bluuebunny/crossref_metadata_2025 huggingface dataset:
Exercise-Based Stroke Rehabilitation: Clinical Considerations Following the COVID-19 Pandemic
Authors: Moncion Kevin , Rodrigues Lynden , MacKay-Lyons Marilyn , Eng Janice J. , Billinger Sandra A. , Ploughman Michelle , Bailey Damian M. , Trivino Michael , Bayley Mark , Thiel Alexander , Roig Marc , Tang Ada
Published: October 2021

Background. The COVID-19 pandemic attributable to the severe acute respiratory syndrome virus (SARS-CoV-2) has had a significant and continuing impact across all areas of healthcare including stroke. Individuals post-stroke are at high risk for infection, disease severity, and mortality after COVID-19 infection. Exercise stroke rehabilitation programs remain critical for individuals recovering from stroke to mitigate risk factors and morbidity associated with the potential long-term consequences of COVID-19. There is currently no exercise rehabilitation guidance for people post-stroke with a history of COVID-19 infection. Purpose. To (1) review the multi-system pathophysiology of COVID-19 related to stroke and exercise; (2) discuss the multi-system benefits of exercise for individuals post-stroke with suspected or confirmed COVID-19 infection; and (3) provide clinical considerations related to COVID-19 for exercise during stroke rehabilitation. This article is intended for healthcare professionals involved in the implementation of exercise rehabilitation for individuals post-stroke who have suspected or confirmed COVID-19 infection and non-infected individuals who want to receive safe exercise rehabilitation. Results. Our clinical considerations integrate pre-COVID-19 stroke (n = 2) and COVID-19 exercise guidelines for non-stroke populations (athletic [n = 6], pulmonary [n = 1], cardiac [n = 2]), COVID-19 pathophysiology literature, considerations of stroke rehabilitation practices, and exercise physiology principles. A clinical decision-making tool for COVID-19 screening and eligibility for stroke exercise rehabilitation is provided, along with key subjective and physiological measures to guide exercise prescription. Conclusion. We propose that this framework promotes safe exercise programming within stroke rehabilitation for COVID-19 and future infectious disease outbreaks.
Motor Network Reorganization After Repetitive Transcranial Magnetic Stimulation in Early Stroke Patients: A Resting State fMRI Study
Authors: Juan Du  , Yao Weihe , Li Jianrui , Yang Fang , Hu Jingze , Xu Qiang , Liu Ling , Lv Qiushi , Liu Rui , Ye Ruidong , Ma Minmin , Zhu Wusheng , Zhang Zhiqiang , Liu Xinfeng
Published: October 2021

Objective

To compare the effects of high-frequency (10 Hz) versus low-frequency (1 Hz) repetitive Transcranial Magnetic Stimulation (rTMS) on motor recovery and functional reorganization of the cortical motor network during the early phase of stroke.

Methods

Forty-six hospitalized, first-ever ischemic stroke patients in early stage (within two weeks) with upper limb motor deficits were recruited. They were randomly allocated to three groups with 10 Hz ipsilesional rTMS, 1 Hz contralesional rTMS, and sham rTMS of five daily session. All patients underwent motor function (Upper Extremity Fugl–Meyer), neurophysiological and resting-state  functional Magnetic Resonance Imaging (fMRI) (rs-fMRI) assessments before and after rTMS intervention. Motor recovery (△Fugl–Meyer Assessment) was defined as motor function changes before and after rTMS intervention. Motor function assessment was reevaluated at time point of three month follow-up.

Results

The two real rTMS groups manifested greater motor improvements than the sham group. The effect sustained for at least 3 months after the end of the treatment sessions. Compared with the sham group, 10 Hz ipsilesional rTMS group presented increased resting-state functional connectivity (FC) between ipsilesional primary motor cortex (M1) and contralesional M1 (P = .007), whereas 1 Hz contralesional rTMS group presented increased FC between contralesional M1 and ipsilesional supplementary motor area (P = .010), which were positively correlated with motor recovery (P < .05).

Conclusion

Beneficial effect of rTMS on motor recovery might be underlaid by increased FC between stimulating site and the remote motor areas, highlighting the motor network reorganization mechanism of rTMS in early post-stroke phase.
Frequency and Types of Complications Encountered in Patients With Nonconvulsive Status Epilepticus in the Neurological ICU: Impact on Outcome
Authors: Dericioglu Nese , Ayvacioglu Cagan Cansu , Sokmen Okan , Arsava Ethem Murat , Topcuoglu Mehmet Akif
Published: October 2021

