bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fish without Tail Fins—Exploring the Function of Tail Morphology of the First Vertebrates
Authors: Rival David E , Yang Wenchao , Caron Jean-Bernard 
Published: February 2021

SynopsisWe use a series of hydrodynamic experiments on abstracted models to explore whether primitive vertebrates may have swum under various conditions without a clearly-differentiated tail fin. Cambrian vertebrates had post-anal stubby tails, some had single dorsal and ventral fins, but none had yet evolved a clearly differentiated caudal fin typical of post-Cambrian fishes, and must have relied on their long and flexible laterally-compressed bodies for locomotion, i.e., by bending their bodies side-to-side in order to propagate waves from head to tail. We approach this problem experimentally based on an abstracted model of Metaspriggina walcotti from the 506-million-year old Burgess Shale by using oscillating thin flexible plates while varying the tail fin geometry from rectangular to uniform, and finally to a no tail–fin condition. Despite a missing tail fin, this study supports the observation that the abstracted Metaspriggina model can generate a strong propulsive force in cruise conditions, both away from, and near the sea bed (in ground effect). However, when the abstracted Metaspriggina model moves in ground effect, a weaker performance is observed, indicating that Metaspriggina may not necessarily have been optimized for swimming near the sea bed. When considering acceleration from rest, we find that the Metaspriggina model's performance is not significantly different from other morphological models (abstracted truncate tail and abstracted heterocercal tail). Statistical analysis shows that morphological parameters, swimming modes, and ground effect all play significant roles in thrust performance. While the exact relationships of Cambrian vertebrates are still debated, as agnathans, they share some general characteristics with modern cyclostomes, in particular an elongate body akin to lampreys. Lampreys, as anguilliform swimmers, are considered to be some of the most efficient swimmers using a particular type of suction thrust induced by the traveling body wave as it travels from head to tail. Our current experiments suggest that Metaspriggina’s ability in acceleration from rest, through possibly a similar type of suction thrust, which is defined as the ability to generate low pressure on upstream facing sections of the body, might have evolved early in response to increasing predator pressure during the Cambrian Explosion.
Measuring Self-Reported Cancer-Related Cognitive Impairment: Recommendations From the Cancer Neuroscience Initiative Working Group
Authors: Henneghan Ashley M , Van Dyk Kathleen , Kaufmann Tara , Harrison Rebecca , Gibbons Christopher , Heijnen Cobi , Kesler Shelli R 
Published: February 2021

Abstract
Cancer and its treatments are associated with increased risk for cancer-related cognitive impairment (CRCI). Methods and measures used to study and assess self-reported CRCI (sr-CRCI), however, remain diverse, resulting in heterogeneity across studies. The Patient-Reported Outcomes Working Group has been formed to promote homogeneity in the methods used to study sr-CRCI. In this report, using a psychometric taxonomy, we inventory and appraise instruments used in research to measure sr-CRCI, and we consider advances in patient-reported outcome methodology. Given its psychometric properties, we recommend the Patient-Reported Outcome Measurement Information System Cognitive Function Short Form 8a for measurement of sr-CRCI in cancer patients and survivors, at a minimum, to increase scientific rigor and progress in addressing CRCI.
Single-cell mapper (scMappR): using scRNA-seq to infer the cell-type specificities of differentially expressed genes
Authors: Sokolowski Dustin J , Faykoo-Martinez Mariela , Erdman Lauren , Hou Huayun , Chan Cadia , Zhu Helen , Holmes Melissa M , Goldenberg Anna , Wilson Michael D 
Published: February 2021

