bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limited resection for stage IA radiologically invasive lung cancer: a real-world nationwide database study
Authors: Soh Junichi , Toyooka Shinichi , Shintani Yasushi , Okami Jiro , Ito Hiroyuki , Ohtsuka Takashi , Mori Takeshi , Watanabe Shun-Ichi , Asamura Hisao , Chida Masayuki , Endo Shunsuke , Nakanishi Ryoichi , Kadokura Mitsutaka , Suzuki Hidemi , Miyaoka Etsuo , Yoshino Ichiro , Date Hiroshi ,   Japanese Joint Committee of Lung Cancer Registry, Toyooka Shinichi , Shintani Yasushi , Okami Jiro , Ito Hiroyuki , Ohtsuka Takashi , Mori Takeshi , Watanabe Shun-Ichi , Asamura Hisao , Chida Masayuki , Endo Shunsuke , Nakanishi Ryoichi , Kadokura Mitsutaka , Suzuki Hidemi , Date Hiroshi 
Published: June 2022

Abstract

OBJECTIVES
Radiologically invasive non-small-cell lung cancer, defined as consolidation size to maximum tumour diameter ratio of over 0.5, is associated with pathological invasiveness and worse prognosis. However, there are no real-world, nationwide database studies on limited resections that consider radiological invasiveness. This study aimed to investigate the prognostic validity of limited resection, such as segmentectomy and wedge resection, in cStage IA (TNM 8th edition) radiologically invasive lung cancer.

METHODS
We conducted a retrospective analysis of patients who underwent complete resection according to the Japanese Joint Committee of Lung Cancer Registry Database. The relationship between surgical procedures and prognosis was examined using stratification by cT factor and radiological invasiveness.

RESULTS
Among the 5,692 patients enrolled, lobectomy, segmentectomy and wedge resection were performed in 4,323 (80.0%), 657 (11.5%) and 712 (12.5%) patients, respectively. Multivariable analysis with or without propensity score matching indicated that older age, poor performance status and wedge resection were significantly associated with worse prognosis and that patients who underwent segmentectomy showed an equivalent prognosis to those who underwent lobectomy. Subset analyses revealed that segmentectomy showed an equivalent prognosis to lobectomy in patients with cT1b or less, but not in those with cT1c, especially for non-pure radiological invasive cT1c; 5-year overall survival rates were 91.4% vs 90.4% in cT1b with non-pure radiological invasiveness and 80.0% vs 83.8% in cT1b with pure radiological invasiveness, respectively.

CONCLUSIONS
Segmentectomy can be an alternative to lobectomy in patients with radiologically invasive lung cancer with cT1b or less but not in those with cT1c.
Variation in gut microbiome structure across the annual hibernation cycle in a wild primate
Authors: Greene Lydia K , Andriambeloson Jean-Basile , Rasoanaivo Hoby A , Yoder Anne D , Blanco Marina B 
Published: June 2022

AbstractThe gut microbiome can mediate host metabolism, including facilitating energy-saving strategies like hibernation. The dwarf lemurs of Madagascar (Cheirogaleus spp.) are the only obligate hibernators among primates. They also hibernate in the subtropics, and unlike temperate hibernators, fatten by converting fruit sugars to lipid deposits, torpor at relatively warm temperatures, and forage for a generalized diet after emergence. Despite these ecological differences, we might expect hibernation to shape the gut microbiome in similar ways across mammals. We, therefore, compare gut microbiome profiles, determined by amplicon sequencing of rectal swabs, in wild furry-eared dwarf lemurs (C. crossleyi) during fattening, hibernation, and after emergence. The dwarf lemurs exhibited reduced gut microbial diversity during fattening, intermediate diversity and increased community homogenization during hibernation, and greatest diversity after emergence. The Mycoplasma genus was enriched during fattening, whereas the Aerococcaceae and Actinomycetaceae families, and not Akkermansia, bloomed during hibernation. As expected, the dwarf lemurs showed seasonal reconfigurations of the gut microbiome; however, the patterns of microbial diversity diverged from temperate hibernators, and better resembled the shifts associated with dietary fruits and sugars in primates and model organisms. Our results thus highlight the potential for dwarf lemurs to probe microbiome-mediated metabolism in primates under contrasting conditions.
Complex mutation profiles in mismatch repair and ribonucleotide reductase mutants reveal novel repair substrate specificity of MutS homolog (MSH) complexes
Authors: Lamb Natalie A , Bard Jonathan E , Loll-Krippleber Raphael , Brown Grant W , Surtees Jennifer A 
Published: June 2022