Objectives. The frequency and types of complications in patients with nonconvulsive status epilepticus (NCSE) who are followed up in the intensive care unit (ICU), and the impact of these complications on outcome are not well-known. We investigated the complications and their effects on prognosis in NCSE patients. Methods. After reviewing the video-EEG monitoring (VEEGM) reports of all the consecutive patients who were followed up in our ICU between 2009 and 2019, we identified two groups of patients: 1-patients with NCSE (study group) and 2-patients who underwent VEEGM for possible NCSE but did not have ictal recordings (no-NCSE group). Electronic health records were reviewed to identify demographic and clinical data, duration of ICU care, medical and surgical complications, pharmacologic treatment, and outcome. These parameters were compared statistically between the groups. We also investigated the parameters affecting prognosis at discharge. Results. Thirty-two patients with NCSE comprised the study group. Infection developed in 84%. More than half were intubated, had tracheostomy or percutaneous endoscopic gastrostomy application. Refractory NCSE was associated with significantly more frequent complications and worse outcome. There was a higher tendency of infections in the study group ( P = .059). Higher organ failure scores and prolonged stay in ICU predicted worse outcome ( P < .05). Conclusion. The frequency of complications in patients with NCSE who are cared for in the ICU is considerable. Most of the complications are similar to the other patients in ICU, except for the higher frequency of infections. Increased physician awareness about modifiable parameters and timely interventions might help improve prognosis.
Brain Networks With Modified Connectivity in Patients With Neuropathic Pain and Spinal Cord Injury
Authors: Hasan Muhammad A. , Sattar Parisa , Qazi Saad A. , Fraser Matthew , Vuckovic Aleksandra
Published: October 2021

Background. Neuropathic pain (NP) following spinal cord injury (SCI) affects the quality of life of almost 40% of the injured population. The modified brain connectivity was reported under different NP conditions. Therefore, brain connectivity was studied in the SCI population with and without NP with the aim to identify networks that are altered due to injury, pain, or both. Methods. The study cohort is classified into 3 groups, SCI patients with NP, SCI patients without NP, and able-bodied. EEG of each participant was recorded during motor imagery (MI) of paralyzed and painful, and nonparalyzed and nonpainful limbs. Phased locked value was calculated using Hilbert transform to study altered functional connectivity between different regions. Results. The posterior region connectivity with frontal, fronto-central, and temporal regions is strongly decreased mainly during MI of dominant upper limb (nonparalyzed and nonpainful limbs) in SCI no pain group. This modified connectivity is prominent in the alpha and high-frequency bands (beta and gamma). Moreover, oscillatory modified global connectivity is observed in the pain group during MI of painful and paralyzed limb which is more evident between fronto-posterior, frontocentral-posterior, and within posterior and within frontal regions in the theta and SMR frequency bands. Cluster coefficient and local efficiency values are reduced in patients with no reported pain group while increased in the PWP group. Conclusion. The altered theta band connectivity found in the fronto-parietal network along with a global increase in local efficiency is a consequence of pain only, while altered connectivity in the beta and gamma bands along with a decrease in cluster coefficient values observed in the sensory-motor network is dominantly a consequence of injury only. The outcomes of this study may be used as a potential diagnostic biomarker for the NP. Further, the expected insight holds great clinical relevance in the design of neurofeedback-based neurorehabilitation and connectivity-based brain–computer interfaces for SCI patients.
A novel method for asynchronous source localisation based on time of arrival measurements
Authors: Zhu Huijie , Liu Sheng , Yao Zhiqiang , Okonkwo Moses Chukwuka , Peng Zheng
Published: October 2021

Source localisation is an important component in the application of wireless sensor networks, and plays a key role in environmental monitoring, healthcare and battlefield surveillance and so on. In this article, the source localisation problem based on time-of-arrival measurements in asynchronous sensor networks is studied. Because of imperfect time synchronisation between the anchor nodes and the signal source node, the unknown parameter of start transmission time of signal source makes the localisation problem further sophisticated. The derived maximum-likelihood estimator cost function with multiple local minimum is non-linear and non-convex. A novel two-step method which can solve the global minimum is proposed. First, by leveraging dimensionality reduction, the maximum (minimum) distance maximum (minimum) time-of-arrival matching-based second-order Monte Carlo method is applied to find a rough initial position of the signal source with low computational complexity. Then, the rough initial position value is refined using trust region method to obtain the final positioning result. Comparative analysis with state-of-the-art semidefinite programming and min–max criterion-based algorithms are conducted. Simulations show that the proposed method is superior in terms of localisation accuracy and computational complexity, and can reach the optimality benchmark of Cramér–Rao Lower Bound even in high signal-to-noise ratio environments.
Serial dependence of facial identity for own- and other-race faces
Authors: Turbett Kaitlyn , Jeffery Linda , Bell Jason , Digges Andrew , Zheng Yueyuan , Hsiao Janet , Palermo Romina
Published: October 2021

It is well established that individuals are better at recognising faces of their own-race compared with other-races; however, there is ongoing debate regarding the perceptual mechanisms that may be involved and therefore sensitive to face-race. Here, we ask whether serial dependence of facial identity, a bias where the perception of a face’s identity is biased towards a previously presented face, shows an other-race effect. Serial dependence is associated with face recognition ability and appears to operate on high-level, face-selective representations, like other candidate mechanisms (e.g., holistic processing). We therefore expected to find an other-race effect for serial dependence for our Caucasian and Asian participants. While participants showed robust effects of serial dependence for all faces, only Caucasian participants showed stronger serial dependence for own-race faces. Intriguingly, we found that individual variation in own-race, but not other-race, serial dependence was significantly associated with face recognition abilities. Preliminary evidence also suggested that other-race contact is associated with other-race serial dependence. In conclusion, though we did not find an overall difference in serial dependence for own- versus other-race faces in both participant groups, our results highlight that this bias may be functionally different for own- versus other-race faces and sensitive to racial experience.
Brain atrophy and endovascular treatment effect in acute ischemic stroke: a secondary analysis of the MR CLEAN trial
Authors: Luijten Sven PR , Compagne Kars CJ , van Es Adriaan CGM , Roos Yvo BWEM , Majoie Charles BLM , van Oostenbrugge Robert J , van Zwam Wim H , Dippel Diederik WJ , Wolters Frank J , van der Lugt Aad , Bos Daniel
Published: October 2021

