bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of ctDNA Quality Control Materials Through a Precompetitive Collaboration of the Foundation for the National Institutes of Health
Authors: Williams P. Mickey , Forbes Thomas , P. Lund Steven , Cole Kenneth D. , He Hua-Jun , Karlovich Chris , Paweletz Cloud P. , Stetson Daniel , Yee Laura M. , Connors Dana E. , Keating Susan M. , Destenaves Benoit , Cleveland Megan H. , Lau Christie J. , Barrett J. Carl , Kelloff Gary J. , McCormack Robert T. 
Published: June 2021

PURPOSEWe report the results from a Foundation for the National Institutes of Health Biomarkers Consortium project to address the absence of well-validated quality control materials (QCMs) for circulating tumor DNA (ctDNA) testing. This absence is considered a cause of variance and inconsistencies in translating ctDNA results into clinical actions.METHODSIn this phase I study, QCMs with 14 clinically relevant mutations representing single nucleotide variants, insertions or deletions (indels), translocations, and copy number variants were sourced from three commercial manufacturers with variant allele frequencies (VAFs) of 5%, 2.5%, 1%, 0.1%, and 0%. Four laboratories tested samples in quadruplicate using two allele-specific droplet digital polymerase chain reaction and three (amplicon and hybrid capture) next-generation sequencing (NGS) panels.RESULTSThe two droplet digital polymerase chain reaction assays reported VAF values very close to the manufacturers’ claimed concentrations for all QCMs. NGS assays reported most single nucleotide variants and indels, but not translocations, close to the expected VAF values. Notably, two NGS assays reported lower VAF than expected for all translocations in all QCM mixtures, possibly related to technical challenges detecting these variants. The ability to call ERBB2 copy number amplifications varied across assays. All three QCMs provided valuable insight into assay precision. Each assay across all variant types demonstrated dropouts at 0.1%, suggesting that the QCM can serve for testing of an assay’s limit of detection with confidence claims for specific variants.CONCLUSIONThese results support the utility of the QCM in testing ctDNA assay analytical performance. However, unique designs and manufacturing methods for the QCM, and variations in a laboratory’s testing configuration, may require testing of multiple QCMs to find the best reagents for accurate result interpretation.
Two Distinctive POMC Promoters Modify Gene Expression in Cushing Disease
Authors: Araki Takako , Tone Yukiko , Yamamoto Masaaki , Kameda Hiraku , Ben-Shlomo Anat , Yamada Shozo , Takeshita Akira , Yamamoto Masato , Kawakami Yasuhiko , Tone Masahide , Melmed Shlomo 
Published: June 2021

Abstract

Context
Mechanisms underlying pituitary corticotroph adenoma adrenocorticotropin (ACTH) production are poorly understood, yet circulating ACTH levels closely correlate with adenoma phenotype and clinical outcomes.

Objective
We characterized the 5′ ends of proopiomelanocortin (POMC) gene transcripts, which encode the precursor polypeptide for ACTH, in order to investigate additional regulatory mechanisms of POMC gene transcription and ACTH production.

Methods
We examined 11 normal human pituitary tissues, 32 ACTH-secreting tumors, as well as 6 silent corticotroph adenomas (SCAs) that immunostain for but do not secrete ACTH.

Results
We identified a novel regulatory region located near the intron 2/exon 3 junction in the human POMC gene, which functions as a second promoter and an enhancer. In vitro experiments demonstrated that CREB binds the second promoter and regulates its transcriptional activity. The second promoter is highly methylated in SCAs, partially demethylated in normal pituitary tissue, and highly demethylated in pituitary and ectopic ACTH-secreting tumors. In contrast, the first promoter is demethylated in all POMC-expressing cells and is highly demethylated only in pituitary ACTH-secreting tumors harboring the ubiquitin-specific protease 8 (USP8) mutation. Demethylation patterns of the second promoter correlate with clinical phenotypes of Cushing disease.

Conclusion
We identified a second POMC promoter regulated by methylation status in ACTH-secreting pituitary tumors. Our findings open new avenues for elucidating subcellular regulation of the hypothalamic-pituitary-adrenal axis and suggest the second POMC promoter may be a target for therapeutic intervention to suppress excess ACTH production.
Changes in Regional Fat Distribution and Anthropometric Measures Across the Menopause Transition
Authors: Greendale Gail A , Han Weijuan , Finkelstein Joel S , Burnett-Bowie Sherri-Ann M , Huang MeiHua , Martin Deborah , Karlamangla Arun S 
Published: June 2021

Abstract

Context
The relation between the menopause transition (MT) and changes in regional fat distribution is uncertain.

