleton Patrick J , Izydorcyzk Conrad , Clark Shawn , Blanchard Ana , Wang Pauline W , Yau Yvonne , Waters Valerie , Guttman David S 
Published: June 2020

Abstract

Background
We previously identified Pseudomonas aeruginosa isolates with characteristics typical of chronic infection in some early infections in children with cystic fibrosis (CF), suggesting that these isolates may have been acquired from other patients. Our objective was to define the extent of P. aeruginosa strain-sharing in early CF infections and its impact on antibiotic eradication treatment failure rates.

Methods
We performed whole genome sequencing on isolates from early pediatric CF pulmonary infections and from the following comparator groups in the same hospital: chronic CF infection, sink drains, sterile site infections, and asymptomatic carriage. Univariate logistic regression was used to assess factors associated with treatment failure.

Results
In this retrospective, observational study, 1029 isolates were sequenced. The CF clones strain B and clone C were present. In 70 CF patients with early infections, 14 shared strains infected 29 (41%) patients over 5 years; 16% (n = 14) of infections had mixed strains. In the 70 children, approximately one-third of shared-strain infections were likely due to patient-to-patient transmission. Mixed-strain infections were associated with strain-sharing (odds ratio, 8.50; 95% confidence interval, 2.2–33.4; P = .002). Strain-sharing was not associated with antibiotic eradication treatment failure; however, nosocomial strain transmission was associated with establishment of chronic infection in a CF sibling pair.

Conclusions
Although early P. aeruginosa CF infection is thought to reflect acquisition of diverse strains from community reservoirs, we identified frequent early CF strain-sharing that was associated with the presence of mixed strains and instances of possible patient-to-patient transmission.
On Enabling Attribute-Based Encryption to Be Traceable Against Traitors
Authors: Liu Zhen , Huang Qiong , Wong Duncan S 
Published: June 2020

Abstract
Attribute-based encryption (ABE) is a versatile one-to-many encryption primitive, which enables fine-grained access control over encrypted data. Due to its promising applications in practice, ABE schemes with high efficiency, security and expressivity have been continuously emerging. On the other hand, due to the nature of ABE, a malicious user may abuse its decryption privilege. Therefore, being able to identify such a malicious user is crucial towards the practicality of ABE. Although some specific ABE schemes in the literature enjoys the tracing function, they are only proceeded case by case. Most of the ABE schemes do not support traceability. It is thus meaningful and important to have a generic way of equipping any ABE scheme with traceability. In this work, we partially solve the aforementioned problem. Namely, we propose a way of transforming (non-traceable) ABE schemes satisfying certain requirements to fully collusion-resistant black-box traceable ABE schemes, which adds only $O(\sqrt{\mathcal{K}})$ elements to the ciphertext where ${\mathcal{K}}$ is the number of users in the system. And to demonstrate the practicability of our transformation, we show how to convert a couple of existing non-traceable ABE schemes to support traceability.
Out-of-hours primary care in 26 European countries: an overview of organizational models
Authors: Steeman Luca , Uijen Maike , Plat Erik , Huibers Linda , Smits Marleen , Giesen Paul 
Published: June 2020

Abstract

Background
Various models exist to organize out-of-hours primary care (OOH-PC). We aimed to provide an up-to-date overview of prevailing organizational models in the European Union (EU), implemented changes over the last decade and future plans. This baseline overview may provide information for countries considering remodelling their OOH-PC system.

Methods
A cross-sectional web-based questionnaire among 93 key informants from EU countries, Norway and Switzerland. Key informants with expertise in the field of primary health care were invited to participate. Themes in the questionnaire were the existing organizational models for OOH-PC, model characteristics, major organizational changes implemented in the past decade and future plans.

Results
All 26 included countries had different coexisting OOH-PC models, varying from 3 to 10 models per country. ‘GP cooperative was the dominant model in most countries followed by primary care centre and rota group’. There was a large variation in characteristics between the models, but also within the models, caused by differences between countries and regions. Almost all countries had implemented changes over the past 10 years, mostly concerning the implementation of telephone triage and a change of organizational model by means of upscaling and centralization of OOH-PC. Planned changes varied from fine-tuning the prevailing OOH-PC system to radical nationwide organizational transitions in OOH-PC.

Conclusions
Different organizational models for OOH-PC exist on international and national level. Compared with a decade ago, more primary care-oriented organizational models are now dominant. There is a trend towards upscaling and centralization; it should be evaluated whether this improves the quality of health care.