Background

Brain atrophy is suggested to impair the potential for functional recovery after acute ischemic stroke. We assessed whether the effect of endovascular treatment is modified by brain atrophy in patients with acute ischemic stroke due to large vessel occlusion.

Methods

We used data from MR CLEAN, a multicenter trial including patients with acute ischemic stroke due to anterior circulation large vessel occlusion randomized to endovascular treatment plus medical care (intervention) versus medical care alone (control). We segmented total brain volume (TBV) and intracranial volume (ICV) on baseline non-contrast computed tomography (n = 410). Next, we determined the degree of atrophy as the proportion of brain volume in relation to head size (1 − TBV/ICV) × 100%, analyzed as continuous variable and in tertiles. The primary outcome was a shift towards better functional outcome on the modified Rankin Scale expressed as adjusted common odds ratio. Treatment effect modification was tested using an interaction term between brain atrophy (as continuous variable) and treatment allocation.

Results

We found that brain atrophy significantly modified the effect of endovascular treatment on functional outcome (P for interaction = 0.04). Endovascular treatment led to larger shifts towards better functional outcome in the higher compared to the lower range of atrophy (adjusted common odds ratio, 1.86 [95% CI: 0.97–3.56] in the lowest tertile vs. 1.97 [95% CI: 1.03–3.74] in the middle tertile vs. 3.15 [95% CI: 1.59–6.24] in the highest tertile).

Conclusion

Benefit of endovascular treatment is larger in the higher compared to the lower range of atrophy, demonstrating that advanced atrophy should not be used as an argument to withhold endovascular treatment.
Governing a Pandemic: Assessing the Role of Collaboration on Latin American Responses to the COVID-19 Crisis
Authors: Cyr Jennifer , Bianchi Matías , González Lucas , Perini Antonella
Published: October 2021

How do governments address complex, cross-sectoral problems, like the COVID-19 pandemic? Why were some Latin American countries more successful at containing the pandemic's most devastating health outcomes? We argue that national governments that were more collaborative in their response to COVID-19 were more successful in reducing death rates. Our original dataset offers a novel attempt to operationalise collaborative governance (CG). We undertake simple statistical tests to measure the relationship between CG and COVID-19-related mortality rates in Latin America. We then choose three case studies to assess whether collaboration was meaningful in practice. Initial evidence suggests governments that pursued CG were more effective at containing mortality rates early on in the pandemic. The collaboration helped to foster cooperation over resources; buy time to prepare for a potential case surge; and produce a unified message regarding what citizens should do to prevent viral spread.
Overstretching or Overreaction? China’s Rise in Latin America and the US Response
Authors: Pu Xiaoyu , Myers Margaret
Published: October 2021

This article examines how the Chinese elites are interpreting China’s growing presence in the Latin American and Caribbean (LAC) region and the various ways in which the United States is responding to China’s expanding activity in the region. Some of China’s elites caution that China’s international posturing could be overly assertive. Regarding China’s growing role in the LAC, they have made a note of US sensitivities, in addition to China’s challenges and limitations in various Latin American countries. Regarding the US response, some US concerns may be legitimate, and others are less valid. Looking ahead, even though US–China interactions in the LAC will remain competitive, the US and China could potentially avoid counterproductive policies while also pursuing pragmatic co-operation. While China does not yet face a serious problem of strategic overstretching in the LAC, China’s domestic debate on the topic will provide feedback to China’s policymakers and promote fruitful China–LAC relations.
A 4-year old presenting with fever and achiness
Authors: Plott Caroline , Gracie Thomas , Alvis Courtney , Schlefman Amanda , Dudas Robert
Published: October 2021

In children under the age of 5 who have abnormalities in history, physical examination, and laboratory studies indicating multi-system disease, uncovering the correct diagnosis is challenging. Here, we report the course of a 4-year-old girl who presented with a change in behavior, fever, arthralgia, arthritis, and hematuria following three recent hospitalizations for pneumonia and impetigo. Serologic findings were suggestive of a rheumatologic etiology and a renal biopsy was consistent with Membranous Lupus Nephritis Class V which helped secure the diagnosis of pediatric systemic lupus erythematosus. We review the clinical features and diagnostic criteria of early-onset systemic lupus erythematosus and discuss diagnostic considerations and prognosis.
Stream your brain! Speculative economy of the IoT and its pan-kinetic dataveillance
Authors: Ahn Sungyong
Published: October 2021

