bluuebunny/crossref_metadata_2025 huggingface dataset:
Awareness, anchor and adjustment factors in the use of institutional repositories by Nigerian lecturers
Authors: Bamigbola Alice A.
Published: January 2021

Institutional repositories have been established in universities globally because of their immense benefits to various stakeholders, especially lecturers. However, the literature has confirmed that institutional repositories are little used by lecturers. Previous studies have examined attitudes and disciplines, for example, but there seems to be no study on anchor and adjustment factors. This study therefore investigated awareness and anchor and adjustment factors as determinants of use of institutional repositories by lecturers in Nigeria. A descriptive survey and a purposive sampling technique were used to select universities that had had functional institutional repositories for at least four years at the time of data collection. A questionnaire was used to collect data from 857 lecturers. The study reveals that awareness and anchor and adjustment factors are determinants of use of institutional repositories by lecturers in Nigerian universities. The study recommends that more awareness programmes should be organized by libraries and that lecturers should constantly use computers to improve their computer self-efficacy and computer playfulness.
Who’s There? Characterizing Interaction in Virtual Classrooms
Authors: Willermark Sara
Published: January 2021

The Covid-19 crisis changed the educational landscape. In Sweden, as in many other countries, school leaders, teachers, and students faced a completely new situation, as teaching would immediately be conducted remotely. It offered an opportunity to continue teaching in a crisis, while giving rise to new questions and dilemmas. This study aims to explore aspects of interaction in the virtual classroom. The context is four high schools in Sweden. Data includes a teacher survey and ten workshops with teachers and school leaders. The interaction order framework is used as an analytic lens. The results draw a multifaceted picture of interaction that involves both increased and reduced contact with, and control over, the students and their activities. Some students find a place in the virtual classroom that they previously lacked, while others “disappear behind the screen.” Contributions include unpacking the complex role of interaction in the virtual classroom and providing implications for teachers and school leaders.
Calibration of thermopile heat flux gauges using a physically-based equation
Authors: Pountney Oliver J , Patinios Mario , Tang Hui , Luberti Dario , Sangan Carl M , Scobie James A , Owen J Michael , Lock Gary D
Published: January 2021

A thermopile, in which a number of thermocouple junctions are arranged on either side of a thin layer of insulation, is commonly used to determine the heat flux for steady-state measurements. Gauges using this method are available commercially and a new, generic calibration method is described here. For this purpose, an equation based on physical properties has been derived to determine the theoretical relationship between the measured voltage output of the gauge and the heat flux through it. An experimental rig has been built and used to calibrate gauges under steady-state conditions for heat fluxes between 0.5 and 8 kW/m2. The gauge temperature was controlled between 30 and 110 °C, and voltage-flux correlation – based on the theoretical relationship – was determined using maximum likelihood estimation (MLE). For tests with constant gauge temperature, there was a linear relationship between the voltage and heat flux; owing to the temperature dependency of the Seebeck constants of the thermoelectric materials, the voltage increased with increasing gauge temperature. In all cases, there was very good agreement between the measured and correlated values, and the overall uncertainty of the correlation was estimated to be less than 5% of the measured heat flux.
A ball head positioning method based on hybrid force-position control
Authors: Chu Wenmin , Huang Xiang , Li Shuanggao , Lou Peihuang
Published: January 2021

In the digital aircraft assembly system, the large component of aircraft is connected with the numerical control locator through a ball joint composed of a ball head and a ball socket. To ensure the posture adjustment accuracy of large component of aircraft, the clearance between the ball head and the ball socket is very small. Therefore, it is very difficult to accurately guide the ball head of large component of aircraft into the ball socket of the numerical control locator. Aiming at this problem, this article proposes a ball head positioning method based on hybrid force-position control, so that the ball socket can approach the ball head adaptively. First, according to the technical characteristics of the ball head positioning, the axes of the numerical control locator are divided into position control axis and force control axis, and the conditions to ensure the safety of ball head positioning are analyzed. Then the control model of ball head positioning based on hybrid force-position control is established and simulated by Simulink. Finally, a simulated posture adjustment system is built in the laboratory, and a series of ball head positioning experiments based on hybrid force-position control are carried out. The experimental results show that, compared with the traditional ball head positioning method, the ball head positioning process based on hybrid force-position control is more stable and faster, and the method can significantly reduce the lateral force. Moreover, the proposed method can be easily integrated into the existing posture adjustment system without additional hardware cost.
Trace fossils and palynomorphs in Holocene calcareous concretions from Lake Selbusjøen, Mid-Norway: Post-glacial environmental records
Authors: Smelror Morten , Knaust Dirk
Published: January 2021

Trace fossils and palynomorphs are recorded for the first time in Holocene calcareous concretions from Lake Selbusjøen, Central Norway. The described trace fossils can be assigned to the Mermia ichnofacies, characterizing lake deposits with good oxygenation and low depositional energy. The predominance of simple grazing trails and shallow burrows (e.g. Cochlichnus, Helminthoidichnites and Treptichnus) in silty and sandy concretions possibly represent relatively low-energy sublittoral parts of the lake, while the occurrence of Vagorichnus and Arenicolites in sandy substrate points to littoral and shallow sublittoral areas with moderate depositional energy. The trace fossils and palynomorph assemblages from Lake Selbusjøen appear to relate to periods of climatic warming during Pre-Boreal times, and possibly also Atlantic times.
Mechanical and thermomechanical properties of vinyl ester/polyurethane IPN based nano-composites
Authors: Ranjan Jagesh Kumar , Goswami Sudipta
Published: January 2021