Abstract
Determining mutation signatures is standard for understanding the etiology of human tumors and informing cancer treatment. Multiple determinants of DNA replication fidelity prevent mutagenesis that leads to carcinogenesis, including the regulation of free deoxyribonucleoside triphosphate pools by ribonucleotide reductase and repair of replication errors by the mismatch repair system. We identified genetic interactions between rnr1 alleles that skew and/or elevate deoxyribonucleoside triphosphate levels and mismatch repair gene deletions. These defects indicate that the rnr1 alleles lead to increased mutation loads that are normally acted upon by mismatch repair. We then utilized a targeted deep-sequencing approach to determine mutational profiles associated with mismatch repair pathway defects. By combining rnr1 and msh mutations to alter and/or increase deoxyribonucleoside triphosphate levels and alter the mutational load, we uncovered previously unreported specificities of Msh2–Msh3 and Msh2–Msh6. Msh2–Msh3 is uniquely able to direct the repair of G/C single-base deletions in GC runs, while Msh2–Msh6 specifically directs the repair of substitutions that occur at G/C dinucleotides. We also identified broader sequence contexts that influence variant profiles in different genetic backgrounds. Finally, we observed that the mutation profiles in double mutants were not necessarily an additive relationship of mutation profiles in single mutants. Our results have implications for interpreting mutation signatures from human tumors, particularly when mismatch repair is defective.
Natural History Trajectories of Frailty in Community-Dwelling Older Japanese Adults
Authors: Tange Chikako , Nishita Yukiko , Tomida Makiko , Otsuka Rei , Ando Fujiko , Shimokata Hiroshi , Arai Hidenori 
Published: June 2022

Abstract

Background
The gap between the average life expectancy and healthy life expectancy remains wide. Understanding the natural history of frailty development is necessary to prevent and treat frailty to overcome this gap. This study elucidated the trajectories of 5 frailty assessment components using group-based multitrajectory modeling.

Methods
Overall, 845 community-dwelling older adults (aged 65–91 years; 433 males and 412 females) who underwent longitudinal frailty assessments at least 3 times were included in the analysis. The mean follow-up period (±SD, range) was 7.1 (±2.3, 3.8–11.3) years. In each wave, the physical frailty was assessed for the following 5 partially modified components of the Cardiovascular Health Study criteria: shrinking, weakness, exhaustion, slowness, and low activity. Using group-based multitrajectory modeling, we identified subgroups that followed distinctive trajectories regarding the 5 frailty components.

Results
Five frailty trajectory groups were identified: weakness-focused frail progression group (Group 1 [G1]; 10.9%), robust maintenance group (Group 2 [G2]; 43.7%), exhaustion-focused prefrail group (Group 3 [G3]; 24.3%), frail progression group (Group 4 [G4]; 6.7%), and low activity–focused prefrail group (Group 5 [G5]; 14.4%). The Cox proportional hazards model analysis showed that G1, G4, and G5 had significantly higher mortality risks after adjusting for sex and age (G2 was the reference group).

Conclusion
Based on the natural history of frailty, the 5 distinctive trajectory groups showed that some individuals remained robust, while others remained predominantly prefrail or progressed primarily owing to physical mobility decline. Therefore, identifying individuals belonging to these progressive frailty groups and providing interventions according to the characteristics of each group may be beneficial.
Perceived Support Protects Against Negative Affective Experiences of Momentary Solitude: An Ecological Momentary Assessment Study
Authors: Fang Boye , Li Danyu , Chen Beizhuo , Huang Jiaojiao , Hou Yanyan , Liu Huiying 
Published: June 2022

Abstract

Objectives
Momentary solitude (the objective state of being alone) has a strong association with negative affective experiences in older people, but little is known about how the role of social relationship characteristics on relationship between momentary solitude and affect. We examined the momentary association between momentary solitude and negative affect (NA), and whether such association was moderated by the structural and functional aspects of social relationships.

