bluuebunny/crossref_metadata_2025_split huggingface dataset:
A case of hereditary metachronous bilateral triple-negative breast cancer that was highly sensitive to carboplatin
Authors: Wu Rongrong , Adachi Kayo , Koyama Yoichi , Orimoto Kyoko , Okazaki Miki , Asaoka Mariko , Teraoka Saeko , Ueda Ai , Miyahara Kana , Kawate Takahiko , Kaise Hiroshi , Yamada Kimito , Sato Eichi , Ishikawa Takashi 
Published: January 2021

Abstract
A 52-year-old woman with a strong family history of breast cancer was diagnosed as having triple-negative breast cancer (TNBC) in her right breast. Neoadjuvant chemotherapy (NAC; four cycles of epirubicin/cyclophosphamide/5-fluorouracil) was performed, followed by breast-conserving surgery and axillary lymph node dissection. Histopathological analysis of the surgical specimens demonstrated a few focal tumor cells remaining in the stroma, but not a pathological complete response (pCR). Weekly paclitaxel was subsequently added to the treatment regimen. A total of 17 months after the adjuvant treatments, TNBC recurred in her left breast with massive lymph node metastasis. Because of the early recurrence after standard treatment, NAC was administered together with carboplatin and paclitaxel. Histopathological analysis of the partially resected breast and axillary lymph nodes demonstrated a pCR. No recurrent disease was found 2 years after the second TNBC treatment. This case underlines the importance of platinum-based chemotherapy and prophylactic mastectomy for patients with BRCA dysfunction.
Ageing beautifully: can the benefits of seed priming be separated from a reduced lifespan trade-off?
Authors: Fabrissin Isabelle , Sano Naoto , Seo Mitsunori , North Helen M 
Published: January 2021

AbstractGermination performance is affected following seed exposure to a combination of temperature fluctuations and cycles of hydration and dehydration. This has long been exploited in a seed technology termed priming, which increases germination speed and seedling vigour, but these benefits have often been associated with effects on seed lifespan, or longevity, with conflicting evidence for positive and negative effects. Seed longevity is a key seed trait influencing not only the storage of commercial stocks but also in situ and ex situ seed conservation. In the context of increasingly variable environmental conditions faced by both crops and wild species, this has led to renewed interest in understanding the molecular factors that underlie priming. Here, we provide an overview of the literature relating to the effect of priming on seed lifespan, and catalogue the different parameters used for priming treatments and their consequences on longevity for a range of species. Our current limited understanding of the molecular basis for priming effects is also outlined, with an emphasis on recent advances and promising approaches that should lead towards the application and monitoring of the priming process in a less empirical manner.
Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population
Authors: Takou Margarita , Hämälä Tuomas , Koch Evan M , Steige Kim A , Dittberner Hannes , Yant Levi , Genete Mathieu , Sunyaev Shamil , Castric Vincent , Vekemans Xavier , Savolainen Outi , Meaux Juliette de 
Published: January 2021

AbstractDuring range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here, we contrast populations of the European subspecies Arabidopsis lyrata ssp. petraea, which expanded its Northern range after the last glaciation. We document a sharp decline in effective population size in the range-edge population and observe that nonsynonymous variants segregate at higher frequencies. We detect a 4.9% excess of derived nonsynonymous variants per individual in the range-edge population, suggesting an increase of the genomic burden of deleterious mutations. Inference of the fitness effects of mutations and modeling of allele frequencies under the explicit demographic history of each population predicts a depletion of rare deleterious variants in the range-edge population, but an enrichment for fixed ones, consistent with the bottleneck effect. However, the demographic history of the range-edge population predicts a small net decrease in per-individual fitness. Consistent with this prediction, the range-edge population is not impaired in its growth and survival measured in a common garden experiment. We further observe that the allelic diversity at the self-incompatibility locus, which ensures strict outcrossing and evolves under negative frequency-dependent selection, has remained unchanged. Genomic footprints indicative of selective sweeps are broader in the Northern population but not less frequent. We conclude that the outcrossing species A. lyrata ssp. petraea shows a strong resilience to the effect of range expansion.
Compatibility of Evolutionary Responses to Constituent Antibiotics Drive Resistance Evolution to Drug Pairs
Authors: Jahn Leonie Johanna , Simon Daniel , Jensen Mia , Bradshaw Charles , Ellabaan Mostafa Mostafa Hashim , Sommer Morten Otto Alexander 
Published: January 2021