Interpenetrating polymer networks of vinyl ester (VE) resin and polyurethane (PU) were synthesized using blend ratio of 93:7(w/w). Two sets of nanocomposites based on i) pure vinyl ester and ii)VE/PU IPN(93VE), were prepared with organically modified silica nanoparticle (OMS) as filler by 1, 2, 3 and 5% weight of the matrix resin. All the nanocomposites were characterized in terms of mechanical and thermomechanical properties.VE/silica nanocomposite with 2% filler (VES2) showed improvement in ultimate tensile strength by 83.5% and toughness by 42% compared to that of VE resin itself. The IPN based nanocomposite, 93VES2, exhibited 31.14%, 10.8% and 18%greater tensile strength, Young’s modulus and toughness respectively in comparison to that of the base 93VE IPN. IPN based nanocomposites were tougher than VE based nanocomposites. Storage modulus of nanocomposites was lower than that of 93VE and VE matrix system. Higher tanδmax of the 93VE/OMS nanocomposites than that of the 93VE matrix was indication of more elastic nature of the later. Smaller size of dispersed domains was found in SEM micrographs for IPN based nanocomposites than that in micrographs of VE based nanocomposites of corresponding composition.
Outpatient clinical pharmacy practice in the face of COVID-19 at a cancer center in New York City
Authors: Yerram Prakirthi , Thackray Jennifer , Modelevsky Lisa R , Land Josiah D , Reiss Samantha N , Spatz Krisoula H , Levoir Andrea C , Pak Terry K , Dao Phuong H , Buege Michael J , Derespiris Lauren M , Lau Carmen , Orozco Jennifer S , Boparai Manpreet , Koranteng Lauren A , Reichert Kate E , Yan Shirley Q , Daukshus Nicole P , Mathew Sherry , Buie Larry W , Tizon Richard F , Freeswick Scott , Liu Dazhi , Harnicar Stephen
Published: January 2021

Purpose

With the rapid spread of COVID-19 in New York City since early March 2020, innovative measures were needed for clinical pharmacy specialists to provide direct clinical care safely to cancer patients. Allocating the workforce was necessary to meet the surging needs of the inpatient services due to the COVID-19 outbreak, which had the potential to compromise outpatient services. We present here our approach of restructuring clinical pharmacy services and providing direct patient care in outpatient clinics during the pandemic.

Data sources

We conducted a retrospective review of electronic clinical documentation involving clinical pharmacy specialist patient encounters in 9 outpatient clinics from March 1, 2020 to May 31, 2020. The analysis of the clinical pharmacy specialist interventions and the impact of the interventions was descriptive.

Data summary

As hospital services were modified to handle the surge due to COVID-19, select clinical pharmacy specialists were redeployed from the outpatient clinics or research blocks to COVID-19 inpatient teams. During these 3 months, clinical pharmacy specialists were involved in 2535 patient visits from 9 outpatient clinics and contributed a total of 4022 interventions, the majority of which utilized telemedicine. The interventions provided critical clinical pharmacy care during the pandemic and omitted 199 in-person visits for medical care.

Conclusion

The swift transition to telemedicine allowed the provision of direct clinical pharmacy services to patients with cancer during the COVID-19 pandemic.
Inulin gelled emulsion as a fat replacer and fiber carrier in healthier Bologna sausage
Authors: Paglarini Camila de Souza , Vidal Vitor Andre Silva , Ozaki Maristela Midori , Ribeiro Ana Paula Badan , Bernardinelli Oigres Daniel , Câmara Ana Karoline Ferreira Ignácio , Herrero Ana M , Ruiz-Capillas Claudia , Sabadini Edvaldo , Pollonio Marise Aparecida Rodrigues
Published: January 2021

The effects of gelled emulsions (GE) used as animal fat replacers in terms of the nutritional, technological, and sensory properties of Bologna sausages during 60 days of chilled storage have been studied. Samples with GE added exhibited a fat reduction of 31%. Sausages with GE had higher values of L* and lower values of a* compared to the control. Harder sausages were obtained by the addition of GE. Higher lipid oxidation rates were found with increasing amounts of GE in the reformulated products. In addition, the relaxation time was not affected by the reformulation. All samples were deemed acceptable by consumer tests. However, CATA (Check-all-that-apply) tests showed that Bolognas formulated with partial or total pork fat replaced with GE were described as rubbery, not very spicy and firm, appeared to be dry and opaque, and had an aftertaste. Chilled storage significantly affected the Thiobarbituric Acid Reactive Substances (TBARS) values and slightly affected the pH values, texture, color, and NMR data. An important result is that the panelists did not detect the oxidation results in relation to the TBARS values, and the addition of a GE with inulin as dietary fiber may be a good strategy to make Bologna sausage healthier.
The effectiveness of internet-based telerehabilitation among patients after total joint arthroplasty: A systematic review and meta-analysis of randomised controlled trials
Authors: Wang Qingling , Lee Regina L-T , Hunter Sharyn , Chan Sally W-C
Published: January 2021

Introduction

The aim of this review was to systematically evaluate the available evidence on the effectiveness of internet-based telerehabilitation among patients after total joint arthroplasty regarding pain, range of motion, physical function, health-related quality of life, satisfaction, and psychological well-being.