It is now a common belief that the truths of our lives are hidden in the databases streamed from our interactions in smart environments. In this current hype of big data, the Internet of Things has been suggested as the idea to embed small sensors and actuators everywhere to unfold the truths beneath the surfaces of everything. However, remaining the technology that promises more than it can provide thus far, more important for the IoT’s actual expansion to various social domains than the actual discovery of hidden truths has been people’s speculations about the unknown problems, such as hidden security issues or lifestyle concerns, beyond the narrow human knowability but assumed to leave their traces in the IoT-collected big data. This paper discuss this speculation as the concealed cognitive labor of IoT users that projects some fictitious values to the big data IoT companies accumulate. By the term pan-kinetics, the systemic operation of smart actuators is analyzed as the process through which fictitious values of data are converted to the real values as these actuators draw some profitable correlations from physical domains of the IoT. Analyzing smart electroencephalogram (EEG) headsets as the unique IoT devices operating on human brains, it argues how the IoT translates this speculative realism of unknown problems into its big data, which the IoT developers believe to be full of machine-learnable correlations that would lead to the smart solutions of the problems.
Suspicious and fraudulent online survey participation: Introducing the REAL framework
Authors: Lawlor Jennifer , Thomas Carl , Guhin Andrew T , Kenyon Kendra , Lerner Matthew D ,   UCAS Consortium, Drahota Amy
Published: October 2021

Online survey research has significantly increased in popularity in recent years. With its use, researchers have a new set of concerns about data collection and analysis to consider, including the possibility of fraudulent survey submissions. The purpose of this article is to demonstrate to survey researchers an innovative and systematized process for addressing online survey fraud over the course of collecting survey data, especially when respondents collect incentives for participation. We provide the Reflect, Expect, Analyze, Label Framework, which includes four sets of guiding questions for use by online survey researchers to plan for addressing survey fraud and making determinations about the inclusion or exclusion of participant submissions from the dataset based on level of suspicion. We also provide a full case example utilizing the Reflect, Expect, Analyze, Label Framework as an appendix. Those wanting to apply the Reflect, Expect, Analyze, Label Framework should keep in mind several considerations as they apply it, including determining logistical needs ahead of survey implementation, considering the ethical issues related to including or excluding data in a study, and considering the issues related to providing incentives for participating in research. Future research should assess the frequency of survey fraud, investigate the reasons for its occurrence and explore the role social networks may play in fraudulent participants sharing information. We suggest that researchers consider online survey fraud as an issue over the lifespan of their survey and apply the guiding questions we present to address the issue throughout.
Posterior tibialis tendon rupture concomitant with a closed medial malleolar fracture: A case report and literature review
Authors: Talebi Shahin , Sheibani Shirin , Ghaffari Salman , Ghadiri Abolfazl
Published: October 2021

Traumatic rupture of the posterior tibialis tendon is an extremely infrequent condition, which mostly occurred due to a traumatic mechanism of pronation and external rotation, less commonly in direct trauma on the medial side of the ankle. This lesion is overlooked preoperatively most of the time because of the limitation of physical examination owing to acute pain and swelling secondary to a medial malleolar fracture. Early diagnosis and treatment of this injury are very important to prevent the complications like acquired flatfoot deformity. Few cases have been described in the literature for the posterior tibialis tendon rupture associated with a closed ankle fracture. Here we report an acute rupture of the posterior tibialis tendon associated with a closed medial malleolar fracture after a high-energy trauma in a healthy 33-year-old man. We fixed the medial malleolar fracture with two screws and repaired the tendon with a direct end-to-end suture. We hope that our study can be helpful for other colleagues to consider this lesion in similar circumstances.
Cervical spine TB – Current concepts in management
Authors: Shetty Ajoy Prasad , Viswanathan Vibhu Krishnan , Rajasekaran S
Published: October 2021

Objective:

Cervical tubercular disease (CTB) is a rare pathology and constitutes 3–5% of all spinal TB. It includes atlantoaxial TB and sub-axial TB. As the literature evidence on this subject is scarce, majority of issues concerning CTB are still controversial. The current narrative review comprehensively discusses the various aspects related to CTB. Literature search: An elaborate search was made using keywords cervical tuberculosis, atlantoaxial tuberculosis, sub-axial tuberculosis, and cervico-thoracic tuberculosis, on pubmed and google ( scholar.google.com ) databases on 2 December 2020. We identified crucial questions regarding CTB and included relevant articles pertaining to them.

Results:

The initial search using keywords cervical tuberculosis, atlantoaxial tuberculosis, sub-axial tuberculosis, and cervico-thoracic tuberculosis yielded 4128, 76, 3 and 9 articles on ‘pubmed’ database, respectively. A similar search using the aforementioned keywords yielded 1,96,000, 2130, 117 and 728 articles on ‘google scholar’ database. The initial screening resulted in the identification of 178 articles. Full manuscripts were obtained for these articles and thoroughly scrutinised at the second stage. Review articles, randomised controlled trials and level 1 studies were given preference. Overall, 41 articles were included.

