bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noncanonical outcomes of break-induced replication produce complex, extremely long-tract gene conversion events in yeast
Authors: Stewart Joseph A , Hillegass Michael B , Oberlitner Joseph H , Younkin Ellen M , Wasserman Beth F , Casper Anne M 
Published: July 2021

Abstract
Long-tract gene conversions (LTGC) can result from the repair of collapsed replication forks, and several mechanisms have been proposed to explain how the repair process produces this outcome. We studied LTGC events produced from repair collapsed forks at yeast fragile site FS2. Our analysis included chromosome sizing by contour-clamped homogeneous electric field electrophoresis, next-generation whole-genome sequencing, and Sanger sequencing across repair event junctions. We compared the sequence and structure of LTGC events in our cells to the expected qualities of LTGC events generated by proposed mechanisms. Our evidence indicates that some LTGC events arise from half-crossover during BIR, some LTGC events arise from gap repair, and some LTGC events can be explained by either gap repair or “late” template switch during BIR. Also based on our data, we propose that models of collapsed replication forks be revised to show not a one-end double-strand break (DSB), but rather a two-end DSB in which the ends are separated in time and subject to gap repair.
The whole-genome sequence of the novel yeast species Metschnikowia persimmonesis isolated from medicinal plant Diospyros kaki Thunb
Authors: Rahmat Endang , Park Inkyu , Kang Youngmin 
Published: July 2021

Abstract
The new yeast Metschnikowia persimmonesis KCTC 12991BP (KIOM G15050 strain) exhibits strong antimicrobial activity against some pathogens. This activity may be related to the medicinal profile of secondary metabolites that could be found in the genome of this species. Therefore, to explore its future possibility of producing some beneficial activities, including medicinal ability, we report high-quality whole-genome assembly of M. persimmonesis produced by PacBio RS II sequencer. The final draft assembly consisted of 16 scaffolds with GC content of 45.90% and comprised a fairly complete set (82.8%) of BUSCO result using Saccharomycetales lineage data set. The total length of the genome was 16.473 Mb, with a scaffold N50 of 1.982 Mb. Annotation of the M. persimmonesis genome revealed presence of 7029 genes and 6939 functionally annotated proteins. Based on the analysis of phylogenetic relationship and the average nucleotide identities, M. persimmonesis was proved to a novel species within the Metschnikowia genus. This finding is expected to significantly contribute to the discovery of high-value natural products from M. persimmonesis as well as for genome biology and evolution comparative analysis within Metschnikowia species.
Associations Between Elevated Growth Differentiation Factor-15 and Sarcopenia Among Community-dwelling Older Adults
Authors: Kim Miji , Walston Jeremy D , Won Chang Won 
Published: July 2021

Abstract

Background
Growth differentiation factor 15 (GDF-15) is associated with disease progression, mitochondrial dysfunction, and mortality. Elevated GDF-15 level was recently reported to be associated with poorer physical performance in healthy adults. However, the association between serum GDF-15 level and sarcopenia in community-dwelling older adults has not been well characterized.

Methods
We conducted cross-sectional (n = 929) and 2-year prospective analyses (n = 788) among participants aged 70–84 years enrolled in the Korean Frailty and Aging Cohort Study. Participants with an estimated glomerular filtration rate of &lt;60 mL/min/1.73 m2 were excluded. Appendicular lean mass was measured using dual-energy x-ray absorptiometry. Sarcopenia status was determined according to the Asian Working Group for Sarcopenia-2019 algorithm.

Results
At baseline, 16.6% of the participants had sarcopenia. Median GDF-15 concentration was higher in the sarcopenic group than in the non-sarcopenic group (1221 pg/mL vs 1019 pg/mL, p &lt; .001). In the multivariate analysis adjusted for cardiometabolic risk and biological factors, the highest GDF-15 tertile (≥1245 pg/mL) had an increased likelihood of sarcopenia (odds ratio, 1.96; 95% confidence interval, 1.16–3.33) than the lowest tertile (&lt;885 pg/mL). During the 2-year follow-up period, 67 (10.1%) individuals without sarcopenia at baseline developed sarcopenia. There were no significant associations between baseline serum GDF-15 levels and incident sarcopenia or its components (all p &gt; .05).