Abstract
RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on heterogeneous samples and the resulting DEGs do not necessarily indicate the cell-types where the differential expression occurred. While single-cell RNA-seq (scRNA-seq) methods solve this problem, technical and cost constraints currently limit its widespread use. Here we present single cell Mapper (scMappR), a method that assigns cell-type specificity scores to DEGs obtained from bulk RNA-seq by leveraging cell-type expression data generated by scRNA-seq and existing deconvolution methods. After evaluating scMappR with simulated RNA-seq data and benchmarking scMappR using RNA-seq data obtained from sorted blood cells, we asked if scMappR could reveal known cell-type specific changes that occur during kidney regeneration. scMappR appropriately assigned DEGs to cell-types involved in kidney regeneration, including a relatively small population of immune cells. While scMappR can work with user-supplied scRNA-seq data, we curated scRNA-seq expression matrices for ∼100 human and mouse tissues to facilitate its stand-alone use with bulk RNA-seq data from these species. Overall, scMappR is a user-friendly R package that complements traditional differential gene expression analysis of bulk RNA-seq data.
Leptospirosis Followed by Kawasaki-Like Disease: Case Report From an Adult Swiss Patient and Review of the Literature
Authors: Baerlocher Severin , Helfenstein Seth , Mahr Alfred , Crippa Selina , Garcia Boy Regine , Kahlert Christian R , Yurttas Timur , Hatz Christoph , Kohler Philipp 
Published: February 2021

Abstract
Kawasaki disease (KD) is a vasculitis that mostly occurs in children, but rare cases in adults have been reported. We describe the case of a 43-year-old Swiss male who developed symptoms compatible with KD 7 weeks after leptospirosis, which was presumably acquired after swimming in a creek in the Swiss Alps. We performed a literature review and identified 10 other cases (all in children), in which Kawasaki-like disease was diagnosed in the context of leptospirosis. Outcome was favourable in most cases, including our patient. This exceptional case demonstrates both the possibility of autochthonous cases of leptospirosis in Switzerland as well as a possible association of leptospirosis with Kawasaki-like disease.
ClearSeeAlpha: Advanced Optical Clearing for Whole-Plant Imaging
Authors: Kurihara Daisuke , Mizuta Yoko , Nagahara Shiori , Higashiyama Tetsuya 
Published: February 2021

Abstract
To understand how the body of plants is made, it is essential to observe the morphology, structure and arrangement of constituent cells. However, the opaque nature of the plant body makes it difficult to observe the internal structures directly under a microscope. To overcome this problem, we developed a reagent, ClearSee, that makes plants transparent, allowing direct observation of the inside of a plant body without inflicting damage on it, e.g. through physical cutting. However, because ClearSee is not effective in making some plant species and tissues transparent, in this study, we further improved its composition to prevent oxidation, and have developed ClearSeeAlpha, which can be applied to a broader range of plant species and tissues. Sodium sulfite, one of the reductants, prevented brown pigmentation due to oxidation during clearing treatment. Using ClearSeeAlpha, we show that it is possible to obtain clear chrysanthemum leaves, tobacco and Torenia pistils and fertilized Arabidopsis thaliana fruits—tissues that have hitherto been challenging to clear. Moreover, we show that the fluorescence intensity of purified fluorescent proteins emitting light of various colors was unaffected in the ClearSeeAlpha solution; only the fluorescence intensity of TagRFP was reduced by about half. ClearSeeAlpha should be useful in the discovery and analysis of biological phenomena occurring deep inside the plant tissues.
Measurement Properties of Outcome Measures Used to Assess Physical Impairments in Patients After Distal Radius Fracture: A Systematic Review
Authors: Ziebart Christina , Mehta Saurabh P , MacDermid Joy 
Published: February 2021

Abstract

Objectives
Individuals with distal radius fractures (DRF) may experience difficulty with gripping an object, painful wrist movements, sensorimotor difficulties, and swelling around the wrist and hand. A comprehensive review of the existing evidence concerning the measurement properties of common physical impairment measures can provide a valuable resource to guide hand therapy practice while managing DRF. The primary objective was to locate and assess the quality of literature on the measurement properties for the measures of physical impairment used in individuals with DRF.

Methods
Two reviewers searched PubMed, CINAHL, and EMBASE. A combination of DRF, measurement properties, and physical impairments were used as keywords, and articles were independently assessed using the Consensus-Based Standards for the Selection of Health Measurement Instruments critical appraisal tool. Primary studies were included if they examined at least 1 of the following: reliability, validity, responsiveness, or indices of true and meaningful changes for measures of physical impairment in the DRF sample. A total of 19 articles were included in this review. The quality of the studies ranged from 46% to 92%. This review suggests that measures such as assessment of grip strength and supination and pronation range of motion (ROM), using various goniometric devices, showed good intrarater and interrater reliability, construct validity, and responsiveness in individuals with DRF.