Conclusion:

AATB and SACTB constitute 0.3 to 1% and 3% of spinal TB, respectively. The incidence of neuro-deficit in CTB is significantly more than other spinal TB. The general principles of management of CTB are similar to spinal TB elsewhere and medical therapy remains the cornerstone. Surgery is advocated in specific scenarios involving gross neuro-deficit, later stages of disease with significant bony/ligamentous disruptions, altered sagittal balance, drug resistance, and poor response to medications. The surgical approaches for AATB include anterior-alone, posterior-alone and combined approaches, although posterior access is the most preferred. Most of the studies on SACTB have supported the role of anterior approach. Additionally, posterior stabilisation may be necessary in specific scenarios. The overall long-term outcome in CTB is favourable.
Association Between Markerless Motion Capture Screenings and Musculoskeletal Injury Risk for Military Trainees: A Large Cohort and Reliability Study
Authors: Hando Ben R. , Scott W. Casan , Bryant Jacob F. , Tchandja Juste N. , Scott Ryan M. , Angadi Siddhartha S.
Published: October 2021

Background:

Markerless motion capture (MMC) systems used to screen for musculoskeletal injury (MSKI) risk have become popular in military and collegiate athletic settings. However, little is known regarding the test-retest reliability or, more importantly, the ability of these systems to accurately identify individuals at risk for MSKI.

Purpose:

To determine the association between scores from a proprietary MMC movement screen test and the likelihood of suffering a subsequent MSKI and establish the test-retest reliability of the MMC system used.

Study Design:

Cohort study; Level of evidence, 3.

Methods:

Trainees for the Air Force Special Warfare program underwent MMC screenings immediately before entering the 8-week training course. MSKI data were extracted from a database for the surveillance period for each trainee. Logistic regression analyses were performed to identify associations between baseline MMC scores and the likelihood of suffering any MSKI or, specifically, a lower extremity MSKI. The test-retest portion of the study collected MMC scores from 10 separate participants performing 4 trials of the standard test procedures. Reliability was assessed using intraclass correlation coefficients by a single rater.

Results:

Overall, 1570 trainees, of whom 800 (51%) suffered an MSKI, were included in the analysis. MMC scores poorly predicted the likelihood of any or a lower extremity MSKI (odds ratio, 1.01-1.02). Further, receiver operating characteristic curve analyses demonstrated poor sensitivity and specificity for prediction of MSKI with MMC scores (area under the curve = 0.53). Finally, intraclass correlation coefficients from the test-retest analysis of MMC scores ranged from 0.157 to 0.602.

Conclusion:

This MMC system displayed poor to moderate test-retest reliability and did not demonstrate the ability to discriminate between individuals who were and were not likely to suffer an MSKI.
Discrimination in Indian Higher Education: Everyday Exclusion of the Dalit–Adivasi Student
Authors: Kumar Bagesh
Published: October 2021

This study is based on the lived experiences of the Dalit and Adivasi students in an elite higher education institution in India. It describes the everyday struggle undertaken by the students from socially marginalized communities, who experience discrimination, alienation and exclusion due to their identity. The study analyses the narratives of students about their educational experiences to develop an understanding of the regulatory and gate-keeping mechanisms operating in the academic and non-academic spheres in the educational institutions. Further, by revealing the serious limitations of existing practices of inclusion it reflects upon the manifest reproduction of caste inequalities within educational institutions today.
Centrality of drug targets in protein networks
Authors: Viacava Follis Ariele
Published: October 2021

Background

In the pharmaceutical industry, competing for few validated drug targets there is a drive to identify new ways of therapeutic intervention. Here, we attempted to define guidelines to evaluate a target’s ‘fitness’ based on its node characteristics within annotated protein functional networks to complement contingent therapeutic hypotheses.

Results

We observed that targets of approved, selective small molecule drugs exhibit high node centrality within protein networks relative to a broader set of investigational targets spanning various development stages. Targets of approved drugs also exhibit higher centrality than other proteins within their respective functional class. These findings expand on previous reports of drug targets’ network centrality by suggesting some centrality metrics such as low topological coefficient as inherent characteristics of a ‘good’ target, relative to other exploratory targets and regardless of its functional class. These centrality metrics could thus be indicators of an individual protein’s ‘fitness’ as potential drug target. Correlations between protein nodes’ network centrality and number of associated publications underscored the possibility of knowledge bias as an inherent limitation to such predictions.

Conclusions

Despite some entanglement with knowledge bias, like structure-oriented ‘druggability’ assessments of new protein targets, centrality metrics could assist early pharmaceutical discovery teams in evaluating potential targets with limited experimental proof of concept and help allocate resources for an effective drug discovery pipeline.
isoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data
Authors: Barcelona-Cabeza Rosa , Sanseverino Walter , Aiese Cigliano Riccardo
Published: October 2021

Background

Accurate copy number variant (CNV) detection is especially challenging for both targeted sequencing (TS) and whole‐exome sequencing (WES) data. To maximize the performance, the parameters of the CNV calling algorithms should be optimized for each specific dataset. This requires obtaining validated CNV information using either multiplex ligation-dependent probe amplification (MLPA) or array comparative genomic hybridization (aCGH). They are gold standard but time-consuming and costly approaches.