Methods

This was a systematic review with meta-analysis based on the Cochrane Handbook for Systematic Reviews of Interventions guidelines. Studies published in English or Chinese were searched using defined search periods, databases, and search terms. Two reviewers assessed independently the quality of studies. RevMan 5.3 was used for meta-analysis. Heterogeneity was assessed using the χ2 and I2 statistic. A random effect model and mean difference (MD) with 95% confidence interval (CI) was adopted. Standardised mean difference (SMD) was used if the outcome was measured by different scales.

Results

Eleven studies with 1020 participants were analysed. Compared to face-to-face rehabilitation, internet-based telerehabilitation showed no significant difference in outcomes of pain (SMD–0.11, 95% CI–0.32 to 0.10), range of motion in flexion (MD 0.65, 95% CI–1.18 to 2.48) and extension (MD–0.38, 95% CI–1.16 to 0.40), patient-reported physical function (SMD 0.01, 95% CI–0.15 to 0.17), health-related quality of life (SMD–0.09, 95% CI–0.26 to 0.07), satisfaction (SMD–0.04, 95% CI–0.21 to 0.14), and psychological well-being (SMD 0.10, 95% CI–0.13 to 0.33). Internet-based telerehabilitation showed better outcomes in physical functional tests (SMD–0.54, 95% CI–1.08 to–0.01).

Discussion

This review suggests that internet-based telerehabilitation has comparable effectiveness to face-to-face rehabilitation on rehabilitation outcomes among patients after total joint arthroplasty.
Consistent co-rotational framework for Euler-Bernoulli and Timoshenko beam-column elements under distributed member loads
Authors: Tang Yi-Qun , Chen Wen-Feng , Liu Yao-Peng , Chan Siu-Lai
Published: January 2021

Conventional co-rotational formulations for geometrically nonlinear analysis are based on the assumption that the finite element is only subjected to nodal loads and as a result, they are not accurate for the elements under distributed member loads. The magnitude and direction of member loads are treated as constant in the global coordinate system, but they are essentially varying in the local coordinate system for the element undergoing a large rigid body rotation, leading to the change of nodal moments at element ends. Thus, there is a need to improve the co-rotational formulations to allow for the effect. This paper proposes a new consistent co-rotational formulation for both Euler-Bernoulli and Timoshenko two-dimensional beam-column elements subjected to distributed member loads. It is found that the equivalent nodal moments are affected by the element geometric change and consequently contribute to a part of geometric stiffness matrix. From this study, the results of both eigenvalue buckling and second-order direct analyses will be significantly improved. Several examples are used to verify the proposed formulation with comparison of the traditional method, which demonstrate the accuracy and reliability of the proposed method in buckling analysis of frame structures under distributed member loads using a single element per member.
An analytical model of diesel injector’s needle valve eccentric motion
Authors: Wang Chuqiao , Adams Moro , Jin Tianyu , sun Yu , Röll Andreas , Luo Fuqiang , Gavaises Manolis
Published: January 2021

Past experimental studies have shown that the needle valve of high-pressure diesel injectors undergoes lateral movement and deformation, while the continuous increase in injection pressure enlarges the gap of the needle valve assembly. Two different analytical models, considering or omitting this change are presented here, linking the geometries of the needle valve assembly with the magnitude of needle valve tip lateral movement. It is found that the physical dimensions of the needle valve assembly and the injection pressure have a significant impact on the radial displacement of the needle. For example, for nominal clearances between the needle guidance and the needle valve of about 1–3 μm, the magnitude of the radial movement of the needle tip could reach tens of microns. The model that takes into account the variation of the gap between the needle guide and needle valve is found to give predictions closer to the experimental results.
Lymph Node Ratio Rather Than Positive Lymph Node Counts Has Better Prognostic Value in Patients With Testicular Germ Cell Tumors
Authors: Huang Chuyang , Long Qian , Pan Yangxun , Wu Leilei , Wang Xiaonan , Xu Hailin , Zheng Fufu
Published: January 2021

Background:

Testicular cancer represents the most common malignancy in young adult men. In the current study, we sought to analyze and compare the prognostic value of lymph node ratio (LNR) as well as positive lymph node counts (LNC) to understand its clinical significance in testicular germ cell tumors.

Methods:

We employed eligibility criteria to recruit a total of 931 patients, with testicular cancer, from 2010 to 2015 from The Surveillance, Epidemiology, and End Results (SEER) database. We then used the X-Tile program to calculate LNR and LNC cutoff values and discriminate survival. We then calculated the overall and cancer specific survival rates and analyzed the association between LNR/LNC and clinical pathological characteristics using the χ2 test. Finally, we assessed the relationships between clinical pathological factors and patient survival using univariate Cox proportional hazard analysis.

Results:

Univariate analysis revealed a significant association between prognosis with age (HR, 5.169; 95% CI, 1.758-15.200; P = 0.003), AJCC stage (III vs I: HR, 9.298; 95% CI, 2.691-32.131; P < 0.001), M stage (HR, 7.897; 95% CI, 3.417-18.251; P < 0.001) and LNR (HR, 3.009; 95% CI, 1.275-7.098; P = 0.012). On the other hand, LNC (HR, 1.743; 95% CI, 0.687-4.420; P = 0.242) was not significantly associated with prognosis. Analysis of the association between LNR/LNC and clinical pathological characteristics showed that high LNR patients tended to have significantly larger tumor sizes (χ2 = 7.877, P = 0.005), as well as advanced T (χ2 = 13.195, P = 0.004), N ( χ2 = 86.775, P < 0.001), M (χ2 = 19.948, P < 0.001) and 7th AJCC (χ2 = 103.074, P < 0.001) stages. In addition, high LNC patients were significantly associated with T (χ2 = 8.799, P = 0.032), N (χ2 = 74.390, P < 0.001) and 7th AJCC (χ2 = 111.759, P < 0.001) stages.

