bluuebunny/crossref_metadata_2025 huggingface dataset:
A facile and robust T7-promoter-based high-expression of heterologous proteins in Bacillus subtilis
Authors: Ye Jing , Li Yunjie , Bai Yuqing , Zhang Ting , Jiang Wei , Shi Ting , Wu Zijian , Zhang Yi-Heng P. Job
Published: May 2022

To mimic the Escherichia coli T7 protein expression system, we developed a facile T7 promoter-based protein expression system in an industrial microorganism Bacillus subtilis. This system has two parts: a new B. subtilis strain SCK22 and a plasmid pHT7. To construct strain SCK22, the T7 RNA polymerase gene was inserted into the chromosome, and several genes, such as two major protease genes, a spore generation-related gene, and a fermentation foam generation-related gene, were knocked out to facilitate good expression in high-density cell fermentation. The gene of a target protein can be subcloned into plasmid pHT7, where the gene of the target protein was under tight control of the T7 promoter with a ribosome binding site (RBS) sequence of B. subtilis (i.e., AAGGAGG). A few recombinant proteins (i.e., green fluorescent protein, α-glucan phosphorylase, inositol monophosphatase, phosphoglucomutase, and 4-α-glucanotransferase) were expressed with approximately 25–40% expression levels relative to the cellular total proteins estimated by SDS-PAGE by using B. subtilis SCK22/pHT7-derived plasmid. A fed-batch high-cell density fermentation was conducted in a 5-L fermenter, producing up to 4.78 g/L inositol monophosphatase. This expression system has a few advantageous features, such as, wide applicability for recombinant proteins, high protein expression level, easy genetic operation, high transformation efficiency, good genetic stability, and suitability for high-cell density fermentation.

Graphical Abstract
From formic acid to single-cell protein: genome-scale revealing the metabolic network of Paracoccus communis MA5
Authors: Tong Sheng , Zhao Lizhi , Zhu Daling , Chen Wuxi , Chen Limei , Li Demao
Published: May 2022

With the increase in population growth and environmental pollution, the daily protein supply is facing great challenges. Single-cell protein (SCP) produced by microorganism fermentation is a good alternative for substituting plant- and animal-derived proteins. In this study, Paracoccus communis MA5 isolated from soil previously demonstrated an excellent ability to synthesize SCP directly from sodium formate. To investigate the central metabolic network of formic acid assimilation and protein synthesis, genome-scale analyses were performed. Genomic analysis showed that complete tetrahydrofolate cycle-, serine cycle-, glycolytic pathway-, tricarboxylic acid (TCA) cycle- and nitrogen metabolism-relevant genes were annotated in the genome. These pathways play key roles in the conversion of formic acid into proteins. Transcriptional analysis showed that sodium formate stress could stimulate the metabolic pathway in response to environmental stress, but weaken the sulfur metabolic pathway to inhibit amino acid synthesis, resulting in a decrease in protein content (30% vs 44%). However, under culture conditions with ammonium sulfate, metabolic pathways associated with protein synthesis were accelerated, causing an increase in protein content (53% vs 44%); while the tetrahydrofolate cycle associated with formic acid assimilation was inhibited, causing a 62.5% decrease in growth rate (OD600: 0.21 vs 0.56). These results provide evidence of protein synthesis from sodium formate in strain MA5 at the gene level and lay a theoretical foundation for the optimization of fermentation systems using formic acid as a carbon source.