Methods
A sample of 153 late-middle-aged and older adults were recruited and provided a total of 6,742 ecological momentary assessment surveys, of which momentary solitudes were reported for 1,885 (28%) surveys. Hierarchical linear model was used to examine how social networks and social support moderated the association of momentary solitude with NA experiences.

Results
The association of momentary solitude with NA experiences was significant among middle-aged and older adults (b = 0.025, SE = 0.008, p &lt; .01). Family networks had the main effect on NA. Perceived social support buffered against increased NA in momentary solitude: Individuals with a higher level of perceived support reported fewer increases in NA during momentary solitude than those perceiving a lower level of support.

Discussion
Momentary solitude was experienced less negatively for middle-aged and older persons embedded in a context of higher levels of perceived social support. Practitioners need to pay more attention to the promotion of social resources when delivering programs to improve the subjective well-being of late-middle-aged and older adults.
Dual-Task Zumba Gold for Improving the Cognition of People With Mild Cognitive Impairment: A Pilot Randomized Controlled Trial
Authors: Parial Laurence Lloyd , Kor Patrick Pui Kin , Sumile Earl Francis , Leung Angela Yee Man 
Published: June 2022

Abstract

Background and Objectives
Integrating mental activities with physical exercises (e.g., dual-tasking) may potentially improve cognition in older adults and people with mild cognitive impairment (MCI). This study investigated the preliminary efficacy of a new intervention called dual-task Zumba Gold (DTZ) on people with MCI to guide an adequately-powered full-scale trial.

Research Design and Methods
This is a 2-arm pilot randomized controlled trial with 60 people with MCI assigned to a 12-week DTZ intervention or control group (health education). We hypothesized that DTZ would facilitate significant improvements in global cognition (primary outcome) and other psychological/physical measures at postintervention (T1) and 6-week follow-up (T2). Generalized estimating equations with an intention-to-treat approach were used to evaluate intervention effects. Postintervention qualitative interviews explored the participants’ program perceptions.

Results
Fifty-one participants completed the study, with no adverse events reported. DTZ participants showed significant improvements in global cognition (p &lt; .001, d = 0.75–0.78), executive function (p &lt; .001, d = 0.28–0.33), immediate recall (p &lt; .001, d = 0.50–0.54), delayed recall (p = .003, d = 0.66–0.71), quality of life (p = .027, d = 0.59–0.63), and mobility (p = .005, d = 0.53–0.56) at T1 and T2. There were nonsignificant changes in working memory, depressive symptoms, blood pressure, body mass index, and waist circumference. Participants conveyed intervention acceptability, including challenges/barriers, enablers, and future recommendations.

Discussion and Implications
DTZ is a potentially feasible intervention for people with MCI that may improve cognition, quality of life, and mobility. A full-scale trial is recommended for confirmatory evaluation.

Clinical Trial Registration Number
NCT04788238
Tensor-based reconstruction applied to regularized time-lapse data
Authors: Popa Jonathan , Minkoff Susan E , Lou Yifei 
Published: June 2022

SUMMARY
Repeatedly recording seismic data over a period of months or years is one way to identify trapped oil and gas and to monitor CO2 injection in underground storage reservoirs and saline aquifers. This process of recording data over time and then differencing the images assumes the recording of the data over a particular subsurface region is repeatable. In other words, the hope is that one can recover changes in the Earth when the survey parameters are held fixed between data collection times. Unfortunately, perfect experimental repeatability almost never occurs. Acquisition inconsistencies such as changes in weather (currents, wind) for marine seismic data are inevitable, resulting in source and receiver location differences between surveys at the very least. Thus, data processing aimed at improving repeatability between baseline and monitor surveys is extremely useful. One such processing tool is regularization (or binning) that aligns multiple surveys with different source or receiver configurations onto a common grid. Data binned onto a regular grid can be stored in a high-dimensional data structure called a tensor with, for example, x and y receiver coordinates and time as indices of the tensor. Such a higher-order data structure describing a subsection of the Earth often exhibits redundancies which one can exploit to fill in gaps caused by sampling the surveys onto the common grid. In fact, since data gaps and noise increase the rank of the tensor, seeking to recover the original data by reducing the rank (low-rank tensor-based completion) successfully fills in gaps caused by binning. The tensor nuclear norm (TNN) is defined by the tensor singular value decomposition (tSVD) which generalizes the matrix SVD. In this work we complete missing time-lapse data caused by binning using the alternating direction method of multipliers (or ADMM) to minimize the TNN. For a synthetic experiment with three parabolic events in which the time-lapse difference involves an amplitude increase in one of these events between baseline and monitor data sets, the binning and reconstruction algorithm (TNN-ADMM) correctly recovers this time-lapse change. We also apply this workflow of binning and TNN-ADMM reconstruction to a real marine survey from offshore Western Australia in which the binning onto a regular grid results in significant data gaps. The data after reconstruction varies continuously without the large gaps caused by the binning process.
DNA Metabarcoding Across Disciplines: Sequencing Our Way to Greater Understanding Across Scales of Biological Organization
Authors: Forsman Anna M , Savage Anna E , Hoenig Brandon D , Gaither Michelle R 
Published: June 2022