Abstract
Antibiotic combinations are considered a relevant strategy to tackle the global antibiotic resistance crisis since they are believed to increase treatment efficacy and reduce resistance evolution (WHO treatment guidelines for drug-resistant tuberculosis: 2016 update.). However, studies of the evolution of bacterial resistance to combination therapy have focused on a limited number of drugs and have provided contradictory results (Lipsitch, Levin BR. 1997; Hegreness et al. 2008; Munck et al. 2014). To address this gap in our understanding, we performed a large-scale laboratory evolution experiment, adapting eight replicate lineages of Escherichia coli to a diverse set of 22 different antibiotics and 33 antibiotic pairs. We found that combination therapy significantly limits the evolution of de novode novo resistance in E. coli, yet different drug combinations vary substantially in their propensity to select for resistance. In contrast to current theories, the phenotypic features of drug pairs are weak predictors of resistance evolution. Instead, the resistance evolution is driven by the relationship between the evolutionary trajectories that lead to resistance to a drug combination and those that lead to resistance to the component drugs. Drug combinations requiring a novel genetic response from target bacteria compared with the individual component drugs significantly reduce resistance evolution. These data support combination therapy as a treatment option to decelerate resistance evolution and provide a novel framework for selecting optimized drug combinations based on bacterial evolutionary responses.
Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome
Authors: Guiblet Wilfried M , Cremona Marzia A , Harris Robert S , Chen Di , Eckert Kristin A , Chiaromonte Francesca , Huang Yi-Fei , Makova Kateryna D 
Published: January 2021

AbstractApproximately 13% of the human genome can fold into non-canonical (non-B) DNA structures (e.g. G-quadruplexes, Z-DNA, etc.), which have been implicated in vital cellular processes. Non-B DNA also hinders replication, increasing errors and facilitating mutagenesis, yet its contribution to genome-wide variation in mutation rates remains unexplored. Here, we conducted a comprehensive analysis of nucleotide substitution frequencies at non-B DNA loci within noncoding, non-repetitive genome regions, their ±2 kb flanking regions, and 1-Megabase windows, using human-orangutan divergence and human single-nucleotide polymorphisms. Functional data analysis at single-base resolution demonstrated that substitution frequencies are usually elevated at non-B DNA, with patterns specific to each non-B DNA type. Mirror, direct and inverted repeats have higher substitution frequencies in spacers than in repeat arms, whereas G-quadruplexes, particularly stable ones, have higher substitution frequencies in loops than in stems. Several non-B DNA types also affect substitution frequencies in their flanking regions. Finally, non-B DNA explains more variation than any other predictor in multiple regression models for diversity or divergence at 1-Megabase scale. Thus, non-B DNA substantially contributes to variation in substitution frequencies at small and large scales. Our results highlight the role of non-B DNA in germline mutagenesis with implications to evolution and genetic diseases.
Preliminary, Real-world, Multicenter Experience With Omadacycline for Mycobacterium abscessus Infections
Authors: Morrisette Taylor , Alosaimy Sara , Philley Julie V , Wadle Carly , Howard Catessa , Webb Andrew J , Veve Michael P , Barger Melissa L , Bouchard Jeannette , Gore Tristan W , Lagnf Abdalhamid M , Ansari Iman , Mejia-Chew Carlos , Cohen Keira A , Rybak Michael J 
Published: January 2021