Objective
To determine whether the MT is associated with the development of central adiposity.

Design
Longitudinal analysis from the Study of Women’s Health Across the Nation, spanning 1996-2013 (median follow-up 11.8 years).

Setting
Community-based.

Participants
380 women with regional body composition measures by dual energy X-ray absorptiometry. Mean baseline age was 45.7 years; racial/ethnic composition was 16% Black, 41% Japanese and 43% White.

Outcomes
Changes in android, gynoid and visceral fat and waist and hip circumferences.

Results
Android fat increased by 1.21% per year (py) and 5.54% py during premenopause and the MT, respectively (each P &lt; 0.05). Visceral and gynoid fat began increasing at the MT, annualized changes were 6.24% and 2.03%, respectively (each P &lt; 0.05). Postmenopausal annual trajectories decelerated to 1.47% (visceral), 0.90% (android), and -0.87% (gynoid), (all non-zero, P &lt; 0.05). Waist girth grew during premenopause (0.55% py), the MT (0.96% py), and postmenopause (0.55% py) (all non-zero, P &lt; 0.05; not statistically different from each other). Hip girth grew during premenopause (0.20% py) and the MT (0.35% py) (each non-zero, P &lt; 0.05; not statistically different from each other) and decelerated to zero slope in postmenopause. Results are for the White referent; there were statistically significant differences in some trajectories in Black and Japanese women.

Conclusions
The MT is associated with the development of central adiposity. Waist or hip circumferences are less sensitive to changes in fat distribution.
Opposing effects of Wnt/β-catenin signaling on epithelial and mesenchymal cell fate in the developing cochlea
Authors: Billings Sara E. , Myers Nina M. , Quiruz Lee , Cheng Alan G. 
Published: June 2021

ABSTRACT
During embryonic development, the otic epithelium and surrounding periotic mesenchymal cells originate from distinct lineages and coordinate to form the mammalian cochlea. Epithelial sensory precursors within the cochlear duct first undergo terminal mitosis before differentiating into sensory and non-sensory cells. In parallel, periotic mesenchymal cells differentiate to shape the lateral wall, modiolus and pericochlear spaces. Previously, Wnt activation was shown to promote proliferation and differentiation of both otic epithelial and mesenchymal cells. Here, we fate-mapped Wnt-responsive epithelial and mesenchymal cells in mice and found that Wnt activation resulted in opposing cell fates. In the post-mitotic cochlear epithelium, Wnt activation via β-catenin stabilization induced clusters of proliferative cells that dedifferentiated and lost epithelial characteristics. In contrast, Wnt-activated periotic mesenchyme formed ectopic pericochlear spaces and cell clusters showing a loss of mesenchymal and gain of epithelial features. Finally, clonal analyses via multi-colored fate-mapping showed that Wnt-activated epithelial cells proliferated and formed clonal colonies, whereas Wnt-activated mesenchymal cells assembled as aggregates of mitotically quiescent cells. Together, we show that Wnt activation drives transition between epithelial and mesenchymal states in a cell type-dependent manner.
An optogenetic method for interrogating YAP1 and TAZ nuclear–cytoplasmic shuttling
Authors: Dowbaj Anna M. , Jenkins Robert P. , Williamson Daniel , Heddleston John M. , Ciccarelli Alessandro , Fallesen Todd , Hahn Klaus M. , O'Dea Reuben D. , King John R. , Montagner Marco , Sahai Erik 
Published: June 2021