Abstract
DNA metabarcoding describes the use of targeted DNA (i.e., amplicon) sequencing to identify community constituents from a complex sample containing genetic material from multiple organisms, such as water, soil, gut contents, microbiomes, or biofilms. This molecular approach for characterizing mixed DNA samples relies on the development of “universal primers” that allow for effective amplification of target sequences across a broad range of taxa. Armed with optimized lab protocols and rigorous bioinformatics tools, DNA metabarcoding can produce a wealth of information about the hidden biodiversity of various sample types by probing for organisms’ molecular footprints. DNA metabarcoding has received considerable popular press over the last few years because of gut microbiome studies in humans and beyond. However, there are many other applications that are continually integrating molecular biology with other fields of study to address questions that have previously been unanswerable, for both prokaryotic and eukaryotic targets. For example, we can now sample mostly digested gut contents from virtually any organism to learn about ontogeny and foraging ecology. Water samples collected from different locations can be filtered to extract eDNA (i.e., environmental DNA), revealing the biodiversity of fish and other taxa targeted by carefully selected primer sets. This universal primer metabarcoding approach has even been extended to looking at diverse gene families within single species, which is particularly useful for complex immune system genetics. The purpose of this SICB symposium was to bring together researchers using DNA metabarcoding approaches to (a) showcase the diversity of applications of this technique for addressing questions spanning ecology, evolution, and physiology, and (b) to spark connections among investigators from different fields that are utilizing similar approaches to facilitate optimization and standardization of metabarcoding methods and analyses. The resulting manuscripts from this symposium represent a great diversity of metabarcoding applications and taxonomic groups of interest.
Timing of Antiretroviral Therapy
Authors: Quinn M K , Williams Paige L , Muhihi Alfa , Duggan Christopher P , Ulenga Nzovu , Alwy Al-Beity Fadhlun M , Perumal Nandita , Aboud Said , Fawzi Wafaie W , Manji Karim P , Sudfeld Christopher R 
Published: June 2022

Abstract

Background
Combination antiretroviral therapy (cART) initiation during pregnancy reduces the risk of perinatal human immunodeficiency virus (HIV) transmission; however, studies have suggested that there may be unintended adverse consequences on birth outcomes for selected cART regimens.

Methods
We analyzed adverse birth outcomes among a prospective cohort of 1307 pregnant women with HIV in Dar es Salaam who initiated cART during the first or second trimester of a singleton pregnancy. Our primary analysis compared birth outcomes by gestational age at cART initiation among these women initiating cART in pregnancy.

Results
Among women who initiated cART in pregnancy, there was no relationship of gestational age at cART initiation with the risk of fetal death or stillbirth. However, women who initiated cART before 20 weeks of gestation compared with after 20 weeks had increased risk of preterm birth (risk ratio [RR], 1.30; 95% confidence interval [CI], 1.03–1.67) but decreased risk of small-for-gestational age birth (RR, 0.71; 95% CI, .55–.93).

Conclusions
With increasing use of cART preconception and early in pregnancy, clinicians should be aware of the benefits and potential risks of cART regimens to optimize birth outcomes.
Clonal relationship of tet(X4)-positive Escherichia coli ST761 isolates between animals and humans
Authors: Zhai Weishuai , Wang Tao , Yang Dawei , Zhang Qidi , Liang Xiao , Liu Zhihai , Sun Chengtao , Wu Congming , Liu Dejun , Wang Yang 
Published: June 2022

Abstract

Objectives
To characterize the relationship of tet(X4)-positive isolates from different hosts and environments.