Results

We present isoCNV which optimizes the parameters of DECoN algorithm using only NGS data. The parameter optimization process is performed using an in silico CNV validated dataset obtained from the overlapping calls of three algorithms: CNVkit, panelcn.MOPS and DECoN. We evaluated the performance of our tool and showed that increases the sensitivity in both TS and WES real datasets.

Conclusions

isoCNV provides an easy-to-use pipeline to optimize DECoN that allows the detection of analysis-ready CNV from a set of DNA alignments obtained under the same conditions. It increases the sensitivity of DECoN without the need for orthogonal methods. isoCNV is available at https://gitlab.com/sequentiateampublic/isocnv.
Comparative transcriptome analysis uncovers cell wall reorganization and repressed cell division during cotton fiber initiation
Authors: Liu Wenyuan , Lv Yanjia , Li Xiaoyue , Feng Zongqin , Wang Lichen
Published: October 2021

Background

Tetraploid cotton plants serve as prime natural fiber source for the textile industry. Although various omics studies have revealed molecular basis for fiber development, a better understanding of transcriptional regulation mechanism regulating lint fiber initiation is necessary to meet global natural fiber demand.

Results

Here, we aimed to perform transcriptome sequencing to identify DEGs (differentially expressed genes) in ovules of the cotton variety Xu142 and its fibreless mutantXu142flduring early lint fiber initiation period. Totally, 5516 DEGs including 1840 upregulated and 3676 downregulated were identified. GO enrichment analysis revealed that the downregulated DEGs were mainly associated with biological processes such as transcription related biosynthesis and metabolism, organic cyclic compound biosynthesis and metabolism, photosynthesis, and plant cell wall organization, with molecular functions involving transcription related binding, organic cyclic compound binding, and dioxygenase activity, while the upregulated DEGs were associated with DNA replication and phospholipid biosynthetic related processes. Among the 490 DEGs annotated as transcription factor genes, 86.5% were downregulated in the mutant including theMalvaceae-specificMMLs, expression patterns of which were confirmed during the central period of lint fiber initiation. Investigation of the 16 genes enriched in the cell wall organization revealed that 15 were EXPA coding genes.

Conclusions

Overall, our data indicate that lint fiber initiation is a complicated process involving cooperation of multiple transcription factor families, which might ultimately lead to the reorganization of the cell wall and terminated cell division of the differentiating fiber initials.
A linkage disequilibrium-based approach to position unmapped SNPs in crop species
Authors: Yadav Seema , Ross Elizabeth M. , Aitken Karen S. , Hickey Lee T. , Powell Owen , Wei Xianming , Voss-Fels Kai P. , Hayes Ben J.
Published: October 2021

Background

High-density SNP arrays are now available for a wide range of crop species. Despite the development of many tools for generating genetic maps, the genome position of many SNPs from these arrays is unknown. Here we propose a linkage disequilibrium (LD)-based algorithm to allocate unassigned SNPs to chromosome regions from sparse genetic maps. This algorithm was tested on sugarcane, wheat, and barley data sets. We calculated the algorithm’s efficiency by masking SNPs with known locations, then assigning their position to the map with the algorithm, and finally comparing the assigned and true positions.

Results

In the 20-fold cross-validation, the mean proportion of masked mapped SNPs that were placed by the algorithm to a chromosome was 89.53, 94.25, and 97.23% for sugarcane, wheat, and barley, respectively. Of the markers that were placed in the genome, 98.73, 96.45 and 98.53% of the SNPs were positioned on the correct chromosome. The mean correlations between known and new estimated SNP positions were 0.97, 0.98, and 0.97 for sugarcane, wheat, and barley. The LD-based algorithm was used to assign 5920 out of 21,251 unpositioned markers to the current Q208 sugarcane genetic map, representing the highest density genetic map for this species to date.

Conclusions

Our LD-based approach can be used to accurately assign unpositioned SNPs to existing genetic maps, improving genome-wide association studies and genomic prediction in crop species with fragmented and incomplete genome assemblies. This approach will facilitate genomic-assisted breeding for many orphan crops that lack genetic and genomic resources.
Removal of EpCAM-positive tumor cells from blood collected during major oncological surgery using the Catuvab device- a pilot study
Authors: Winter Andreas , Zacharowski Kai , Meybohm Patrick , Schnitzbauer Andreas , Ruf Peter , Kellermann Claudia , Lindhofer Horst
Published: October 2021

Background

Intraoperative blood salvage (IBS) is regarded as an alternative to allogeneic blood transfusion excluding the risks associated with allogeneic blood. Currently, IBS is generally avoided in tumor surgeries due to concern for potential metastasis caused by residual tumor cells in the erythrocyte concentrate.

Methods

The feasibility, efficacy and safety aspects of the new developedCatuvabprocedure using the bispecific trifunctional antibody Catumaxomab was investigated in an ex-vivo pilot study in order to remove residual EpCAM positive tumor cells from the autologous erythrocyte concentrates (EC) from various cancer patients, generated by a IBS device.

