bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of confound adjustment methods in the construction of gene co-expression networks
Authors: Cote Alanna C. , Young Hannah E. , Huckins Laura M. 
Published: February 2022

AbstractAdjustment for confounding sources of expression variation is an important preprocessing step in large gene expression studies, but the effect of confound adjustment on co-expression network analysis has not been well-characterized. Here, we demonstrate that the choice of confound adjustment method can have a considerable effect on the architecture of the resulting co-expression network. We compare standard and alternative confound adjustment methods and provide recommendations for their use in the construction of gene co-expression networks from bulk tissue RNA-seq datasets.
Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation
Authors: Pei Liuling , Huang Xianhui , Liu Zhenping , Tian Xuehan , You Jiaqi , Li Jianying , Fang David D. , Lindsey Keith , Zhu Longfu , Zhang Xianlong , Wang Maojun 
Published: February 2022

Abstract
Background
Despite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications in this process.

Results
To interrogate its significance, we establish the dynamic three-dimensional (3D) genome architecture of the allotetraploid cotton fiber, representing a typical single cell undergoing staged development in plants. We show that the subgenome-relayed switching of the chromatin compartment from active to inactive is coupled with the silencing of developmentally repressed genes, pinpointing subgenome-coordinated contribution to fiber development. We identify 10,571 topologically associating domain-like (TAD-like) structures, of which 25.6% are specifically organized in different stages and 75.23% are subject to partition or fusion between two subgenomes. Notably, dissolution of intricate TAD-like structure cliques showing long-range interactions represents a prominent characteristic at the later developmental stage. Dynamic chromatin loops are found to mediate the rewiring of gene regulatory networks that exhibit a significant difference between the two subgenomes, implicating expression bias of homologous genes.

Conclusions
This study sheds light on the spatial-temporal asymmetric chromatin structures of two subgenomes in the cotton fiber and offers a new insight into the regulatory orchestration of cell differentiation in plants.
Combined quadriceps tendon reconstruction and total knee replacement with computer navigation: a case report
Authors: Abdulkareem Imran Haruna , Liu Perry , Adhikhari Ajeya , Kader Deiary 
Published: February 2022

Abstract
Background
Chronic quadriceps tendon rupture is technically challenging for surgeons due to scarring and tendon retraction. The presence of concurrent ipsilateral knee osteoarthritis compounds the issue even further. Although a combined presentation is rare, treatment options to manage each coexisting pathology simultaneously are scarcely reported. We describe the case of a 67-year-old Caucasian male who had such a presentation, and was subsequently treated with a one-stage extensor mechanism autograft reconstruction and total knee replacement with computer navigation.

Case
The patient was a 67-year-old male Caucasian, who had previously sustained an acute rupture of his right quadriceps tendon that was adequately repaired 6 months prior. Despite an initial satisfactory result, he reported deterioration in his mobility in the few months thereafter, with worsening knee pain. His comorbidities consisted of hypertension, asthma, and a body mass index of 40.4 kg/m2. Otherwise, there were no risk factors for tendon rerupture. Clinical examination later revealed a large palpable gap in the right suprapatellar region and weakness of active knee extension. No traumatic cause for this new presentation was identified. Suspicion of a chronic quadriceps tendon rupture was confirmed on radiological imaging, but the investigations also noted the presence of severe tricompartmental osteoarthritis of the ipsilateral, native knee joint. The combined procedure took place in one surgical sitting. The total knee replacement with patella resurfacing was performed first and assisted by computer navigation. The quadriceps tendon reconstruction was then conducted sequentially using the patient’s hamstring tendons (semitendinosus and gracilis). The tensile strength was reinforced with use of a Ligament Augmentation and Reconstruction System (LARS) ligament. Initial outcomes were excellent, and these results were maintained at 6 months postoperatively, with the patient reporting no pain and having full range of movement.