Conclusion:

LNR was a better predictor for long-term prognosis and was closely associated with clinical pathological characteristics than LNC in patients with testicular germ cell tumors.
Frequency and Significance of Maneuvers to Dissect the Distal Internal Carotid Artery During Carotid Endarterectomy
Authors: Kakkos Stavros K. , Papageorgopoulou Chrysanthi P. , Papadoulas Spyros , Nikolakopoulos Konstantinos M. , Kouri Anastasia , Salmas Marios , Siampalioti Athina , Zotou Anastasia , Ellul John , Tsolakis Ioannis
Published: January 2021

Objectives:

To describe the frequency, factors associated with, and significance of surgical dissection maneuvers of the distal internal carotid artery (ICA) during carotid endarterectomy (CEA).

Methods:

In this retrospective analysis of prospectively collected information in patients undergoing CEA, we recorded information on demographics, risk factors and comorbidities, dissection maneuvers of the distal ICA, other operative variables and neurological outcome measures.

Results:

During the period July 2008 and February 2020 inclusive, 218 consecutive patients (180 males, median age 69.5 years) underwent 240 CEAs. In 117 (48.8%) of them, CEA was performed for a symptomatic stenosis. Dissection maneuvers of the distal ICA were required in 77 cases (32.1%), including division and ligation of the sternocleidomastoid vessels in 66 cases (27.5%), mobilization of the XII cranial nerve in 69 cases (28.7%, with concomitant transection of the superior root of the ansa cervicalis in 11 cases, 4.6%) and division of the posterior belly of the digastric muscle in 8 cases (3.3%). Styloid osteotomy was not required in any case. Smoking was the single predictive factor associated with the use of an adjunctive dissection maneuver (odds ratio 2.23, p = 0.009). The use of a patch was more common in smokers (16% vs 7.1% in non-smokers, odds ratio 2.48, p = 0.05). Perioperative stroke and/or death rate was 0%, not allowing testing for associations with maneuver performance. Two patients (0.8%) developed a transient ischemic attack and 4 patients (1.7%) a cranial nerve injury (CNI), including 2 patients with recurrent laryngeal nerve palsy, diagnosed on routine laryngoscopy during planning of a contralateral CEA. There was no association between CNI and dissection of the distal ICA using an operative adjunct (p = 0.60).

Conclusions:

Several surgical maneuvers are often required to accomplish dissection of the distal ICA beyond the point of atherosclerotic disease. When dictated by operative findings, such maneuvers are deemed safe.
Ultrasound Evaluation of Endo-AVF Using a Dialysis Access Clamp
Authors: Karbo Jenna R. , Eidt John F. , Hohmann Stephen E.
Published: January 2021

Percutaneous endovascular arteriovenous fistula (Endo-AVF) is a minimally invasive alternative to conventional surgical dialysis access. Endo-AVF may represent a significant advance in the creation of dialysis access but may require a variety of additional procedures to achieve adequate flow. To maximize flow through the cephalic vein, usually the preferred vessel, it may be necessary to permanently occlude competing outflow branches such as the brachial or basilic vein. Ultrasound monitoring of cephalic vein flow in the vascular lab can be used to predict the efficacy of basilic vein ligation but requires 2 operators to perform. We developed a simple technique to temporarily obstruct basilic vein outflow using a standard dialysis clamp that can be performed by a single vascular technologist. With the patient in the supine position, the spring-loaded dialysis clamp is positioned over the basilic vein in the upper arm using ultrasound guidance. The clamp applies mild, painless obstruction of the basilic vein without interfering with arterial inflow or cephalic vein outflow. Cephalic vein peak systolic velocity, intraluminal diameter, and flow volume are recorded. This technique was used in 6 patients, 4 to 6 weeks, following the initial Endo-AVF procedure. Ultrasound surveillance confirmed that the basilic vein outflow was effectively occluded in all 6 cases. The same ultrasound machine was used in all 6 studies. Cephalic vein flow increased significantly in each case (pre-clamp cephalic flow volume 301 ± 66.8 mL/min vs post-clamp 702 ± 156.5 mL/min after, P = 1.0). Ultrasound observation of the basilic vein post-clamp application concluded there were no complications related to the use of the dialysis clamp. The average duration of the procedure was less than 20 minutes. We have successfully developed a simple non-invasive technique to predict the effect of basilic vein occlusion on cephalic vein flow that can be accomplished by a sole vascular technologist. This technique can be used to guide the need for embolization of the basilic vein.
Management of esophageal strictures after endoscopic resection for early neoplasia
Authors: Abou Ali Einas , Belle Arthur , Hallit Rachel , Terris Benoit , Beuvon Frédéric , Leconte Mahaut , Dohan Anthony , Leblanc Sarah , Dermine Solène , Palmieri Lola-Jade , Coriat Romain , Chaussade Stanislas , Barret Maximilien
Published: January 2021

Background:

Endoscopic resection of extensive esophageal neoplastic lesions is associated with a high rate of esophageal stricture. Most studies have focused on the risk factors for post-endoscopic esophageal stricture, but data on the therapeutic management of these strictures are scarce. Our aim is to describe the management of esophageal strictures following endoscopic resection for early esophageal neoplasia.