Conclusions
Elevated GDF-15 was associated with prevalent sarcopenia but not able to predict incident sarcopenia in the 2-year follow-up. Further studies are needed to explore the pathophysiological roles of GDF-15 in the development of sarcopenia.
Later-Life Living Arrangements of Americans With and Without Children: A Life Table Approach
Authors: Raymo James M , Xu Xiao , Kim BoRin , Liang Jersey , Ofstedal Mary Beth 
Published: July 2021

Abstract

Objectives
This study describes living arrangement-specific life expectancy for older Americans with and without children, by sex and race/ethnicity.

Method
We use life tables from the Human Mortality Database and data from the Health and Retirement Study over a 17-year period (2000–2016) to calculate living arrangement-specific life expectancy at age 65 using Sullivan’s method. Results describe the lives of older Americans aged 65 and older with and without children in terms of the number of expected years of life in different living arrangements.

Results
With the exception of Hispanic men, older Americans without children spend over half of their remaining life living alone. Among the childless, it is White women and Black men who spend the largest percent of remaining life living alone (65% and 57%, respectively). Relative to parents, childless older Americans have an overall life expectancy at age 65 that is 1 year lower and spend 5–6 years more living alone and fewer years living with a spouse (8 years less for men and 5 years less for women). Childless older Americans spend more time in nursing homes, but average expected duration in this living arrangement is short and differences between those with and without children are small.

Discussion
This descriptive analysis demonstrates the fundamental ways in which children shape the lives of older Americans by showing that later-life living arrangements of childless Americans differ markedly from their counterparts with children. These results provide a valuable empirical foundation for broader efforts to understand relationships between childlessness, living arrangements, and well-being at older ages.
Combinatorial Ricci Flows with Applications to the Hyperbolization of Cusped 3-Manifolds
Authors: Feng Ke , Ge Huabin , Hua Bobo , Xu Xu 
Published: July 2021

Abstract
In this paper, we adopt combinatorial Ricci flow to study the existence of hyperbolic structure on cusped 3-manifolds. The long-time existence and the uniqueness for the extended combinatorial Ricci flow are proven for general pseudo 3-manifolds. We prove that the extended combinatorial Ricci flow converges to a decorated hyperbolic polyhedral metric if and only if there exists a decorated hyperbolic polyhedral metric of zero Ricci curvature, and the flow converges exponentially fast in this case. For an ideally triangulated cusped 3-manifold admitting a complete hyperbolic metric, the flow provides an effective algorithm for finding the hyperbolic metric.
On C0-Continuity of the Spectral Norm for Symplectically Non-Aspherical Manifolds
Authors: Kawamoto Yusuke 
Published: July 2021

Abstract
The purpose of this paper is to study the relation between the $C^0$-topology and the topology induced by the spectral norm on the group of Hamiltonian diffeomorphisms of a closed symplectic manifold. Following the approach of Buhovsky–Humilière–Seyfaddini, we prove the $C^0$-continuity of the spectral norm for complex projective spaces and negative monotone symplectic manifolds. The case of complex projective spaces provides an alternative approach to the $C^0$-continuity of the spectral norm proven by Shelukhin. We also prove a partial $C^0$-continuity of the spectral norm for rational symplectic manifolds. Some applications such as the Arnold conjecture in the context of $C^0$-symplectic topology are also discussed.
Incidence of Chronic Obstructive Pulmonary Disease in People With Human Immunodeficiency Virus and Their Parents and Siblings in Denmark
Authors: Ronit Andreas , Omland Lars H , Kronborg Gitte , Pedersen Gitte , Nielsen Lars , Mohey Rajesh , Wiese Lothar , Obel Niels , Ahlström Magnus G 
Published: July 2021

AbstractBackgroundPeople with human immunodeficiency virus (PWH) may be at increased risk of several respiratory syndromes including chronic obstructive pulmonary disease (COPD). In matched cohort studies, we examined risk factors for COPD in PWH and their parents and siblings compared with population controls.MethodsUsing data from national registries, competing risk regression models were constructed and used to calculate adjusted hazard ratios (aHRs) for COPD. We evaluated the effect of human immunodeficiency virus characteristics, smoking, and educational attainment on COPD incidence in PWH.ResultsA total of 226 PWH and 1029 population controls were diagnosed with COPD during 63 661 and 562 171 person-years of follow-up. PWH had increased risk of being diagnosed with COPD compared to controls (aHR, 2.02 [95% confidence interval, 1.75–2.33]). Parents and siblings of PWH were also more likely to be diagnosed with COPD compared to controls. CD4+ T-cell counts were not associated with COPD, but unsuppressed viral replication, smoking status, and educational attainment were associated with COPD in PWH. No COPD diagnoses were registered in PWH with high educational attainment and absence of smokingConclusionsPWH have an increased risk of being diagnosed with COPD, as have their parents and siblings. This seems to be driven primarily by smoking and low socioeconomic status.
Gender differences in survival among low birthweight newborns and infants in sub-Saharan Africa: a systematic review
Authors: Gebremeskel Akalewold T , Fantaye Arone W , Faust Lena , Obegu Pamela , Yaya Sanni 
Published: July 2021