Conclusion
Our techniques used have not previously been reported, but are successful options in treating coexisting chronic quadriceps tendon rupture and ipsilateral knee osteoarthritis. The advantage of using computer navigation with an extramedullary femoral jig can lead to improved accuracy of bone cuts, which is important in the presence of anatomical disruption. Chronic failures of the extensor mechanism require different approaches depending on the inherent and underlying pathology. We feel that the multidisciplinary team approach to the management and use of two surgeons with differing expertise added to the successful outcome of this complex case.
The new Veterinary Medicines Regulation: rising to the challenge
Authors: More Simon J. , McCoy Finola , McAloon Catherine I. 
Published: February 2022

AbstractThis article focuses on the new Veterinary Medicines Regulation, which is applicable across all Member States of the European Union, including Ireland, from 28 January 2022. From this date, prophylactic use of antimicrobials (AMs) in groups of animals is banned, metaphylactic use in groups of animals is restricted, and certain AMs are reserved for humans only. In the Irish dairy industry, as elsewhere, successful implementation of the Regulation will require a high level of mastitis control across all herds, and measures to support high standards in antibiotic stewardship. National actions will be critical, to support optimal mastitis control throughout the national herd. For private veterinary practitioners (PVPs), the Regulation will lead to specific prescribing changes, including the requirement to shift from blanket to selective dry cow therapy. Further, prescribing choices will need to be guided by the categorisation for AMs developed by the European Medicines Agency (EMA). More broadly, the Regulation requires a fundamental shift in thinking both in terms of AM usage and of the role of the PVP. Given the close association between mastitis control and intramammary AM stewardship, it is imperative that prescribing and mastitis control decisions are made concurrently. A herd health approach will be critical, within a Client-Patient-Practice Relationship as outlined by the Veterinary Council of Ireland. On those farms with sub-optimal mastitis control, mastitis issues need to be sustainably resolved. A detailed farm investigation by the PVP, in partnership with the farmer and other milk quality professionals, is essential, to understand the epidemiology and on-farm drivers of mastitis, to develop farm-specific action plans, and to facilitate ongoing monitoring of progress. It is vital that PVPs provide leadership, with the provision of a holistic, herd health approach to inform both prescribing and mastitis control decisions in herds under their care.
The need to improve antimicrobial susceptibility testing capacity in Ugandan health facilities: insights from a surveillance primer
Authors: Chaplain Duku , Asutaku Butti Ben , Mona Muhammad , Bulafu Douglas , Aruhomukama Dickson 
Published: February 2022

Abstract
Background
Lab-based surveillance (LBS) of antimicrobial resistance (AMR) is not systematically implemented in Uganda. We aimed to identify the gaps in establishing regular LBS of AMR in Uganda.

Methods
This was a retrospective records review. It was done at Mulago Hospital (MH) Microbiology Lab (MHL). It analyzed lab records on bacteria and their antimicrobial susceptibility profiles (ASPs) over 6 months. Since MH is the national referral hospital, we hypothesized that (1) MHL is the best resourced and that any limitations seen here are amplified in labs at regional referral hospitals (RRHs) and health centers (HCs); (2) data from MHL on LBS mirrors that from labs at RRHs and HCs; (3) the state of records from MHL show lab performance and the presence or absence of standard operating procedures (SOPs), as would be the case at RRHs and HCs.

Results
The lab got 1760 samples over the six months. The most common sample was urine (659, 37.4%). From the 1760 samples, data on 478 bacterial isolates were available. Urine gave the most isolates (159, 33.3%). Most of the isolates were gram-negative (267, 55.9%). Escherichia coli (100, 37%) was the most common gram-negative (of the Enterobacteriaceae). Pseudomonas aeruginosa (17, 6%) was the most common gram-negative (of the non-Enterobacteriaceae). The gram-negative bacteria were highly resistant to β-lactams. These were highly sensitive to carbapenems. The Staphylococcus aureus were highly resistant to β-lactams. The gram-positive bacteria were highly sensitive to vancomycin. ASPs for all bacterial categories were incomplete.