Methods:

We included all patients with an endoscopic resection for early esophageal neoplasia followed by endoscopic dilatation at a tertiary referral center. We recorded the demographic, endoscopic, and histological characteristics, and the outcomes of the treatment of the strictures.

Results:

Between January 2010 and December 2019, we performed 166 endoscopic mucosal resections and 261 endoscopic submucosal dissections for early esophageal neoplasia, and 34 (8.0%) patients developed an esophageal stricture requiring endoscopic treatment. The indication for endoscopic resection was Barrett’s neoplasia in 15/34 (44.1%) cases and squamous cell neoplasia (SCN) in 19/34 (55.9%) cases. The median [(interquartile range) (IQR)] number of endoscopic dilatations was 2.5 (2.0–4.0). Nine of 34 (26.5%) patients required only one dilatation, and 22/34 (65%) had complete dysphagia relief following three endoscopic treatment sessions. The median number of dilatations was significantly higher for SCN [3.0 (2–7); range 1–17; p = 0.02], and in the case of circumferential resection [4.0 (3.0–7.0); p = 0.03]. Endoscopic dilatation allowed a sustained dysphagia relief in 33/34 (97.0%) patients after a mean follow-up of 25.3 ± 22 months.

Conclusion:

Refractory post-endoscopic esophageal stricture is a rare event. After a median of 2.5 endoscopic dilatations, 97.0% of patients were permanently relieved of dysphagia. Circumferential endoscopic esophageal resections should be considered when indicated.
From Save The Crew to Saved The Crew: Constitutive Rhetoric, Myth, and Fan Opposition to Sports Team Relocation
Authors: Andon Stephen P.
Published: January 2021

Sports franchise relocation is a hallmark of the American sports landscape. Teams relocate at their owners’ whims, leaving fans with little more to do than voice their angst. When the Columbus Crew of Major League Soccer announced in 2017 that ownership was set to move the team to Austin, a group of the Crew’s most ardent supporters initially seemed resigned to the franchise’s predetermined fate. However, over the course of months, those fans embarked on a grass roots campaign that generated attention worldwide and, ultimately, convinced a new ownership group to purchase the team and keep it in Columbus. This paper analyzes the efforts of these supporters through the lens of constitutive rhetoric, an ideologically-based concept that can galvanize disparate communities, shift their collective perspective, and set them on a course for action. In using this approach, the Save The Crew movement used myth to deploy a unique rhetorical power that successfully opposed the powerful capitalist logic of team relocation.
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms
Authors: Shaw Dipan , Chen Hao , Xie Minzhu , Jiang Tao
Published: January 2021

Background

Long non-coding RNAs (lncRNAs) regulate diverse biological processes via interactions with proteins. Since the experimental methods to identify these interactions are expensive and time-consuming, many computational methods have been proposed. Although these computational methods have achieved promising prediction performance, they neglect the fact that a gene may encode multiple protein isoforms and different isoforms of the same gene may interact differently with the same lncRNA.

Results

In this study, we propose a novel method, DeepLPI, for predicting the interactions between lncRNAs and protein isoforms. Our method uses sequence and structure data to extract intrinsic features and expression data to extract topological features. To combine these different data, we adopt a hybrid framework by integrating a multimodal deep learning neural network and a conditional random field. To overcome the lack of known interactions between lncRNAs and protein isoforms, we apply a multiple instance learning (MIL) approach. In our experiment concerning the human lncRNA-protein interactions in the NPInter v3.0 database, DeepLPI improved the prediction performance by 4.7% in term of AUC and 5.9% in term of AUPRC over the state-of-the-art methods. Our further correlation analyses between interactive lncRNAs and protein isoforms also illustrated that their co-expression information helped predict the interactions. Finally, we give some examples where DeepLPI was able to outperform the other methods in predicting mouse lncRNA-protein interactions and novel human lncRNA-protein interactions.

Conclusion

Our results demonstrated that the use of isoforms and MIL contributed significantly to the improvement of performance in predicting lncRNA and protein interactions. We believe that such an approach would find more applications in predicting other functional roles of RNAs and proteins.
MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning
Authors: Dhungel Eliza , Mreyoud Yassin , Gwak Ho-Jin , Rajeh Ahmad , Rho Mina , Ahn Tae-Hyuk
Published: January 2021

Background

Diverse microbiome communities drive biogeochemical processes and evolution of animals in their ecosystems. Many microbiome projects have demonstrated the power of using metagenomics to understand the structures and factors influencing the function of the microbiomes in their environments. In order to characterize the effects from microbiome composition for human health, diseases, and even ecosystems, one must first understand the relationship of microbes and their environment in different samples. Running machine learning model with metagenomic sequencing data is encouraged for this purpose, but it is not an easy task to make an appropriate machine learning model for all diverse metagenomic datasets.

Results

We introduce MegaR, an R Shiny package and web application, to build an unbiased machine learning model effortlessly with interactive visual analysis. The MegaR employs taxonomic profiles from either whole metagenome sequencing or 16S rRNA sequencing data to develop machine learning models and classify the samples into two or more categories. It provides various options for model fine tuning throughout the analysis pipeline such as data processing, multiple machine learning techniques, model validation, and unknown sample prediction that can be used to achieve the highest prediction accuracy possible for any given dataset while still maintaining a user-friendly experience.