Abstract
Twelve patients were treated with omadacycline (OMC) as part of a multidrug regimen for Mycobacterium abscessus. The majority of infections were of pulmonary origin (7/12; 58.3%). The median (interquartile range) duration of OMC was 6.2 (4.2–11.0) months. Clinical success occurred in 9/12 (75.0%) patients. Three patients experienced a possible adverse effect while on therapy.
Pain and fatigue are longitudinally and bi-directionally associated with more sedentary time and less standing time in rheumatoid arthritis
Authors: O’Brien Ciara M , Ntoumanis Nikos , Duda Joan L , Kitas George D , Veldhuijzen van Zanten Jet J C S , Metsios George S , Fenton Sally A M 
Published: January 2021

Abstract

Objectives
The aims of this study were to examine the longitudinal and bi-directional associations of pain and fatigue with sedentary, standing and stepping time in RA.

Methods
People living with RA undertook identical assessments at baseline (T1, n = 104) and 6-month follow-up (T2, n = 54). Participants completed physical measures (e.g. height, weight, BMI) and routine clinical assessments to characterize RA disease activity (DAS-28). Participants also completed questionnaires to assess physical function (HAQ), pain (McGill Pain Questionnaire) and fatigue (Multidimensional Assessment of Fatigue Scale). Participants’ free-living sedentary, standing and stepping time (min/day) were assessed over 7 days using the activPAL3µ™. For the statistical analysis, hierarchical regression analysis was employed to inform the construction of path models, which were subsequently used to examine bi-directional associations of pain and fatigue with sedentary, standing and stepping time. Specifically, where significant associations were observed in longitudinal regression analysis, the bi-directionality of these associations was further investigated via path analysis. For regression analysis, bootstrapping was applied to regression models to account for non-normally distributed data, with significance confirmed using 95% CIs. Where variables were normally distributed, parametric, non-bootstrapped statistics were also examined (significance confirmed via β coefficients, with P &lt; 0.05) to ensure all plausible bi-directional associations were examined in path analysis.

Results
Longitudinal bootstrapped regression analysis indicated that from T1 to T2, change in pain, but not fatigue, was positively associated with change in sedentary time. In addition, change in pain and fatigue were negatively related to change in standing time. Longitudinal non-bootstrapped regression analysis demonstrated a significant positive association between change in fatigue with change in sedentary time. Path analysis supported the hypothesized bi-directionality of associations between change in pain and fatigue with change in sedentary time (pain, β = 0.38; fatigue, β = 0.44) and standing time (pain, β = –0.39; fatigue, β = –0.50).

Conclusion
Findings suggest pain and fatigue are longitudinally and bi-directionally associated with sedentary and standing time in RA.
The distribution of indirect cost recovery in academic research
Authors: Graddy-Reed Alexandra , Feldman Maryann , Bercovitz Janet , Langford W. Scott 
Published: January 2021

AbstractResearch universities rely heavily on external funding to advance knowledge and generate economic growth. In the USA, tens of billions of dollars are spent each year on research and development with the federal government contributing over half of these funds. Yet a decline in relative federal funding highlights the role of other funders and their varying contractual terms. Specifically, nonfederal funders provide lower recovery of indirect costs. Using project-level university-sponsored research administrative records from four institutions, we examine indirect cost recovery. We find significant variation in the amount of indirect funding recovered—both across and within funders, as well as to different academic fields within a university. The distribution of sponsors in the overall research funding portfolio also impacts indirect cost recovery. The recovery variation has important implications for the sustainability and cross-subsidization of the university research enterprise. Together, our results show where universities are under-recovering indirect costs.
A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses
Authors: Lloyd Graeme T , Slater Graham J 
Published: January 2021

AbstractPhylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins, and allies). Our trees extend sampling from the $\sim 90$ extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios, we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.[Extinction; macroevolution; matrix representation with parsimony; morphology; supertree.]
It’s more than climate change and active transport—physical activity’s role in sustainable behavior
Authors: Nigg Carina , Nigg Claudio R 
Published: January 2021