ABSTRACT
The shuttling of transcription factors and transcriptional regulators into and out of the nucleus is central to the regulation of many biological processes. Here we describe a new method for studying the rates of nuclear entry and exit of transcriptional regulators. A photo-responsive LOV (light–oxygen–voltage) domain from Avena sativa is used to sequester fluorescently labelled transcriptional regulators YAP1 and TAZ (also known as WWTR1) on the surface of mitochondria and to reversibly release them upon blue light illumination. After dissociation, fluorescent signals from the mitochondria, cytoplasm and nucleus are extracted by a bespoke app and used to generate rates of nuclear entry and exit. Using this method, we demonstrate that phosphorylation of YAP1 on canonical sites enhances its rate of nuclear export. Moreover, we provide evidence that, despite high intercellular variability, YAP1 import and export rates correlate within the same cell. By simultaneously releasing YAP1 and TAZ from sequestration, we show that their rates of entry and exit are correlated. Furthermore, combining the optogenetic release of YAP1 with lattice light-sheet microscopy reveals high heterogeneity of YAP1 dynamics within different cytoplasmic regions, demonstrating the utility and versatility of our tool to study protein dynamics.
This article has an associated First Person interview with Anna M. Dowbaj, joint first author of the paper.
Twinfilin1 controls lamellipodial protrusive activity and actin turnover during vertebrate gastrulation
Authors: Devitt Caitlin C. , Lee Chanjae , Cox Rachael M. , Papoulas Ophelia , Alvarado José , Shekhar Shashank , Marcotte Edward M. , Wallingford John B. 
Published: June 2021

ABSTRACT
The dynamic control of the actin cytoskeleton is a key aspect of essentially all animal cell movements. Experiments in single migrating cells and in vitro systems have provided an exceptionally deep understanding of actin dynamics. However, we still know relatively little of how these systems are tuned in cell-type-specific ways, for example in the context of collective cell movements that sculpt the early embryo. Here, we provide an analysis of the actin-severing and depolymerization machinery during vertebrate gastrulation, with a focus on Twinfilin1 (Twf1) in Xenopus. We find that Twf1 is essential for convergent extension, and loss of Twf1 results in a disruption of lamellipodial dynamics and polarity. Moreover, Twf1 loss results in a failure to assemble polarized cytoplasmic actin cables, which are essential for convergent extension. These data provide an in vivo complement to our more-extensive understanding of Twf1 action in vitro and provide new links between the core machinery of actin regulation and the specialized cell behaviors of embryonic morphogenesis.
Divergent estimates of the ratio between Na+-Ca2+ current densities in t-tubular and surface membranes of rat ventricular cardiomyocytes
Authors: Pásek Michal , Šimurda Jiří , Bébarová Markéta , Christé Georges 
Published: June 2021

ABSTRACT
The ratio between Na+-Ca2+ exchange current densities in t-tubular and surface membranes of rat ventricular cardiomyocytes (JNaCa-ratio) estimated from electrophysiological data published to date yields strikingly different values between 1.7 and nearly 40. Possible reasons for such divergence were analysed by Monte Carlo simulations assuming both normal and log-normal distribution of the measured data. The confidence intervals CI95 of the mean JNaCa-ratios computed from the reported data showed an overlap of values between 1 and 3, and between 0.3 and 4.3 in the case of normal and log-normal distribution, respectively. Further analyses revealed that the published high values likely result from a large scatter of data due to transmural differences in JNaCa, dispersion of cell membrane capacitances and variability in incomplete detubulation. Taking into account the asymmetric distribution of the measured data, the reduction of mean current densities after detubulation and the substantially smaller CI95 of lower values of the mean JNaCa-ratio, the values between 1.6 and 3.2 may be considered as the most accurate estimates. This implies that 40 to 60% of Na+-Ca2+ exchanger is located at the t-tubular membrane of adult rat ventricular cardiomyocytes.
Bearded dragons (Pogona vitticeps) with reduced scalation lose water faster but do not have substantially different thermal preferences
Authors: Sakich Nicholas B. , Tattersall Glenn J. 
Published: June 2021