Conclusions
The findings from MHL suggest that there is a need to improve antimicrobial susceptibility testing capacity. They also suggest that the situation at RRHs and HCs around the country could be worse. So, there is a need to extend the political will, which already exists, into operational and implementation action.
Mapping socio-physical legacies of Emirati villas: contingency and spatial continuity or rift
Authors: Rashid Mamun , Ara Dilshad Rahat , Abdalla Salem Buhashima 
Published: February 2022

AbstractUAE urban housing and planning history discourses commonly assume a sharp division between the pre-oil (before the 1950s) and the post-oil (since the 1960s) eras. It is a misleading assumption that flattens historical legacies and exempts pre-oil tribal and maritime built landscape from having a bearing on the emergence of more recent ‘iconic’ villas for the Emiratis/UAE citizens. Besides, status quo urban narratives are further dismissive of non-iconic citizen centric modern housing prototypes of the late 1960s. In this context, our approach is to illustrate the intertwined evolution of contingent driven dwelling features, changes as well as continuities across the pre-oil and post-oil eras. By interconnecting history with user-led spatial changes in current Emirati houses, we argue that, while sustainability has become more of a catchphrase and the ‘iconic' villa façade—the marketing brand, the concept, acceptance, and spatial realization are indeed set by historical overlays of local and transnational experimentation, arbitration, and adaptation. Thus, the current design and policy led national housing prototypes would be corrective, regenerative and successful if assembled through an iterative design process that accommodates emerging sustainable frameworks as well as user-driven spatial interventions. This approach sustains the socio-physical legacies of the Emirati houses and their cultural legitimacy in the built-environment.
A mathematical determination of foveal attachment in primary rhegmatogenous retinal detachment when obscured by bullous retina
Authors: Kousha Obaid , Tarafdar Sonali , Ellis John 
Published: February 2022

AbstractIn primary rhegmatogenous retinal detachment (RRD), the foveal attachment is an important prognostic factors for post-operative vision. When the fovea is obscured by the RRD, its attachment status is considered uncertain. Using a model of the reduced emmetropic and − 10 dioptre myopic eye and the physical properties of the detached retina, we aimed to mathematically ascertain if it is clinically possible for the fovea to be attached while it is obscured by the primary RRD. With the patient upright, a primary RRD due to a 12 o’clock break directly above the fovea was considered. Mathematically, once the trough of the RRD touches the visual axis the edge of the RRD nearest to fovea is $$2.77\,{\text{mm}}$$

2.77

mm

away from fovea in emmetropic eye and $$2.89\;\,{\text{mm}}$$

2.89

mm

in myopic eye. When the RRD reaches the fovea, its trough is $$2.20{\text{ mm}}$$

2.20

mm

below the visual axis in emmetropic eye and $$2.29{\text{ mm}}$$

2.29

mm

in myopic eye. However, in vivo the RRD makes an acute angle with the retinal pigment epithelium and the corrugation of the retina in RRD shortens the retina. When these in vivo constraints are considered, in both of the above situations the fovea will be detached. If the fovea is obscured by an RRD, the fovea is very likely to be detached. In idiomatic terms, if the fovea cannot be seen, the fovea cannot see. This is an important clinical diagnosis for appropriate triage of the patient.
Loss to Follow-Up and the Care Cascade for Cervical Cancer Care in Rural Guatemala: A Cross-Sectional Study
Authors: Garcia Andrea , Juarez Michel , Sacuj Neftali , Tzurec Evelyn , Larson Karen , Miller Ann , Rohloff Peter 
Published: February 2022

PURPOSE More than 80% of cervical cancer cases and deaths occur in low- and middle-income countries. Here, we analyze a large geographically extensive cross-sectional data set from the Western rural highlands of Guatemala. Our objective is to better characterize weak points in care along the cervical cancer care continuum and investigate sociodemographic and clinical correlates of loss to follow-up. METHODS We conducted a retrospective review of electronic health records data from July 21, 2015, through December 10, 2020 for a cytology-based screening and cervical cancer treatment program. We used a care cascade analysis to characterize the progression of individuals through screening, confirmatory testing, and treatment. We examined demographic and clinical factors correlated with screening and loss to follow-up using multivariate logistic regression. RESULTS A total of 8,872 individuals were included in the analysis. Five thousand nine hundred thirteen cervical cancer screenings were conducted. 4.1% of all screening tests were abnormal, including 0.61% cervical intraepithelial neoplasia or overt cervical cancer. Care cascade analysis showed that 67% of eligible women accepted screening. Of those requiring confirmatory testing or treatment, 73% completed recommended follow-up. In adjusted multivariable analysis, prior history of sexual transmitted infection, prior experience with cervical cancer screening, older age, and current contraceptive use were associated with accepting screening. Age and contraceptive use were also associated with retention in care after a positive first screen. CONCLUSION In a large rural Guatemalan retrospective cohort, a care continuum analysis showed that both declining the opportunity to receive cervical cancer screening as well as declining confirmatory testing after a first positive screen were both important weak points along the care continuum. These data support the need for comprehensive and culturally appropriate initiatives to improve screening uptake and retention in care.
The Safety and Effectiveness of the Contour Neurovascular System (Contour) for the Treatment of Bifurcation Aneurysms: The CERUS Study
Authors: Liebig Thomas , Killer-Oberpfalzer Monika , Gal Gyula , Schramm Peter , Berlis Ansgar , Dorn Franziska , Jansen Olav , Fiehler Jens , Wodarg Fritz 
Published: February 2022