Graphical Abstract
A possible mechanism for spontaneous cyclic back-arc spreading
Authors: Ishii Kazuhiko , Wallis Simon R.
Published: May 2022

Back-arc spreading is a non-steady-state process exemplified by the repeated cycles of spreading of the South Fiji and the Lau Basins behind the Tonga arc, and the Parece Vela Basin and the Mariana Trough behind the Mariana arc. Spreading in these regions starts with rifting within the volcanic arc before shifting to the back-arc region where it develops into a phase of well-defined spreading. 2D thermo-mechanical subduction modeling incorporating phase transitions at depths of 410 km and 660 km suggests the presence of a low-viscosity and low-density mantle wedge is an important condition for arc rifting to occur. Back-arc spreading starts when a nearly vertical slab impinges upon the 660 km discontinuity causing downdip compressive stress that is transmitted up the slab resulting in extensional within-arc stress. Trench retreat during a phase of back-arc spreading causes a decrease in slab dip angle and buckling of the slab. Back-arc spreading ceases during this buckling phase. Rifting starts once more when the nearly vertically dipping ‘heel’ of the buckled slab again impinges upon the 660-km boundary. The second phase of rifting initially focuses within the arc but subsequently shifts to the back-arc region leading to renewed back-arc spreading. Our modeling predicts that subduction of thick (old age) and weak (small yield stress) slabs, which have intermediate resistance to slab bending, leads to cyclic back-arc spreading. In contrast, continuous back-arc spreading is predicted for thick and strong slabs with a large resistance to bending, and no back-arc spreading is predicted for slabs with a small resistance to bending (thin slabs). Geological processes such as toroidal mantle flow around the lateral edges of a slab, collisions with buoyant lithosphere and interactions with third plates may have important roles in the development of cyclic back-arc spreading in specific cases. However, the presence of a common timescale of ~ 20 Myr suggests there a general underlying control on back-arc basin formation that is common to many if not all subduction zones. The new model presented here can account for the main features of cyclic back-arc spreading seen in the Tonga-Kermadec and the Calabrian arcs.
“Nourish to Flourish”: complementary feeding for a healthy infant gut microbiome—a non-randomised pilot feasibility study
Authors: Lovell Amy L. , Eriksen Hannah , McKeen Starin , Mullaney Jane , Young Wayne , Fraser Karl , Altermann Eric , Gasser Olivier , Kussmann Martin , Roy Nicole C. , McNabb Warren C. , Wall Clare R.
Published: May 2022

Background

The introduction of complementary foods and changes in milk feeding result in modifications to gastrointestinal function. The interplay between indigestible carbohydrates, host physiology, and microbiome, and immune system development are areas of intense research relevant to early and later-life health.

Methods

This 6-month prospective non-randomised feasibility study was conducted in Auckland, New Zealand (NZ), in January 2018. Forty parents/caregivers and their infants were enrolled, with 30 infants allocated to receive a prebiotic NZ kūmara (flesh and skin; a type of sweet potato) prepared as a freeze-dried powder, and ten infants allocated to receive a commercially available probiotic control known to show relevant immune benefits (109 CFU Bifidobacterium lactis BB-12®). The primary outcome was the study feasibility measures which are reported here.

Results

Recruitment, participant retention, and data collection met feasibility targets. Some limitations to biological sample collection were encountered, with difficulties in obtaining sufficient plasma sample volumes for the proposed immune parameter analyses. Acceptability of the kūmara powder was met with no reported adverse events.

Conclusion

This study indicates that recruiting infants before introducing complementary foods is feasible, with acceptable adherence to the food-based intervention. These results will inform the protocol of a full-scale randomised controlled trial (RCT) with adjustments to the collection of biological samples to examine the effect of a prebiotic food on the prevalence of respiratory tract infections during infancy.

Trial registration

Australia New Zealand Clinical Trials Registry ACTRN12618000157279. Prospectively registered on 02/01/2018.
Raynaud’s phenomenon and positive antinuclear antibodies as first manifestation of POEMS syndrome (polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin changes): a case report
Authors: Torres-Saavedra Fabio , León-Sierra Lina
Published: May 2022

Background

POEMS syndrome is a rare paraneoplastic syndrome caused by plasma cell disorder almost always lambda restricted. Secondary Raynaud’s phenomenon is an overlooked skin manifestation of the disease even though it is present in twenty percent of patients. On POEMS syndrome have not been described positive antinuclear antibodies (ANA) and this could lead to a misdiagnosis of autoimmune disease, mainly systemic sclerosis.