Results

Tumor cells in intraoperative blood were detected in 10 of 16 patient samples in the range of 69–2.6 × 105but no residual malignant cells in the final erythrocyte concentrates afterCatuvabprocedure. IL-6 and IL-8 as pro-inflammatory cytokines released during surgery, were lowered in mean 28-fold and 52-fold during theCatuvabprocedure, respectively, whereas Catumaxomab antibody was detected in 8 of 16 of the final EC products at a considerable decreased and uncritical residual amount (37 ng in mean).

Conclusion

The preliminary study results indicate efficacy and feasibility of the new medical deviceCatuvaballowing potentially the reinfusion of autologous erythrocyte concentrates (EC) produced by IBS device during oncological high blood loss surgery. An open-label, multicenter clinical study on the removal of EpCAM-positive tumor cells from blood collected during tumor surgery using theCatuvabdevice is initiated to validate these encouraging results.
The 10-year incidence of hypertension across blood pressure categories in a population-based cohort in southwestern Sweden
Authors: Lindblad Ulf , Lundholm Klara , Eckner Jenny , Li Ying , Råstam Lennart , Hellgren I. Margareta , Daka Bledar
Published: October 2021

Background

To explore the determinants of incident hypertension, and especially the impact of baseline blood pressure categories, in a representative Swedish population.

Methods

A 10-year longitudinal study of residents aged 30–74. Blood pressures were measured and categorized according to ESH guidelines with optimal blood pressure < 120/80 mmHg, normal 120–129/80–84 mmHg, and high normal 130–139/85–89 mmHg. Incident hypertension was defined as ongoing treatment or three consecutive blood pressure readings ≥ 140/ ≥ 90 mmHg (one or both) at follow-up, while those with ≥ 140 and/or ≥ 90 mmHg at only one or two visits were labelled as unstable. After excluding subjects with hypertension, ongoing blood pressure lowering medication or a previous CVD event at baseline, 1099 remained for further analyses.

Results

Sixteen (2.6%) subjects with optimal baseline blood pressure had hypertension at follow up. Corresponding numbers for subjects with normal, high normal and unstable blood pressure were 55 (19.4%), 50 (39.1%) and 46 (74.2%), respectively. Compared with subjects in optimal group those in normal, high normal and unstable blood pressure categories had significantly higher risk to develop manifest hypertension with odds ratios OR and (95% CI) of 7.04 (3.89–12.7), 17.1 (8.88–33.0) and 84.2 (37.4–190), respectively, with adjustment for age, BMI and family history for hypertension. The progression to hypertension was also independently predicted by BMI (p < 0.001), however, not by age.

Conclusions

Subjects with high normal or unstable blood pressure should be identified in clinical practice, evaluated for global hypertension risk and offered personalized advice on lifestyle modification for early prevention of manifest hypertension and cardiovascular disease.
Factors associated with quality of care in inflammatory bowel diseases: a view from patient’s side using the IQCARO quality of care decalogue
Authors: Casellas F. , Calvet Xavier , Carpio D. , Vera I. , Saldaña R. , Mínguez M. , Marín L. , Juliá B. ,   GETECCU, GETEII and ACCU
Published: October 2021

Background

Quality of care (QoC) is a highly important topic in inflammatory bowel disease (IBD). We recently elaborated a decalogue of QoC indicators (IQCARO-QoC) developed by IBD patients. The aim of the present study was to assess the factors associated with patients’ evaluation of QoC in Spain using the IQCARO-QoC Decalogue recently developed by IBD patients.

Methods

A survey including patients’ socio-demographic and clinical characteristics, and the IQCARO-QoC Decalogue, was completed by IBD patients. We described patients’ assessment of QoC across Spanish patients. A univariable and multivariable analysis was performed to explore the associations between patients’ characteristics and QoC.

Results

Questionnaires from 788 participant patients were analysed. Participants’ mean age was 43.4 years, 63% were females and 58% had Crohn’s disease. The mean QoC score was 8.1 (± 2.4 SD) points out of a maximum of 10. Items with the lowest score were related to the provision of information and the implication of the medical team throughout the entire patient care. Factors associated with better QoC scores included: being employed better disease control, fewer numbers of unscheduled visits, and being followed by a gastroenterologist specialized in IBD.

Conclusions

Spanish patients’ reported QoC seems to be globally good although there is room for improvement, especially in providing adequate information to patients. Care provided by specialized IBD gastroenterologists seems to be related with higher QoC scores.
A case report of delayed lower intestinal bleeding after organophosphate poisoning
Authors: Hung Wei , Tsai Tsung-Heng , Chen Jian-Han
Published: October 2021

Background

Organophosphate poisoning is a serious issue and it results in significant casualties in developing countries. Since agriculture remains an important and necessary sector of human society and organophosphate are commonly used in agriculture, it is difficult to prevent organophosphate poisoning. Gastrointestinal bleeding is not a common but life threatening symptom of organophosphate poisoning. We report a rare case of gastrointestine bleeding due to organophosphate poisoning.