Conclusion
Acceptable reliability and responsiveness were reported in grip and wrist ROM assessments for measuring changes in wrist and hand function after DRF; however, wrist ROM assessed using traditional goniometric techniques were less reliable in individuals with DRF.

Impact
This study provides insight into which objective tools might be better suited for measuring outcomes related to DRF.
CAP measures towards environmental sustainability—Trade opportunities for Africa?
Authors: Latka Catharina , Heckelei Thomas , Kuhn Arnim , Witzke Heinz-Peter , Kornher Lukas 
Published: February 2021

AbstractEnvironmental sustainability is a core aspect of the proposed future EU Common Agricultural Policy (CAP). Policy changes must not compromise socioeconomic development in low-income countries, whereas the extensification of EU agriculture may also create trade opportunities abroad. We apply a global agricultural-economic model to assess EU–African trade-related impacts of potential, environmentally motivated CAP changes. Restrictions on livestock density and nitrogen application reveal reduced EU production levels of meat. This lowers the EU's agricultural environmental burden and share in agricultural trade flows to Africa. However, overall food supply in Africa is not projected to deteriorate substantially, as imports from other world regions and increasing domestic production fill the gap. While this weakens the global emission reduction potential, net livestock producers in Africa may benefit from increasing producer prices. How far potentials for domestic production and trade can be used in African regions depends at least partly on their competitiveness vis-á-vis substituting importers.
The circadian clock: a central mediator of cartilage maintenance and osteoarthritis development?
Authors: Poulsen Raewyn C , Hearn James I , Dalbeth Nicola 
Published: February 2021

Abstract
The circadian clock is a specialized cell signalling pathway present in all cells. Loss of clock function leads to tissue degeneration and premature ageing in animal models demonstrating the fundamental importance of clocks for cell, tissue and organism health. There is now considerable evidence that the chondrocyte circadian clock is altered in OA. The purpose of this review is to summarize current knowledge regarding the nature of the change in the chondrocyte clock in OA and the implications of this change for disease development. Expression of the core clock component, BMAL1, has consistently been shown to be lower in OA chondrocytes. This may contribute to changes in chondrocyte differentiation and extracellular matrix turnover in disease. Circadian clocks are highly responsive to environmental factors. Mechanical loading, diet, inflammation and oxidative insult can all influence clock function. These factors may contribute to causing the change in the chondrocyte clock in OA.
von Willebrand Factor Multimer Formation Contributes to Immunothrombosis in Coronavirus Disease 2019
Authors: Doevelaar Adrian A. N. , Bachmann Martin , Hölzer Bodo , Seibert Felix S. , Rohn Benjamin J. , Bauer Frederic , Witzke Oliver , Dittmer Ulf , Bachmann Michael , Yilmaz Serap , Dittmer Rita , Schneppenheim Sonja , Babel Nina , Budde Ulrich , Westhoff Timm H. 
Published: February 2021

OBJECTIVES:
Prevention and therapy of immunothrombosis remain crucial challenges in the management of coronavirus disease 2019, since the underlying mechanisms are incompletely understood. We hypothesized that endothelial damage may lead to substantially increased concentrations of von Willebrand factor with subsequent relative deficiency of a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13 (ADAMTS13).

DESIGN:
Prospective controlled cross-over trial.

SETTING:
Blood samples of patients with confirmed coronavirus disease 2019 and healthy controls were obtained in three German hospitals and analyzed in a German hemostaseologic laboratory.

PATIENTS:
Seventy-five patients with confirmed coronavirus disease 2019 of mild to critical severity and 30 healthy controls.

MEASUREMENTS AND MAIN RESULTS:
von Willebrand factor antigen, ADAMTS13, and von Willebrand factor multimer formation were analyzed. von Willebrand factor antigen was 4.1 times higher in COVID-19 patients compared with healthy controls (p < 0.0001), whereas ADAMTS13 activities were not significantly different (p = 0.18). The ADAMTS13/von Willebrand factor antigen ratio was significantly lower in COVID-19 than in the control group (24.4 ± 20.5 vs 82.0 ± 30.7; p < 0.0001). Fourteen patients (18.7%) undercut a critical ratio of 10 as described in thrombotic thrombocytopenic purpura. Gel analysis of multimers resembled a thrombotic thrombocytopenic purpura pattern with loss of the largest multimers in 75% and a smeary triplet pattern in 39% of the patients. The ADAMTS13/von Willebrand factor antigen ratio decreased continuously from mild to critical disease (analysis of variance p = 0.026). Furthermore, it differed significantly between surviving patients and those who died from COVID-19 (p = 0.001) yielding an area under the curve of 0.232 in receiver operating characteristic curve curve analysis.