Case presentation

A 47-year-old man presented with color changes on fingertips consistent with biphasic Raynaud’s phenomenon; an antinuclear antibody test was positive (at 1:320 titers in a speckled pattern) with normal nailfold capillaroscopy. Clinical features of systemic sclerosis were absent. Twenty-four months later, the patient presented symmetric sensorimotor demyelinating polyneuropathy, and he was diagnosed with Guillain–Barre syndrome; treatment with intravenous gammaglobulin had an incomplete response. Raynaud’s phenomenon persisted associated with acrocyanosis, white nails, and positive ANA (1:1280 in a nucleolar pattern). POEMS syndrome was suspected, and serum protein electrophoresis (SPEP) was done. The SPEP revealed polyclonal gammopathy, and serum immunofixation showed monoclonal (M)-protein (IgG lambda). Serum vascular endothelial growth factor concentration showed increased levels. The patient was diagnosed with POEMS syndrome, and treatment with lenalidomide and dexamethasone improved the Raynaud’s phenomenon, acrocyanosis, and white nails, but the neurological response was partial.

Conclusions

POEMS syndrome may mimic clinical manifestations of systemic sclerosis v.g. Raynaud’s phenomenon, skin thickening, telangiectasia, and positive ANA. Raynaud’s phenomenon may precede other clinical manifestations of POEMS syndrome by several months. It is necessary to have a high index of suspicion for the diagnosis, especially in patients with peripheral polyneuropathy and monoclonal paraprotein. The significance of positive ANA in this condition is unknown and deserves further investigation.
How and why adults use cannabis during physical activity
Authors: Ogle Whitney L. , Gold Gregg J. , Coppen Lukas E. , Copriviza Claire
Published: May 2022

Background

With increased legalization of cannabis, users are combining cannabis with exercise. The purpose of this study is to understand how and why people use cannabis when participating in physical activity.

Methods

A convenience sample of cannabis users participated in an anonymous online survey created by the authors regarding exercise habits while under the influence of cannabis, perceived benefits, unanticipated experiences related to cannabis and exercise, and demographics.

Results

One hundred thirty-one respondents (18–55 years) were eligible and began the survey. Nearly 60 physical activities under the influence of cannabis were reported. The most frequently reported modes of exercise included hiking (60%), yoga (58%), and aerobic machines (50%). The primary reasons for using cannabis before exercise were “helping to focus/concentrate” (66%), “helping enjoy the exercise experience” (65%), and “enhancing mind-body-spirit connection” (65%). Thirty-three participants reported “yes” or “maybe” regarding having an experience they “didn’t anticipate or desire while exercising under the influence of cannabis.”

Discussion

Participants’ reasons for exercising with cannabis span the physiological, psychological, neuromotor, and even spiritual domains. However, some reported an undesired experience when pairing cannabis with exercise. While this was an online survey with a small sample size, our results agree with and contribute to the growing research investigating cannabis use and physical activity participation.

Conclusion

We found considerable heterogeneity in types of physical activity participation under the influence of cannabis, as well as perceived benefits of use. This study provides directions to further explore the risks and benefits of combining cannabis with physical activity.
Traditional fermented foods and beverages in Iraq and their potential for large-scale commercialization
Authors: Muhialdin Belal J. , Filimonau Viachaslau , Qasem Jamal M. , Ibrahim Salam A. , Algboory Hussein L.
Published: May 2022

The tradition of making fermented foods and beverages in Iraq dates back to 7500 BC. These fermented foods and beverages are represented by meat-, milk-, vegetable-, and fruit-based products reflecting diversity of agricultural production in ancient Iraq (Mesopotamia). Although the recipes for some fermented foods and beverages were lost throughout history, those remaining foods and beverages occupy a noticeable position in modern Iraqi cuisine. In this review, knowledge and techniques for preparation of 5 traditional fermented foods, i.e. Basturma, Smoked Liban,Aushari cheese, Turshi, and Sour Khobz, and 3 fermented beverages, i.e. Shanina, Sharbet Zbeeb, and Erk Sous in Iraq, are documented. Traditional fermented foods and beverages have multiple health benefits because of high content of probiotics and bioactive compounds. Traditional fermented foods and beverages are made using the back-slopping technique which ensures safety of production and maintains organoleptic properties. The review highlights the potential of fermented foods and beverages for their large-scale commercialization.
Preparation and characterization of polymyxin B- and histidine-coupled magnetic nanoparticles for purification of biologics from acquired endotoxin contamination
Authors: Salah Al-Shaimaa M. , Hassan Lamiaa A. , Fathallaa Faten , Al-Ghobashy Medhat A. , Nebsen Marianne
Published: May 2022