Case presentation

A 78-year-old woman presented to our hospital approximately 12 h after ingesting a mouthful of organophosphate and benzodiazepines in a suicide attempt. Six weeks after successful medical treatment for respiratory failure, she developed recurring melena. Colonoscopy and esophagogastroduodenoscopy findings were negative for ulcers or bleeding. Enteroscopy revealed severe circumferential ulcers with luminal narrowing 10 cm proximal to the ileocecal valve. The patient underwent a 100-cm ileum resection after failed medical treatment and recovered uneventfully. The resected terminal ileum demonstrated severe inflammation and a sharp transitional zone between the healthy and injured mucosa approximately 50 cm proximal to the ileocecal valve. Pathological examination revealed an injured mucosa with inflammatory cell infiltration and structural damage. This case highlights a rare event of OP poisoning with late-onset lower gastrointestinal bleeding, which prolonged the patient’s recovery course and parenteral alimentation period.

Conclusion

We report a rare case of a patient with organophosphate poisoning, with late-onset lower GI tract bleeding, which raised clinical awareness regarding the organophosphate poisoning that induce intestinal symptoms.
The length of susceptibility vessel sign predicts early neurological deterioration in minor acute ischemic stroke with large vessel occlusion
Authors: He Lanying , Wang Jian , Wang Feng , Zhang Lili , Zhang Lijuan , Zhao Wang , Weng Xiechuan , Xu Fan
Published: October 2021

Background

Patients with acute large vessel occlusion (LVO) presenting with minor stroke are at risk of early neurological deterioration (END). The present study aimed to evaluate the frequency and potential predictors of END in patients with medical management and LVO presenting with minor stroke. The relationship between SVS length and END was also investigated.

Methods

This was a prospective multicenter study. Consecutive patients were collected with anterior circulation. LVO presented with minor stroke [National Institutes of Health Stroke Scale (NIHSS) ≤ 4] within 24 h following onset. END was defined as a deterioration of NIHSS ≥4 within 24 h, without parenchymal hemorrhage. The length of the susceptibility vessel sign (SVS) was measured using the T2* gradient echo imaging.

Results

A total of 134 consecutive patients with anterior circulation LVO presenting with minor stroke were included. A total of 27 (20.15%) patients experienced END following admission. Patients with END exhibited longer SVS and higher baseline glucose levels compared with subjects lacking END (P < 0.05). ROC curve analysis indicated that the optimal cutoff point SVS length for END was SVS ≥ 9.45 mm. Multivariable analysis indicated that longer SVS [adjusted odds ratio (aOR), 2.03; 95% confidence interval (CI), 1.45–2.84; P < 0.001] and higher baseline glucose (aOR,1.02; 95% CI, 1.01–1.03; P = 0.009) levels were associated with increased risk of END. When SVS ≥ 9.45 mm was used in the multivariate logistic regression, SVS ≥ 9.45 mm (aOR, 5.41; 95%CI, 1.00–29.27; P = 0.001) and higher baseline glucose [aOR1.01; 95%CI, 1.00–1.03; P = 0.021] were associated with increased risk of END.

Conclusions

END was frequent in the minor stroke patients with large vessel occlusion, whereas longer SVS and higher baseline glucose were associated with increased risk of END. SVS ≥ 9.45 mm was a powerful independent predictor of END.
Universal versus selective screening for gestational diabetes mellitus among antenatal clinic attendees in Abakaliki: using the one-step 75 gram oral glucose tolerance test
Authors: Nwali Silas Alegu , Onoh Robinson Chukwudi , Dimejesi Ikechukwu Bo , Obi Vitus Okwuchukwu , Jombo Sunday Emmanuel , Edenya Oghenevwogaga Obukohwo
Published: October 2021

Aim

To compare universal screening with selective risk factor based screening for GDM, using the one-step 75 g oral glucose tolerance test (OGTT).

Materials and method

A cross-sectional, comparison between universal and selective risk factor based screening for GDM, among 400 antenatal care clients at Alex-Ekwueme Federal University Teaching Hospital Abakaliki (AE-FUTHA). All the participants had 75 g OGTT at 24–28 weeks of gestation and risk factor screening for GDM. All 400 participants formed the universal group while participants with one or more of the considered risk factors formed the selective risk factor group.

Data were analyzed using IBM SPSS version 20. Statistical comparison was done using t- test for continuous variables. Logistics regression was used to determine the level of associations of the independent predictors for hyperglycemia. Level of significance was set atP < 0.05.

Results

The point prevalence of GDM using universal and selective screening were 11.51 and 7.93% respectively, giving a selective screening miss rate of 31.11%. The sensitivity, specificity, positive predictive value and negative predictive value were 73.58, 48.82, 19.12 and 92.51% respectively for the selective risk factor based screening compared to universal screening.

On multivariate analysis; age ≥ 35 years, weight ≥ 90 kg, history of previous GDM and hypertension were significantly related to the development of hyperglycemia.

Conclusion

Selective risk factor based screening missed 31.11% of patients with GDM when compare to Universal screening with one step 75 g OGTT. Universal screening for GDM using the one step 75 g OGTT is recommended for pregnant women and more studies are needed to compare pregnancy outcomes for pregnant women diagnosed with GDM with and without risk factors.