Conclusions

Metagenomic sample classification and phenotype prediction is important particularly when it applies to a diagnostic method for identifying and predicting microbe-related human diseases. MegaR provides various interactive visualizations for user to build an accurate machine-learning model without difficulty. Unknown sample prediction with a properly trained model using MegaR will enhance researchers to identify the sample property in a fast turnaround time.
Correction to: Characterization of a vacuolar sucrose transporter, HbSUT5, from Hevea brasiliensis: involvement in latex production through regulation of intracellular sucrose transport in the bark and laticifers
Authors: Long Xiangyu , Li Heping , Yang Jianghua , Xin Lusheng , Fang Yongjun , He Bin , Huang Debao , Tang Chaorong
Published: January 2021

An amendment to this paper has been published and can be accessed via the original article.
Identification and molecular characterization of Subramaniula asteroides causing human fungal keratitis: a case report
Authors: Cultrera Rosario , Torelli Riccardo , Sarnicola Caterina , Segala Daniela , Mengoli Andrea , Chiaretto Giuseppina , Perri Paolo , Sanguinetti Maurizio
Published: January 2021

Background

Keratitis due to by filamentous fungi are not easy to diagnose thus causing a delay in correct therapy. There are many descriptions of keratitis due to Candida, Fusarium and Aspergillus genera. Subramaniula genus has only recently been reported to cause human infections and there are few descriptions of eye infections due to this filamentous fungus. Diagnosis of fungal keratitis is usually based on microscopic and cultural techniques of samples obtained by corneal swabbing or scraping. Considering the amount of time required to obtain culture results it is wise to use other diagnostic methods, such as molecular analyses. Therapeutic options against these fungi are limited by low tissue penetration in the eye due to ocular barriers. We describe the first case of S. asteroides human keratitis treated with isavuconazole.

Case presentation

We describe a rare case of fungal keratitis unresponsive to antimicrobial treatment in a 65-year-old male patient without a history of diabetes or immunological diseases. He reported that the onset of symptoms occurred during a long holiday in Cape Verde Island. Initial treatment with topical antibiotics associated to steroids were ineffective, allowing a slow clinical progression of disease to corneal perforation. On admission in our Hospital, slit-lamp examination of the left eye showed conjunctival congestion and hyperemia, a large inferior corneal ulceration with brown pigment, corneal edema, about 3 mm of hypopyon and irido-lenticular synechiae. The slow clinical progression of the disease to corneal perforation and the aspect of the ulcer were consistent with a mycotic etiology. Molecular methods used on fungal colonies isolated by Sabouraud’s dextrose agar cultures allowed the identification of Subramaniula asteroids from corneal scraping. Antimicrobial test showed a good susceptibility of this filamentous fungus to voriconazole and isavuconazole. Moreover, this fungal keratitis was successfully treated with isavuconazole, without side effects, observing a progressive clinical improvement.

Conclusions

Molecular methods may be useful for the identification of filamentous fungal keratitis on scraping samples thus shortening the time of diagnosis. Systemic therapy by isavuconazole could be useful to treat the filamentous fungal keratitis, reducing the possible adverse effects due to the use of voriconazole by systemic administration.
Dynamic changes in lymphocyte subsets and parallel cytokine levels in patients with severe and critical COVID-19
Authors: Liu Yangli , Tan Weiping , Chen Haihong , Zhu Ying , Wan Li , Jiang Ke , Guo Yubiao , Tang Kejing , Xie Canmao , Yi Hui , Kuang Yukun , Luo Yifeng
Published: January 2021

Background

The lack of knowledge regarding the pathogenesis and host immune response during SARS-CoV-2 infection has limited the development of effective treatments. Thus, we longitudinally investigated the dynamic changes in peripheral blood lymphocyte subsets and parallel changes in cytokine levels in COVID-19 patients with different disease severities to further address disease pathogenesis.

Methods

A total of 67 patients (10 moderate, 38 severe and 19 critical cases) with COVID-19 admitted to a tertiary care hospital in Wuhan from February 8th to April 6th, 2020 were retrospectively studied. Dynamic data of lymphocyte subsets and inflammatory cytokines were collected.

Results

On admission, compared with moderate cases, severe and critical cases showed significantly decreased levels of total lymphocytes, T lymphocytes, CD4+ T cells, CD8+ T cells, B cells and NK cells. IL-6 and IL-10 were significantly higher in the critical group. During the following hospitalization period, most of the lymphocyte subsets in the critical group began to recover to levels comparable to those in the severe group from the fourth week after illness onset, except for NK cells, which recovered after the sixth week. A sustained decrease in the lymphocyte subsets and an increase in IL-6 and IL-10 were observed in the nonsurvivors until death. There was a strong negative correlation between IL-6 and IL-10 and total lymphocytes, T lymphocytes, CD4+ T cells, CD8+ T cells and NK cells.