ABSTRACT
Whether scales reduce cutaneous evaporative water loss in lepidosaur reptiles (Superorder Lepidosauria) such as lizards and snakes has been a contentious issue for nearly half a century. Furthermore, while many studies have looked at whether dehydration affects thermal preference in lepidosaurs, far fewer have examined whether normally hydrated lepidosaurs can assess their instantaneous rate of evaporative water loss and adjust their thermal preference to compensate in an adaptive manner. We tested both of these hypotheses using three captive-bred phenotypes of bearded dragon (Pogona vitticeps) sourced from the pet trade: ‘wild-types’ with normal scalation, ‘leatherbacks’ exhibiting scales of reduced prominence, and scaleless bearded dragons referred to as ‘silkbacks’. Silkbacks on average lost water evaporatively at about twice the rate that wild-types did. Leatherbacks on average were closer in their rates of evaporative water loss to silkbacks than they were to wild-types. Additionally, very small (at most ∼1°C) differences in thermal preference existed between the three phenotypes that were not statistically significant. This suggests a lack of plasticity in thermal preference in response to an increase in the rate of evaporative water loss, and may be reflective of a thermal ‘strategy’ as employed by thermoregulating bearded dragons that prioritises immediate thermal benefits over the threat of future dehydration. The results of this study bolster an often-discounted hypothesis regarding the present adaptive function of scales and have implications for the applied fields of animal welfare and conservation.
Direct anterior approach has short-term functional benefit and higher resource requirements compared with the posterior approach in primary total hip arthroplasty
Authors: Awad Mohamed E. , Farley Brendan J. , Mostafa Gamal , Saleh Khaled J. 
Published: June 2021

Aims It has been suggested that the direct anterior approach (DAA) should be used for total hip arthroplasty (THA) instead of the posterior approach (PA) for better early functional outcomes. We conducted a value-based analysis of the functional outcome and associated perioperative costs, to determine which surgical approach gives the better short-term outcomes and lower costs. Methods This meta-analysis was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol and the Cochrane Handbook. Several online databases were searched. Non-stratified and stratified meta-analyses were conducted to test the confounding biases in the studies which were included. The mean cost and probability were used to determine the added costs of perioperative services. Results The DAA group had significantly longer operating times (p < 0.001), reduced length of hospital stay by a mean of 13.4 hours (95% confidence interval (CI) 9.12 to 18; p < 0.001), and greater blood loss (p = 0.030). The DAA group had significantly better functional outcome at three (p < 0.001) and six weeks (p = 0.006) postoperatively according to the Harris Hip Score (HHS). However, there was no significant difference between the groups for the HHS at six to eight weeks (p = 0.230), 12 weeks (p = 0.470), six months (p = 0.740), and one year (p = 0.610), the 12-Item Short Form Survey (SF-12) physical score at six weeks (p = 0.580) and one year (p = 0.360), SF-12 mental score at six weeks (p = 0.170) and one year (p = 0.960), and University of California and Los Angeles (UCLA) activity scale at 12 weeks (p = 0.250). The mean non-stratified and stratified difference in costs for the operating theatre time and blood transfusion were $587.57 (95% CI 263.83 to 1,010.29) to $887.04 (95% CI 574.20 to 1,298.88) and $248.38 (95% CI 1,003.40 to 1,539.90) to $1,162.41 (95% CI 645.78 to 7,441.30), respectively, more for the DAA group. However, the mean differences in costs for the time in hospital were $218.23 and $192.05, respectively, less for the DAA group. Conclusion The use of the DAA, rather than the PA, in THA has earlier benefits for function and pain. However, these are short-lasting, with no significant differences seen at later intervals. In addition the limited benefits were obtained with higher cumulative costs for DAA. Cite this article: Bone Joint J 2021;103-B(6):1078–1087.
Patients follow three distinct outcome trajectories following total knee arthroplasty
Authors: Hamilton David F. , Shim Joanna , Howie Colin R. , Macfarlane Gary J. 
Published: June 2021

Aims Although total knee arthroplasty (TKA) is a highly successful procedure, about 20% of patients remain dissatisfied postoperatively. This proportion is derived from dichotomous models of the assessment of surgical success or failure, which may not reflect the spectrum of outcomes. The aim of this study was to explore differing responses to surgery, and assess whether there are distinct groups of patients with differing patterns of outcome. Methods This was a secondary analysis of a UK multicentre TKA longitudinal cohort study. We used a group-based trajectory modelling analysis of Oxford Knee Score (OKS) in the first year following surgery with longitudinal data involving five different timepoints and multiple predictor variables. Associations between the derived trajectory groups and categorical baseline variables were assessed, and predictors of trajectory group membership were identified using Poisson regression and multinomial logistic regression, as appropriate. The final model was adjusted for sociodemographic factors (age, sex) and baseline OKS. Results Data from 731 patients were available for analysis. Three distinct trajectories of outcome were identified: “poor” 14.0%, “modest” 39.1%, and “good” 46.9%. The predicted probability of membership for patients assigned to each trajectory group was high (0.89 to 0.93). Preoperative mental, physical health, and psychosocial factors determined which trajectory is likely to be followed. Poor responders were characterized by a comparatively small number of factors, preoperative expectations of pain and limitations, coping strategies, and a lower baseline physical health status, while the good responders were characterized by a combination of clinical, psychosocial, mental health, and quality of life factors. Conclusion We identified three distinct response trajectories in patients undergoing TKA. Controlling for baseline score, age, and sex, psychosocial factors such as expectations of pain and limited function and poor coping strategies differentiated the trajectory groups, suggesting a role for preoperative psychosocial support in optimizing the clinical outcome. Cite this article: Bone Joint J 2021;103-B(6):1096–1102.
Open reduction and internal fixation versus nonoperative treatment for closed, displaced, intra-articular fractures of the calcaneus: long-term follow-up from the HeFT randomized controlled trial
Authors: Dickenson Edward J. , Parsons Nick , Griffin Damian R. 
Published: June 2021