BACKGROUND:
The Contour is a novel intra-aneurysmal flow disrupting device to treat intracranial aneurysms.

OBJECTIVE:
To evaluate the safety and effectiveness of the Contour device for treatment of nonruptured intracranial bifurcation aneurysms through a prospective, multicenter, single-arm study.

METHODS:
Thirty-four patients were enrolled. Primary end points were successful occlusion at 6 mo for efficacy and any major stroke or nonaccidental death up to 30 d or major disabling stroke within 6 mo for safety. Secondary end points were occlusion at 12 mo, retreatment rate, procedure time, and procedure-related/device-related adverse events. Procedural and follow-up imaging was reviewed by an independent core laboratory. Adverse events were reviewed and adjudicated by a clinical events committee.

RESULTS:
In total, 32 of 34 aneurysms were successfully implanted and, 2 of 34 in the intention-to-treat (ITT) group did not receive the Contour and were excluded from follow-up after 30 d. In addition, 2 of 32 were lost to angiographic follow-up and regarded as treatment failure. The primary safety end point was met in 2 patients in the ITT group. In the perprotocol (PP) group, complete occlusion was seen in 14 of 32 (44%) at 6 mo and 22 of 32 (69%) at 12 mo. Adequate occlusion (Raymond–Roy [RR] 1 and 2) was reached in 84% at a last available follow-up. One patient from the ITT group and 1 from the PP group received additional treatment during follow-up.

CONCLUSION:
The Contour seems to be both safe and effective in the treatment of intracranial bifurcation aneurysms.
Optimal Glucose Target After Aneurysmal Subarachnoid Hemorrhage: A Matched Cohort Study
Authors: Eagles Matthew E. , Newton Braedon D. , Rosgen Brianna K. , Ayling Oliver G. S. , Muram Sandeep , Tso Michael K. , Mitha Alim P. , Macdonald R. Loch 
Published: February 2022

BACKGROUND:
Hyperglycemia has been associated with poor outcomes in patients with aneurysmal subarachnoid hemorrhage (aSAH). However, there remains debate as to what optimal glucose targets should be in this patient population.

OBJECTIVE:
To assess whether we could identify an optimal glucose target for patients with aSAH.

METHODS:
We performed a post hoc analysis of the “clazosentan to overcome neurological ischemia and infarction occurring after subarachnoid hemorrhage” trial data set. Patients had laboratory results drawn daily for the entirety of their intensive care unit stay. Maximum blood glucose levels were assessed for a relationship with unfavorable outcomes using multiple logistic regression analysis. Maximum blood glucose levels were dichotomized based on the Youden index, which identified a maximum level of <9.2 mmol/L as the optimal cut point for prediction of unfavorable outcomes. Nearest neighbor matching was used to assess the relationship between maintaining glucose levels below the cut point and unfavorable functional outcomes (defined as a modified Rankin score of >2 at 3 mo post-aSAH). The matching was performed after calculation of a propensity score based on identified predictors of outcome and glucose levels.

RESULTS:
Three hundred eighty-nine patients were included in the matched analysis. Propensity scores were balanced on both the covariates and outcomes of interest. There was a significant average treatment effect (−0.143: 95% confidence interval −0.267 to −0.019) for patients who maintained glucose levels <9.2 mmol/L.