Conclusion:
COVID-19 is associated with a substantial increase in von Willebrand factor levels, which can exceed the ADAMTS13 processing capacity resulting in the formation of large von Willebrand factor multimers indistinguishable from thrombotic thrombocytopenic purpura. The ADAMTS13/von Willebrand factor antigen ratio is an independent predictor of severity of disease and mortality. These findings provide a rationale to consider plasma exchange as a therapeutic option in COVID-19 and to include von Willebrand factor and ADAMTS13 in the diagnostic workup.
Prone Positioning and Survival in Mechanically Ventilated Patients With Coronavirus Disease 2019–Related Respiratory Failure*
Authors: Mathews Kusum S. , Soh Howard , Shaefi Shahzad , Wang Wei , Bose Sonali , Coca Steven , Gupta Shruti , Hayek Salim S. , Srivastava Anand , Brenner Samantha K. , Radbel Jared , Green Adam , Sutherland Anne , Leonberg-Yoo Amanda , Shehata Alexandre , Schenck Edward J. , Short Samuel A.P. , Hernán Miguel A. , Chan Lili , Leaf David E. 
Published: February 2021

OBJECTIVES:
Therapies for patients with respiratory failure from coronavirus disease 2019 are urgently needed. Early implementation of prone positioning ventilation improves survival in patients with acute respiratory distress syndrome, but studies examining the effect of proning on survival in patients with coronavirus disease 2019 are lacking. Our objective was to estimate the effect of early proning initiation on survival in patients with coronavirus disease 2019–associated respiratory failure.

DESIGN:
Data were derived from the Study of the Treatment and Outcomes in Critically Ill Patients with coronavirus disease 2019, a multicenter cohort study of critically ill adults with coronavirus disease 2019 admitted to 68 U.S. hospitals. Using these data, we emulated a target trial of prone positioning ventilation by categorizing mechanically ventilated hypoxemic (ratio of Pao
2 over the corresponding Fio
2 ≤ 200 mm Hg) patients as having been initiated on proning or not within 2 days of ICU admission. We fit an inverse probability–weighted Cox model to estimate the mortality hazard ratio for early proning versus no early proning. Patients were followed until death, hospital discharge, or end of follow-up.

SETTING:
ICUs at 68 U.S. sites

PATIENTS:
Critically ill adults with laboratory-confirmed coronavirus disease 2019 receiving invasive mechanical ventilation with ratio of Pao
2 over the corresponding Fio
2 less than or equal to 200 mm Hg.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Among 2,338 eligible patients, 702 (30.0%) were proned within the first 2 days of ICU admission. After inverse probability weighting, baseline and severity of illness characteristics were well-balanced between groups. A total of 1,017 (43.5%) of the 2,338 patients were discharged alive, 1,101 (47.1%) died, and 220 (9.4%) were still hospitalized at last follow-up. Patients proned within the first 2 days of ICU admission had a lower adjusted risk of death compared with nonproned patients (hazard ratio, 0.84; 95% CI, 0.73–0.97).

CONCLUSIONS:
In-hospital mortality was lower in mechanically ventilated hypoxemic patients with coronavirus disease 2019 treated with early proning compared with patients whose treatment did not include early proning.
Bacterial growth and recovery on hospital biometric devices: effect of two types of disinfectants
Authors: Norton Pedro , Guimarães João Tiago , Pinho Paulo , Ribeiro Manuela , Martins Natália , Mendes Carlos Pedro 
Published: February 2021

Abstract

Objectives:
The aim of the study was to evaluate the presence of bacterial contamination on biometric identification devices in a public hospital; identify the species of bacteria implicated in the contamination and assess bacterial recovery after the use of 2 types of disinfectants: alcohol 70% and isopropyl alcohol chlorhexidine.

Design:
Before and after trial.

Setting:
Public hospital, tertiary referral center.