Methods
PCR and MALDI-TOF MS were used to identify the tet(X4)-positive isolates. The MICs of 13 antimicrobial agents were determined by broth microdilution. Illumina technology was used to sequence all of the isolates. One isolate was randomly selected from Escherichia coli ST761 clones for long-read sequencing to obtain plasmid sequences. Bioinformatics analysis was used to determine the phylogeny of 46 tet(X4)-positive E. coli ST761 strains.

Results
A total of 12 tet(X4)-positive isolates, 8 E. coli and 4 Aeromonas simiae, were obtained from six lairages of a slaughterhouse. These isolates exhibited resistance to at least three classes of antimicrobials, including tigecycline. The majority of them, seven E. coli and three A. simiae, represent separate clonal groups. Notably, the seven E. coli isolates belonged to ST761, a common ST carrying the tet(X4) gene that has been identified in 39 isolates from animals, meat, wastewater and humans from seven Chinese provinces. All 46 tet(X4)-positive E. coli ST761 strains from various sources have a close phylogenetic relationship (0–72 SNPs), with a high nucleotide sequence similarity of resistance genes and the tet(X4)-carrying IncX1-IncFIA(HI1)-IncFIB(K) hybrid plasmid, indicating a clonal relationship of tet(X4)-positive E. coli ST761 among animals, food, the environment and humans.

Conclusions
The clonal relationship of tet(X4)-positive E. coli ST761 between humans and animals poses a previously underestimated threat to public health. To the best of our knowledge, this is the first description of tet(X4)-positive A. simiae.
Dalbavancin in Gram-positive periprosthetic joint infections
Authors: Simon Sebastian , Frank Bernhard J H , Hartmann Susana , Hinterhuber Laetitia , Reitsamer Michael , Aichmair Alexander , Dominkus Martin , Söderquist Bo , Hofstaetter Jochen G 
Published: June 2022

Abstract

Objectives
The unique properties of dalbavancin (DAL) emphasize the need to explore its clinical benefits to treat periprosthetic joint infections (PJIs). The present study aimed to compare the treatment outcome of dalbavancin with Standard of Care (SoC) in hip and knee PJIs.

Methods
Eighty-nine patients were selected for each group of this study based on our prospectively maintained PJI database. A 1:1 propensity score-matching was performed between patients who received at least two doses of dalbavancin and those who received SoC. Patients were matched based on demographics, joint, patient risk factors, Musculoskeletal Infection Society (MSIS) criteria, surgical management and type of infection. Treatment outcome was evaluated considering re-infection and re-revision rates, safety and tolerability of dalbavancin after a minimum of 1 year follow-up.

Results
Infection eradication was achieved in 69 (77.5%) and 66 (74.2%) patients of the DAL and SoC groups, respectively. Thirteen (14.6%) patients in the DAL group and 12 (13.5%) patients in the SoC group had an infection-related re-revision. The most prevalent microorganisms among the two groups were Staphylococcus epidermidis (32.3%), Staphylococcus aureus (13.8%) and Cutibacterium spp. (11.3%). There were significantly less Gram-positive bacteria (P = 0.03) detected in patients who received dalbavancin (17.4%) treatment compared with those treated with SoC (48.0%) in culture-positive re-revisions.

Conclusions
Dalbavancin treatment for Gram-positive PJIs resulted in a similar outcome to SoC, with excellent safety and low rate of adverse effects. Dalbavancin seems to be a promising antimicrobial against PJIs by reducing the risk of Gram-positive re-infections and allowing a less frequent dosage with potential outpatient IV treatment.
Two new species of freshwater crabs of the genera Huananpotamon Dai & Ng, 1994 and Minpotamon Dai & Türkay, 1997 (Decapoda: Brachyura: Potamidae) from eastern China
Authors: Wang Ru-Xiao , Pan Da , Sun Hong-Ying 
Published: June 2022

Abstract
Two new Chinese species of potamid freshwater crabs, Huananpotamon shangyouensesp. nov. and Minpotamon auritumsp. nov., are described from Fujian and Jiangxi, eastern China, respectively. The two new species can be distinguished from their closest congeners by carapace features and structures of the male first gonopods. Phylogenetic analyses based on mitochondrial 16S rDNA sequences support the establishment of the two new species.