Conclusions

A sustained decrease in lymphocyte subsets, especially CD4+ T cells and NK cells, interacting with proinflammatory cytokine storms was associated with severe disease and poor prognosis in COVID-19.
A child with Imerslund-Gräsbeck syndrome concealed by co‐existing α-thalassaemia presenting with subacute combined degeneration of the spinal cord: a case report
Authors: Arunath Visvalingam , Hoole Thabitha Jebaseeli , Rathnasri Asanka , Muthukumarana Oshanie , Kumarasiri Ishara Minuri , Liyanage Nishadi Dananjani , Costa Yasintha , Mettananda Sachith
Published: January 2021

Background

Imerslund-Gräsbeck syndrome is a rare genetic disease characterised by vitamin B12deficiency and proteinuria.

Case presentation

A 4-year old Sri Lankan boy presented with gradually worsening difficulty in walking for two weeks duration. He was previously diagnosed and managed as having non-transfusion-dependent α-thalassaemia based on the presence of hypochromic microcytic anaemia, haemoglobin H inclusion bodies in the blood film and compound heterozygous α-thalassaemia genotype with a gene deletion. However, his transfusion requirement increased over the past three months and he gradually lost his motor developmental milestones during two weeks before admission. The neurological examination revealed generalised hypotonia, exaggerated knee jerks and extensor plantar response. His complete blood count showed pancytopenia, and bone marrow biopsy revealed megaloblastic changes. Serum vitamin B12and red blood cell folate levels were low. MRI revealed sub-acute combined degeneration of the spinal cord with characteristic ‘inverted V sign’. Urine analysis showed non-nephrotic range proteinuria. The diagnosis of Imerslund-Gräsbeck syndrome was made due to the presence of non-nutritional vitamin B12deficiency and asymptomatic proteinuria. He showed a rapid haematological and neurological improvement to intramuscular hydroxocobalamin.

Conclusions

This case report presents a rare occurrence of severe vitamin B12deficiency due to Imerslund-Gräsbeck syndrome masked by co-existent α-thalassaemia, resulting in serious consequences. It highlights the need for a high index of suspicion in evaluating children with severe anaemia, especially in the presence of mixed pathologies.
Unprecedented tibial bone lengthening of 33.5 cm by distraction osteogenesis for the reconstruction of a subtotal tibial bone defect. A case report and literature review
Authors: Ali Abdulnassir , Ren Ying , Zhou Chun-Hao , Fang Jia , Qin Cheng-He
Published: January 2021

Background

We present a case of an immense unprecedented tibial bone lengthening of 33.5 cm. The management of chronic osteomyelitis of the right tibia with subtotal tibial bone defect, talus defect and equinus ankle deformity. We demonstrate limb reconstruction by distraction osteogenesis and correction of ankle deformity with the Ilizarov technique. Limb salvage was preferred as an alternative to amputation to restore basic limb function.

Case presentation

A 16-year-old male patient fell and injured his right lower leg. He attempted to treat the symptoms with traditional home remedies. During 15 months of self-treating, he developed osteomyelitis of the right tibia and had lost function in his foot. Radiology revealed immense bone defect of the right tibia, including talus bone defect and equinus deformity of the calcaneus. The patient’s right tibia was non weight-bearing, had drainage sinus just below his knee and a large scar anteriorly along the entire length of the tibia.

Conclusion

Upon completion of treatment, the patient was able to avoid amputation of his leg with partially restored function for weight-bearing. He carried himself without assistance after 3 years of lost function in his right leg. Tibial bone distraction osteogenesis of 33.5 cm was done after 90% of the tibial length was defected. To the best of our best knowledge, this case is one of a kind to achieve distraction of tibial bone to such length.
The effect of the sagittal plane osteotomy inclination on the posterior tibial slope in medial open wedge HTO: experimental study with a square column model
Authors: Moon Sang Won , Ryu Ji Young , Lee Sung-Jae , Woo Sang Won , Park Sin Hyung , Choi Young
Published: January 2021

Background

Medial open-wedge high tibial osteotomy (HTO) is an effective and safe treatment method for medial osteoarthritis of the knee. However, unintended changes in the posterior tibial slope (PTS) may occur. Several factors cause PTS alterations after medial open-wedge HTO; however, research on sagittal-plane osteotomy inclination (SPOI) in relation to the PTS is sparse. The purpose of this study was to evaluate whether the SPOI affects changes in the PTS after medial open-wedge HTO. The hypothesis was that an SPOI parallel to the PTS causes no change in the PTS after medial open-wedge HTO.

Methods

A square column model with a 10° posterior slope was produced using two three-dimensional (3D) programs and a 3D printer. Then, a series of medial open-wedge HTO procedures was performed on the square column model through virtual simulation using the two 3D programs, and an actual simulation was conducted using a 3D printer, a testing machine and a measurement system. The SPOI was divided into four types: ① SPOI 20° (posterior-inclined 10° osteotomy), ② SPOI 10° (osteotomy parallel to posterior slope), ③ SPOI 0° (anterior-inclined 10° osteotomy), and ④ SPOI − 10° (anterior-inclined 20° osteotomy). The correction angle was increased at intervals of 5° from 0° to 30°. The change in posterior slope was measured in the sagittal plane.

Results

The posterior slope was increased in SPOI 20° (posterior-inclined 10° osteotomy), maintained in SPOI 10° (osteotomy parallel to posterior slope), and decreased in SPOI 0° (anterior-inclined 10° osteotomy) and SPOI − 10° (anterior-inclined 20° osteotomy) based on the correction angle.