Participants:
All existing biometric identification devices in the hospital (n = 20).

Methods:
Collection of 2 microbiological samples from the fingerprint reading surface of biometric devices immediately before and after applying the solution with alcohol 70% and in separate time periods with isopropyl alcohol chlorhexidine.

Results:
It have been identified 21 different bacterial species in a total of 78 samples, mostly Staphylococcus epidermidis (32 samples) and S aureus (7 samples). S epidermidis was eliminated in 61.5% of the samples after disinfecting with alcohol 70% and in 92.3% of the samples disinfected with isopropyl alcohol chlorhexidine. S aureus was eliminated in 33.3% and 100% of the samples, respectively. We found no bacterial growth in 10% of the devices after disinfection with 70% alcohol and in 78.9% of devices after disinfection with isopropyl alcohol chlorhexidine. We also found that there was a decrease in the frequency of species isolated after using both disinfection solutions, although isopropyl alcohol chlorhexidine appeared to be more effective.

Conclusions:
The biometric identification devices used in this hospital seem to be safe regardless of the products used for its cleaning. The majority of the bacteria found are commensal skin microorganisms. We did not find pathogenic bacteria for immunocompetent individuals, in particular methicillin-resistant S aureus.
Rare popliteal mass following retrograde nailing of ballistic femur fracture: a case report
Authors: Court Tannor , Gusho Charles A. , Graf Alexander , Schmeling Gregory 
Published: February 2021

Abstract

Introduction:
Civilian ballistic injuries are commonly associated with fracture, vascular injury, and soft tissue trauma. Posttraumatic pseudoaneurysms represent an extremely rare subset of vascular injuries following ballistic fractures.

Case:
We present the rare case of a posttraumatic pseudoaneurysm that occurred after retrograde femoral nailing of a ballistic distal femur fracture. The patient presented in clinic postoperatively with a pulsatile popliteal mass. Distal pulses were intact but subsequent ultrasound and angiography revealed a pseudoaneurysm of the distal superficial femoral artery. The pseudoaneurysm was subsequently treated with a covered stent and the patient's recovery was uncomplicated.

Conclusion:
Due to the potential life and limb-threating complications from pseudoaneurysm rupture, this case report emphasizes the early recognition and expeditious management of vascular complications following ballistic fractures in the civilian population.
Low CD4+ cell count nadir exacerbates the impacts of APOE ε4 on functional connectivity and memory in adults with HIV
Authors: Yang Fan Nils , Bronshteyn Margarita , Flowers Sarah A. , Dawson Matthew , Kumar Princy , Rebeck George William , Turner Raymond Scott , Moore David J. , Ellis Ronald J. , Jiang Xiong 
Published: February 2021

Objective:
Nearly half of individuals living with HIV in the USA are now 50 or older. This rapidly ageing populace may be at an increasingly greater risk of Alzheimer's disease. However, the potential interaction between HIV-disease and Alzheimer's disease pathogenesis (i.e. Alzheimer's disease genetic risk factors) on brain function remains an open question. The present study aimed to investigate the impact of APOE ε4 on brain function in middle-aged to older people with HIV (PWH), as well as the putative interaction between ε4 and HIV disease severity.

Methods:
Ninety-nine PWH participated in a cross-sectional study (56.3 ± 6.5 years, range 41–70 years, 27 women, 26 ε4 carriers and 73 noncarriers). Structural MRI and resting-state functional MRI were collected to assess alterations in brain structure and functional connectivity, respectively.

Results:
APOE ε4 was associated with worse memory performance and reduced functional connectivity in the memory network. The functional connectivity reduction was centred at the caudate nucleus rather than hippocampus and correlated with worse memory performance. In ε4 carriers, low CD4+ cell count nadir was associated with reduced functional connectivity in the memory network, but this association was absent in noncarriers. Furthermore, there was an indirect detrimental impact of ε4 on memory performance through memory network functional connectivity. However, this indirect effect was contingent on CD4+ cell count nadir, that is the indirect effect of ε4 on memory was only significant when CD4+ cell count nadir was low.

Interpretation:
APOE ε4 is associated with reduced memory and reduced functional connectivity within the memory network, and low CD4+ cell count nadir -- indicating a history of severe immunosuppression -- may exacerbate the effects of ε4.