AbstractIn sub-Saharan Africa, low birthweight (LBW) accounts for three-quarters of under-five mortality and morbidity. However, gender differences in survival among LBW newborns and infants have not yet been systematically examined. This review examines gender differences in survival among LBW newborns and infants in the region. Ovid Medline, Embase, CINAHL, Scopus and Global Health databases were searched for qualitative, quantitative and mixed methods studies. Studies that presented information on differences in mortality or in morbidity between LBW male and female newborns or infants were eligible for inclusion. The database search yielded 4124 articles, of which 11 were eligible for inclusion. A narrative synthesis method was used to summarize the findings of the included studies. Seven studies reported more LBW male deaths, three studies reported more LBW female deaths and one study did not disaggregate the deaths by gender. Nine of the 11 studies that examined gender differences in mortality did not find significant evidence of gender differences in mortality among LBW newborns and infants. Likewise, no significant differences were found for gender differences in morbidity among this population. The review findings suggest a need for further research on this topic given the potential significance on child health and developmental goals.
Comparison of phenotypic antimicrobial susceptibility testing results and WGS-derived genotypic resistance profiles for a cohort of ESBL-producing Escherichia coli collected from Canadian hospitals: CANWARD 2007–18
Authors: Golden Alyssa R , Karlowsky James A , Walkty Andrew , Baxter Melanie R , Denisuik Andrew J , McCracken Melissa , Mulvey Michael R , Adam Heather J , Bay Denice , Zhanel George G 
Published: July 2021

Abstract

Objectives
To determine whether the genotypic resistance profile inferred from WGS could accurately predict phenotypic resistance for ESBL-producing Escherichia coli isolated from patient samples in Canadian hospital laboratories.

Methods
As part of the ongoing CANWARD study, 671 E. coli were collected and phenotypically confirmed as ESBL producers using CLSI M100 disc testing criteria. Isolates were sequenced using the Illumina MiSeq platform, resulting in 636 high-quality genomes for comparison. Using a rules-based approach, the genotypic resistance profile was compared with the phenotypic resistance interpretation generated using the CLSI broth microdilution method for ceftriaxone, ciprofloxacin, gentamicin and trimethoprim/sulfamethoxazole.

Results
The most common genes associated with non-susceptibility to ceftriaxone, gentamicin and trimethoprim/sulfamethoxazole were CTX-M-15 (n = 391), aac(3)-IIa + aac(6′)-Ib-cr (n = 121) and dfrA17 + sul1 (n = 169), respectively. Ciprofloxacin non-susceptibility was most commonly attributed to alterations in both gyrA (S83L + D87N) and parC (S80I + E84V), with (n = 187) or without (n = 197) aac(6′)-Ib-cr. Categorical agreement (susceptible or non-susceptible) between actual and predicted phenotype was 95.6%, 98.9%, 97.6% and 88.8% for ceftriaxone, ciprofloxacin, gentamicin and trimethoprim/sulfamethoxazole, respectively. Only ciprofloxacin results (susceptible or non-susceptible) were predicted with major error (ME) and very major error (VME) rates of &lt;3%: ciprofloxacin (ME, 1.5%; VME, 1.1%); gentamicin (ME, 0.8%–31.7%; VME, 4.8%); ceftriaxone (ME, 81.8%; VME, 3.0%); and trimethoprim/sulfamethoxazole (ME, 0.9%–23.0%; VME, 5.2%–8.5%).

Conclusions
Our rules-based approach for predicting a resistance phenotype from WGS performed well for ciprofloxacin, with categorical agreement of 98.9%, an ME rate of 1.5% and a VME rate of 1.1%. Although high categorical agreements were also obtained for gentamicin, ceftriaxone and trimethoprim/sulfamethoxazole, ME and/or VME rates were ≥3%.
User-centered design of a scalable, electronic health record-integrated remote symptom monitoring intervention for patients with asthma and providers in primary care
Authors: Rudin Robert S , Perez Sofia , Rodriguez Jorge A , Sousa Jessica , Plombon Savanna , Arcia Adriana , Foer Dinah , Bates David W , Dalal Anuj K 
Published: July 2021

Abstract

Objective
To determine user and electronic health records (EHR) integration requirements for a scalable remote symptom monitoring intervention for asthma patients and their providers.