Conclusions

In this study using a square column model, the SPOI affected the change in the PTS, and an SPOI parallel to the PTS caused no change in the PTS after medial open-wedge HTO.
PCR-based genotyping assays to detect germline APC variant associated with hereditary gastrointestinal polyposis in Jack Russell terriers
Authors: Yoshizaki Kyoko , Hirata Akihiro , Matsushita Hiroyuki , Nishii Naohito , Kawabe Mifumi , Mori Takashi , Sakai Hiroki
Published: January 2021

Background

The prevalence of gastrointestinal (GI) neoplastic polyps in Jack Russell terriers (JRTs) has increased in Japan since the late 2000s. Recently, we demonstrated that JRTs with GI polyps harbor identical germline variant in the APC gene (c.[462_463delinsTT]) in the heterozygous state. Thus, this disease is an autosomal dominant hereditary disorder. Although the affected JRTs have distinct features, such as the development of multiple GI polyps and an early age of disease onset, genetic testing is indispensable for a definitive diagnosis. Here, polymerase chain reaction (PCR)-based assays capable of detecting germline APC variant were designed and validated using synthetic wild-type and mutant DNAs and genomic DNAs from carrier and non-carrier dogs.

Result

First, the PCR-restriction fragment length polymorphism (PCR-RFLP) assay was developed by taking advantage of the germline APC variant creating a new restriction site for MseI. In the PCR-RFLP assay, the 156-bp region containing the variant site was amplified by PCR and subsequently digested with MseI, yielding diagnostic 51 and 58 bp fragments from the mutant allele and allowing determination of the APC genotypes. It was possible to determine the genotypes using genomic DNA extracted from the peripheral blood, buccal swab, or formalin-fixed paraffin-embedded tissue. Next, a TaqMan duplex real-time PCR assay was developed, where a 78-bp region flanking the variant was amplified in the presence of wild-type allele- and mutant allele-specific fluorescent probes. Using blood-derived DNA, altogether 40 cycles of PCR amplification determined the APC genotypes of all examined samples by measuring the fluorescence intensities. Importantly, false-positive and false-negative errors were never detected in both assays.

Conclusion

In this study, we developed highly reliable genetic tests for hereditary GI polyposis in JRTs, providing accurate assessment of the presence of the causative germline APC variant. The genotyping assays could contribute to the diagnosis and prevention of hereditary GI polyposis in dogs.
LRIG1 expression and colorectal cancer prognosis
Authors: Bakherad Maryam , Salimi Mahdieh , Angaji Seyed Abdolhamid , Mahjoubi Frouzandeh , Majidizadeh Tayebeh
Published: January 2021

Background

To make the right treatment decisions about colorectal cancer (CRC) patients reliable predictive and prognostic data are needed. However, in many cases this data is not enough. Some studies suggest that LRIG1 gene (leucine-rich repeats and immunoglobulin-like domains1) has prognostic implications in different kinds of cancers.

Methods

One hundred and two patients with colorectal cancer were retrospectively analyzed for LRIG1 expression at both mRNA and protein levels. SYBR Green Real-Time RT-PCR technique was used for mRNA expression analyses and Glyceraldehyde-3-Phosphate Dehydrogenase gene (GAPDH) was considered as a reference gene for data normalization. LRIG1 protein expression was analyzed using Immunohistochemistry. Additionally, appropriate statistic analyses were used to assess the expression of LRIG1 in test and control groups. The prognostic significance of LRIG1 expression was analyzed using the univariate and multivariate analyses.

Results

The data revealed that the expression of LRIG1 in both mRNA and protein levels was down regulated in colorectal tumor tissues (P < 0.01) but is not clinically relevant prognostic indicator in CRC.

Conclusions

Therefore, it is suggested that LRIG1 expression analyses may not be considered as an important issue when making informed and individualized clinical decisions regarding the management of colorectal cancer patients.
Hereditary leiomyomatosis and renal cell carcinoma: a case series and literature review
Authors: Chayed Zahraa , Kristensen Lone Krøldrup , Ousager Lilian Bomme , Rønlund Karina , Bygum Anette
Published: January 2021

Background

Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is a rare genodermatosis characterized by cutaneous leiomyoma (CLM), uterine leiomyoma (ULM) and renal cell carcinoma (RCC). Five HLRCC patients are presented with a compiled database of published HLRCC cases to increase understanding of HLRCC. Furthermore, a surveillance program is suggested. Our review is based on a PubMed search which retrieved case reports and cohort studies published before November 2019. The search yielded 97 original papers with a total of 672 HLRCC patients.

Results

CLMs were present in 474 patients (71.5%), developed at the mean age of 28 years. Five patients had cutaneous leiomyosarcomas. ULMs were present in 356 women (83%), while two had uterine leiomyosarcoma. ULMs were diagnosed at a mean age of 32 years, with the youngest diagnosed at age 17 years. The most common surgical treatment for ULMs was hysterectomy, performed at a mean age of 35 years, with the youngest patient being 19 years old. RCCs were present in 189 patients (34.9%), of which half had metastatic disease. The mean age of diagnosis was 36 years with the youngest patient diagnosed with RCC at the age of 11 years.

Conclusion

We suggest a surveillance program for HLRCC including a dermatological examination once every 2 years, annual magnetic resonance imaging starting at the age of 10 years to monitor for early RCCs, annual gynecological examinations from the age of 15 years and counseling regarding risk of hysterectomy and family planning at the age of 18 years. CLMs are often the earliest manifestation of HLRCC, which is why recognizing these lesions, performing a biopsy, and making a prompt referral to genetic counseling is important in order to diagnose HLRCC early.