Aims We report the long-term outcomes of the UK Heel Fracture Trial (HeFT), a pragmatic, multicentre, two-arm, assessor-blinded, randomized controlled trial. Methods HeFT recruited 151 patients aged over 16 years with closed displaced, intra-articular fractures of the calcaneus. Patients with significant deformity causing fibular impingement, peripheral vascular disease, or other significant limb injuries were excluded. Participants were randomly allocated to open reduction and internal fixation (ORIF) or nonoperative treatment. We report Kerr-Atkins scores, self-reported difficulty walking and fitting shoes, and additional surgical procedures at 36, 48, and 60 months. Results Overall, 60-month outcome data were available for 118 patients (78%; 52 ORIF, 66 nonoperative). After 60 months, mean Kerr-Atkins scores were 79.2 (SD 21.5) for ORIF and 76.4 (SD 22.5) for nonoperative. Mixed effects regression analysis gave an estimated effect size of -0.14 points (95% confidence interval -8.87 to 8.59; p = 0.975) in favour of ORIF. There were no between group differences in difficulty walking (p = 0.175), or on the type of shoes worn (p = 0.432) at 60 months. Additional surgical procedures were conducted on ten participants allocated ORIF, compared to four in the nonoperative group (p = 0.043). Conclusion ORIF of displaced intra-articular calcaneal fractures, not causing fibular impingement, showed no difference in outcomes at 60 months compared to nonoperative treatment, but with an increased risk of additional surgery. Cite this article: Bone Joint J 2021;103-B(6):1040–1046.
The surgical treatment of spinal deformity in children with non-ambulatory myelomeningocele
Authors: Tsirikos Athanasios I. , Wordie Sarah J. 
Published: June 2021

Aims To report the outcome of spinal deformity correction through anterior spinal fusion in wheelchair-bound patients with myelomeningocele. Methods We reviewed 12 consecutive patients (7M:5F; mean age 12.4 years (9.2 to 16.8)) including demographic details, spinopelvic parameters, surgical correction, and perioperative data. We assessed the impact of surgery on patient outcomes using the Spina Bifida Spine Questionnaire and a qualitative questionnaire. Results The mean follow-up was 5.4 years (2 to 14.9). Nine patients had kyphoscoliosis, two lordoscoliosis, and one kyphosis. All patients had a thoracolumbar deformity. Mean scoliosis corrected from 89.6° (47° to 151°) to 46.5° (17° to 85°; p < 0.001). Mean kyphosis corrected from 79.5° (40° to 135°) to 49° (36° to 65°; p < 0.001). Mean pelvic obliquity corrected from 19.5° (8° to 46°) to 9.8° (0° to 20°; p < 0.001). Coronal and sagittal balance restored to normal. Complication rate was 58.3% (seven patients) with no neurological deficits, implant failure, or revision surgery. The degree of preoperative spinal deformity, especially kyphosis and lordosis, correlated with increased blood loss and prolonged hospital/intensive care unit stay. The patients reported improvement in function, physical appearance, and pain after surgery. The parents reported decrease in need for everyday care. Conclusion Anterior spinal fusion achieved satisfactory deformity correction with high perioperative complication rates, but no long-term sequelae among children with high level myelomeningocele. This resulted in physical and functional improvement and high reported satisfaction. Cite this article: Bone Joint J 2021;103-B(6):1133–1141.