Methods
Guided by the Non-Adoption, Abandonment, Scale-up, Spread, and Sustainability (NASSS) framework, we conducted a user-centered design process involving English- and Spanish-speaking patients and providers affiliated with an academic medical center. We conducted a secondary analysis of interview transcripts from our prior study, new design sessions with patients and primary care providers (PCPs), and a survey of PCPs. We determined EHR integration requirements as part of the asthma app design and development process.

Results
Analysis of 26 transcripts (21 patients, 5 providers) from the prior study, 21 new design sessions (15 patients, 6 providers), and survey responses from 55 PCPs (71% of 78) identified requirements. Patient-facing requirements included: 1- or 5-item symptom questionnaires each week, depending on asthma control; option to request a callback; ability to enter notes, triggers, and peak flows; and tips pushed via the app prior to a clinic visit. PCP-facing requirements included a clinician-facing dashboard accessible from the EHR and an EHR inbox message preceding the visit. PCP preferences diverged regarding graphical presentations of patient-reported outcomes (PROs). Nurse-facing requirements included callback requests sent as an EHR inbox message. Requirements were consistent for English- and Spanish-speaking patients. EHR integration required use of custom application programming interfaces (APIs).

Conclusion
Using the NASSS framework to guide our user-centered design process, we identified patient and provider requirements for scaling an EHR-integrated remote symptom monitoring intervention in primary care. These requirements met the needs of patients and providers. Additional standards for PRO displays and EHR inbox APIs are needed to facilitate spread.
Influence of a novel consensus bacterial 6-phytase variant on mineral digestibility and bone ash in young growing pigs fed diets with different concentrations of phytate-bound phosphorus
Authors: Espinosa Charmaine D , Oliveira Maryane S F , Velayudhan Deepak E , Dersjant-Li Yueming , Stein Hans H 
Published: July 2021

AbstractA 20-d experiment was conducted to test the hypothesis that phytase increases nutrient digestibility, bone ash, and growth performance of pigs fed diets containing 0.23%, 0.29%, or 0.35% phytate-bound P. Within each level of phytate, five diets were formulated to contain 0, 500, 1,000, 2,000, or 4,000 phytase units (FTU)/kg of a novel phytase (PhyG). Three reference diets were formulated by adding a commercial Buttiauxella phytase (PhyB) at 1,000 FTU/kg to diets containing 0.23%, 0.29%, or 0.35% phytate-bound P. A randomized complete block design with 144 individually housed pigs (12.70 ± 4.01 kg), 18 diets, and 8 replicate pigs per diet was used. Pigs were adapted to diets for 15 d followed by 4 d of fecal collection. Femurs were collected on the last day of the experiment. Results indicated that diets containing 0.35% phytate-bound P had reduced (P &lt; 0.01) digestibility of Ca, P, Mg, and K compared with diets containing less phytate-bound P. Due to increased concentration of total P in diets with high phytate, apparent total tract digestible P and bone ash were increased by PhyG to a greater extent in diets with 0.29% or 0.35% phytate-bound P than in diets with 0.23% phytate-bound P (interaction, P &lt; 0.05). At 1,000 FTU/kg, PhyG increased P digestibility and bone P more (P &lt; 0.05) than PhyB. The PhyG increased (P &lt; 0.01) pig growth performance, and pigs fed diets containing 0.35% or 0.29% phytate-bound P performed better (P &lt; 0.01) than pigs fed the 0.23% phytate-bound P diets. In conclusion, the novel phytase (i.e., PhyG) is effective in increasing bone ash, mineral digestibility, and growth performance of pigs regardless of dietary phytate level.
Migration and invention in the Age of Mass Migration
Authors: Diodato Dario , Morrison Andrea , Petralia Sergio 
Published: July 2021

AbstractMore than 30 million people migrated to the USA between late-ninetieth and early-twentieth century, and thousands became inventors. Drawing on a novel dataset of immigrant inventors in the USA, we assess the city-level impact of immigrants’ patenting and their contribution to the technological specialization of the receiving US regions between 1870 and 1940. Our results show that native inventors benefited from the inventive activity of immigrants. In addition, we show that the knowledge transferred by immigrants gave rise to new and previously not exiting technological fields in the US regions where immigrants moved to.
History of the AsianLymantriaspecies Program: A Unique Pathway Risk Mitigation Strategy
Authors: Mastro Victor C , Munson A Steve , Wang Baode , Freyman Tamara , Humble Leland M 
Published: July 2021