Abstract
Considering the interdependence of human’s and nature’s health within the planetary health concept, we evaluated how physical activity (PA) can be conceptualized as sustainable behavior (SuB) and how PA relates to other types of SuBs within the United Nations’ sustainable development goal (SDG) framework. Regarding social SDGs, PA contributes to improving malnutrition (SDG 2), health behaviors (SDG 3), education (SDG 4), reducing inequalities (SDG 10), sustainable cities (SDG 12), and peace (SDG 16). For ecological SDGs, PA contributes to sustainable consumption (SDG 11) and combating climate change (SDG 13). Therefore, PA is more than a health behavior, it contributes to planetary health and sustainable development. However, caution is warranted as PA also has the potential to contribute and reinforce unsustainability. Thus, PA as a SuB requires an own research agenda, investigating (a) PA as social and ecological SuB, (b) sustainable PA promotion, (c) sustainable PA measurement, (d) common underlying constructs of PA and SuB, and (e) technology’s role to assess and promote PA and SuB.
Return to Play Guidelines After Cervical Spine Injuries in American Football Athletes
Authors: Swiatek Peter R. , Nandurkar Tejas S. , Maroon Joseph C. , Cantu Robert C. , Feuer Henry , Bailes Julian E. , Hsu Wellington K. 
Published: January 2021

Study Design
Literature-based review.

Objective
We sought to evaluate clinical and case studies related to return to play (RTP) after cervical spine injuries in elite American football athletes and to formulate guidelines to help health care practitioners manage these conditions.

Summary of Background Data
American football athletes are at unique risk of cervical spine injury and appropriate case-by-case management of cervical spine injuries is necessary for these athletes. Despite this need, no standardized guidelines exist for RTP after cervical spine injury.

Methods
Observational or case-based articles relating to RTP after cervical spine injury in American football athletes were curated from PubMed/EMBASE databases. Primary literature published before December 1, 2019 involving National Football League (NFL) or National Collegiate Athletic Association (NCAA) athletes met inclusion criteria.

Results
The data acquisition process yielded 28 studies addressing cervical spine injuries and RTP in American football athletes. Stingers/burners were the most common injury and placed athletes at higher risk of a more severe re-injury. Transient quadriplegia, cervical stenosis, cervical disc herniation (CDH), and cervical fractures have a more significant impact on the long-term health and career longevity of the American football athlete. As such, the literature offers some guidance for management of these athletes, including average time for RTP in patients treated nonoperatively, thresholds involving cervical stenosis, and postoperative recommendations after spinal decompression and/or fusion surgery.

Conclusion
Elite American football athletes are at high risk for cervical spine injury due to the nature of their sport. The decision to allow these athletes to return to play should involve an understanding of the average RTP time, the potential risks of recurrence or re-injury, and individual characteristics such as position played and pathology on imaging.

Level of Evidence: 3
Diagnostic Yield of Axial Computed Tomography Scans for Pediatric Axial Skeletal Injuries
Authors: Maqsoodi Noorullah , Louis Clauden , Botros Mina , Baldwin Avionna , Jefferson Jamal , Moses Jalea T. , Wakeman Derek , Mesfin Addisu 
Published: January 2021

Study Design
Retrospective cohort study.

Objective
To evaluate the diagnostic yield of computed tomography (CT) imaging of the axial skeleton in pediatric patients evaluated a level I trauma center.

Summary of Background Data
CT imaging has become ubiquitous in the assessment of axial skeletal injuries in trauma patients.

Methods
This is a retrospective study from one Level I trauma center of patients undergoing CT imaging during pediatric trauma assessment. Medical records of pediatric trauma patients 18-year old and younger who underwent axial skeletal CT imaging from 2013 to 2015 were evaluated. The following were assessed: mechanism of injury, age, sex, race/ethnicity, presence of fracture, management of fracture.