CONCLUSION:
Maintaining glucose levels below the identified cut point was associated with a decreased risk for unfavorable outcomes in this retrospective matched study.
Effects of mechanical stimulation on metabolomic profiles of SW1353 chondrocytes: shear and compression
Authors: Welhaven Hope D. , McCutchen Carley N. , June Ronald K. 
Published: February 2022

ABSTRACT
Mechanotransduction is a biological phenomenon where mechanical stimuli are converted to biochemical responses. A model system for studying mechanotransduction are the chondrocytes of articular cartilage. Breakdown of this tissue results in decreased mobility, increased pain, and reduced quality of life. Either disuse or overloading can disrupt cartilage homeostasis, but physiological cyclical loading promotes cartilage homeostasis. To model this, we exposed SW1353 cells to cyclical mechanical stimuli, shear and compression, for different durations of time (15 and 30 min). By utilizing liquid chromatography-mass spectroscopy (LC-MS), metabolomic profiles were generated detailing metabolite features and biological pathways that are altered in response to mechanical stimulation. In total, 1457 metabolite features were detected. Statistical analyses identified several pathways of interest. Taken together, differences between experimental groups were associated with inflammatory pathways, lipid metabolism, beta-oxidation, central energy metabolism, and amino acid production. These findings expand our understanding of chondrocyte mechanotransduction under varying loading conditions and time periods.
This article has an associated First Person interview with the first author of the paper.
A genome-wide CRISPR screen identifies HuR as a regulator of apoptosis induced by dsRNA and virus
Authors: Gao Huixin , Lin Yuxia , Huang Changbai , Li Xiaobo , Diamond Michael S. , Liu Chao , Zhang Rong , Zhang Ping 
Published: February 2022

ABSTRACT
We performed an unbiased whole-genome CRISPR/Cas9 screen in A549 cells to identify potential regulators involved in cell death triggered by double-stranded RNA (dsRNA). Of several top candidate genes, we identified the RNA-binding gene ELAV like protein 1 (256529), which encodes the protein Hu antigen R (HuR). Depletion of HuR led to less cell death induced by dsRNA. HuR is mainly involved in apoptosis, and all of its RNA recognition motifs are essential for its pro-apoptotic function. We further showed that the HuR depletion had no influence on the mRNA level of the anti-apoptotic gene BCL2, but instead that HuR downregulates BCL2 translation in a cap-independent way. Polysome fractionation studies showed that HuR retarded the BCL2 mRNA in the non-translating pool of polysomes. Moreover, protection from dsRNA-induced apoptosis by HuR depletion required the presence of BCL2, indicating that the pro-apoptotic function of HuR is executed by suppressing BCL2. Consistent with this, HuR regulated apoptosis induced by infection of encephalomyocarditis or Semliki Forest virus. Collectively, our work identified a suite of proteins that regulate dsRNA-induced cell death, and elucidated the mechanism by which HuR acts as a pro-apoptotic factor.
Efficient Production of 1,3-Butadiene from 1,4-Butanediol over Yb2O3 Catalyst Prepared through Hydrothermal Aging
Authors: Matsuda Asami , Sato Fumiya , Yamada Yasuhiro , Sato Satoshi 
Published: February 2022

Abstract
Vapor-phase catalytic dehydration of 1,4-butanediol (1,4-BDO) was investigated over rare earth metal oxide (RE2O3) catalysts to produce 1,3-butadiene (BD). Among eight RE2O3, Yb2O3 showed the highest catalytic activity to produce BD via an intermediate 3-buten-1-ol (3B1OL). Hydrothermal (HT) aging of precursor precipitate of Yb2O3 greatly enhanced the catalytic activity and the selectivity to 3B1OL of the resulting Yb2O3 catalyst. It was confirmed that the morphology of Yb2O3 and the catalytic activity varied with the HT conditions. Hydrothermally aged Yb2O3 reduced the formation of propylene, a decomposed product of 3B1OL, even at high temperatures above 400 °C. HT-aged Yb2O3 followed by calcination at 700 °C showed excellent catalytic activity in the dehydration of 1,4-BDO with the highest BD productivity of 34.6 mol kgcat−1 h−1 and a high BD yield of 97.4% at 450 °C.