AbstractChanges in grain trading between Russian Far Eastern ports and North America in the late 1980s and early 1990s led to introductions of Lymantria dispar asiatica (Vnukovskij), formerly called the Asian gypsy moth (AGM), and the recognition of a new pathway for its transport. Unlike the pathways commonly used and regulated for commodities and for packaging material containing pest organisms, this presented a unique pathway for AGM. Vessels departing from the Russia Far East transiting to ports on the west coast of the United States (US) and Canada (CA) were infested with life stages of AGM and related species. Upon arrival in North America, eggs oviposited on the surfaces of the ships and its cargo hatched with larvae ballooning to vegetation surrounding port areas leading to the potential establishment of AGM populations. A multi layered monitoring and inspection program was developed to mitigate this risk of introduction, initially for Russian Far Eastern ports, and eventually to include specified areas of other Asian countries. In this article, we summarize and review the integral parts of this mitigation program, which include: risk assessments, AGM monitoring in foreign and domestic ports, vessel cleaning and certification by a government Plant Protection Organization (PPO) or its proxy, AGM surveillance, and eradication of introduced AGM in ports and other areas within the United States and Canada. The uniqueness of this program is characterized by its complexity, which involves coordinated efforts of PPOs, the use of various inspection organizations, and the support of ocean transportation industries.
Risk of death due to other causes is lower among octogenarians with non-small cell lung cancer after wedge resection than lobectomy/segmentectomy
Authors: Mimae Takahiro , Miyata Yoshihiro , Yoshimura Kenichi , Tsutani Yasuhiro , Imai Kentaro , Ito Hiroyuki , Nakayama Haruhiko , Ikeda Norihiko , Okada Morihito 
Published: July 2021

Abstract

Objective
We aimed to determine the influences of surgical procedures on the postoperative death of octogenarians with clinical Stage IA non-small cell lung cancer excluding cT1mi.

Methods
We compared overall survival and the cumulative incidence of death due to all and other causes among 1 130 279, and 191 consecutive patients aged ≤79 and ≥80 years after lobectomy, segmentectomy and wedge resection at three institutions. Death due to other causes was defined as death due to any cause except non-small cell lung cancer.

Results
The median followup was 53 months. The 5-year overall survival rates for patients aged ≥ 80 and ≤ 79 years after lobectomy, segmentectomy and wedge resection were respectively, 78.0% (95% confidence interval, 63.8%–87.2%) versus 91.2% (95% confidence interval, 89.0%–92.9%), 68.1% (95% confidence interval, 45.2%–83.1%) versus 90.0% (95% confidence interval, 84.6%–93.5%), and 62.7% (95% confidence interval, 44.0–76.7%) versus 84.4% (95% confidence interval, 76.3%–89.9%) (P &lt; 0.01 for all). The cumulative incidence of death due to other causes after wedge resection was similar between patients aged ≥ 80 and ≤ 79 years (P = 0.45), but significantly higher in those aged ≥ 80, than ≤ 79 years after lobectomy or segmentectomy (P = 0.00015 and 0.00091, respectively).

Conclusions
The influence of wedge resection on death due to other causes was lower than that of lobectomy or segmentectomy in patients with non-small cell lung cancer aged ≥ 80 years. Wedge resection might be a useful option for octogenarians even if they can tolerate lobectomy/segmentectomy to avoid postoperative death due to causes other than non-small cell lung cancer.
Deep Learning for Mortgage Risk*
Authors: Sadhwani Apaar , Giesecke Kay , Sirignano Justin 
Published: July 2021

AbstractWe examine the behavior of mortgage borrowers over several economic cycles using an unprecedented dataset of origination and monthly performance records for over 120 million mortgages originated across the United States between 1995 and 2014. Our deep learning model of multi-period mortgage delinquency, foreclosure, and prepayment risk uncovers the highly nonlinear influence on borrower behavior of an exceptionally broad range of loan-specific and macroeconomic variables down to the zip-code level. In particular, most variables strongly interact. Prepayments involve the greatest nonlinear effects among all events. We demonstrate the significant implications of the nonlinearities for risk management, investment management, and mortgage-backed securities.