Results
A total of 831 patients were assessed, there were 355 (42.7%) females and 476 males (57.3%) with an average age of 15.4 (2 mo–18 yrs). 588 (70.8%) were White, 164 (19.7%) were African-American, 12 (1.4%) were Asians, 67 (8.1%) other, and 46 (5.5%) identified as Hispanic. There were 45 patients (5.4%) who sustained 52 fractures. Common mechanisms were motor vehicle accidents (MVA) 28%, sports injuries (18%), and fall from height (15%). 35.9% of fractures were identified on plain radiographs. Nine injuries were treated surgically (one cervical, two thoracic, two lumbar, and four pelvic); three of these were identified on radiographs. From the 14 patients with cervical spine fractures none were detected on radiographs.

Conclusion
In this large series of 831 pediatric patients undergoing axial CT imaging, the rate of axial fractures was 5.4%. The majority of these fractures were managed non-surgically. Only 35.9% of fractures were identified on radiographs.

Level of Evidence: 3
Comparable efficacy of 100 mg aspirin twice daily and rivaroxaban for venous thromboembolism prophylaxis following primary total hip arthroplasty: a randomized controlled trial
Authors: Ren Yi , Cao Shi-Liang , Li Zeng , Luo Tim , Feng Bin , Weng Xi-Sheng 
Published: January 2021

Abstract

Background:
Aspirin has demonstrated safety and efficacy for venous thromboembolism (VTE) prophylaxis following total hip arthroplasty (THA); however, inconsistent dose regimens have been reported in the literature. This study aimed to evaluate and compare the safety and efficacy of 100 mg aspirin twice daily with rivaroxaban in VTE prophylaxis following THA.

Methods:
Patients undergoing elective unilateral primary THA between January 2019 and January 2020 were prospectively enrolled in the study and randomly allocated to receive 5 weeks of VTE prophylaxis with either oral enteric-coated aspirin (100 mg twice daily) or rivaroxaban (10 mg once daily). Medication safety and efficacy were comprehensively evaluated through symptomatic VTE incidence, deep vein thrombosis (DVT) on Doppler ultrasonography, total blood loss (TBL), laboratory bloodwork, Harris hip score (HHS), post-operative recovery, and the incidence of other complications.

Results:
We included 70 patients in this study; 34 and 36 were allocated to receive aspirin and rivaroxaban prophylaxis, respectively. No cases of symptomatic VTE occurred in this study. The DVT rate on Doppler ultrasonography in the aspirin group was not significantly different from that in the rivaroxaban group (8.8% vs. 8.3%, χ
2 = 0.01, P = 0.91), confirming the non-inferiority of aspirin for DVT prophylaxis (χ
2 = 2.29, P = 0.01). The calculated TBL in the aspirin group (944.9 mL [658.5–1137.8 mL]) was similar to that in the rivaroxaban group (978.3 mL [747.4–1740.6mL]) (χ
2 = 1.55, P = 0.12). However, there were no significant inter-group differences in HHS at post-operative day (POD) 30 (Aspirin: 81.0 [78.8–83.0], Rivaroxaban: 81.0 [79.3–83.0], χ
2 = 0.43, P = 0.67) and POD 90 (Aspirin: 90.0 [89.0–92.0], Rivaroxaban: 91.5 [88.3–92.8], χ
2 = 0.77, P = 0.44), the incidence of bleeding events (2.9% vs. 8.3%, χ
2 = 0.96, P = 0.33), or gastrointestinal complications (2.9% vs. 5.6%, χ
2 = 1.13, P = 0.29).

Conclusion:
In terms of safety and efficacy, the prophylactic use of 100 mg aspirin twice daily was not statistically different from that of rivaroxaban in preventing VTE and reducing the risk of blood loss following elective primary THA. This supports the use of aspirin chemoprophylaxis following THA as a less expensive and more widely available option for future THAs.

Trial Registration:
Chictr.org, ChiCTR18000202894; http://www.chictr.org.cn/showproj.aspx?proj=33284