Background

Endotoxin is a major process-related impurity that can act as a strong immunostimulant leading to fever and hypotensive shock. Thus, the US FDA and international quality standards strictly direct the biologics manufacturers to control the endotoxin contamination during the purification process. In this work, a developed method for biologics purification from acquired endotoxin contamination is introduced. This is accomplished by the preparation of dextran-coated magnetic nanoparticles using a facile rapid co-precipitation method.

Results

The resulting magnetic nanoparticles (MNPs) are characterized by dynamic light scattering, transmission electron microscope, Fourier transform infrared spectroscopy, X-ray diffraction, and vibrating sample magnetometry. The dextran-coated magnetic nanoparticles are further coupled to either polymyxin B or histidine to provide a positively charged ligand which enhances the affinity to the negatively charged endotoxin. Both ligands-coupled MNPs are tested for purification efficiency using the chromogenic kinetic assay. The method conditions are optimized using a two-level factorial design to achieve best purification conditions of the contaminated biologics and indicated endotoxin removal percentage 85.12% and maximum adsorption capacity of 38.5 mg/g, for histidine-coupled MNPs.

Conclusions

This developed method is introduced to serve biologics manufacturers to improve their manufacturing processes through providing a simple purifying tool for biologics from acquired endotoxin contamination.

Graphical Abstract
Intercostobrachial neuralgia—a case of bizzare diagnosis?
Authors: Singh Tejinder , Kumar Parijat
Published: May 2022

Background

Intercostobrachial neuralgia is a rare and bizarre diagnosis usually missed by many clinicians. The rare occurrence and absence of clear diagnostic criteria could be a result of this missed diagnosis. The symptoms could range from debilitating pain in the axilla, medial arm, and forearm at rest and with specific shoulder movements. The symptoms are very distinct from axillary web syndrome in which the patient could have thickening of subcutaneous tissue of axilla with affected shoulder mobility but absence of neural symptoms. The diagnostic and treatment procedure involving breast cancer may cause injury or lesion of the intercostobrachial nerve and is of particular interest to the surgeons, pain physicians, and physical therapists. The diagnosis is reached after excluding all the other possible diagnoses. The treatment of this post-surgical intercostobrachial neuralgia can range from cryoneurolysis, ultrasound-guided nerve block, steroid injection, and paravertebral nerve block. Lidocaine injection and avoiding certain positions like flexion and abduction are helpful in certain patients. Unfortunately, there is not much literature available on possible manual therapy treatments of this diagnosis. Therefore, this case report focuses on potential manual therapies to address this intricate diagnosis.

Case presentation

The patient is a 38-year-old Asian female reported to an outpatient orthopedic physical therapy clinic with left medial arm and forearm pain for the past 5 years. Medical history included left breast lump removal surgery 9 years ago and cervical laminectomy C6–C7 with little success. The quick disability arm and hand scale showed a 36% disability score of function. The manual therapy approach targeted the cervicothoracic junction, second and third costovertebral joint, thoracic spine (T1–T8), and atlantooccipital joint (C0–C1). The patient showed significant improvement in function with a DASH score falling to 0% disability with a hands-on approach.

Conclusion

The intercostobrachial neuralgia is usually undiagnosed by various practitioners, physicians, and surgeons. The clinicians must consider manual treatments to the second and third rib and soft tissue mobilizations around the axillary region. The patient demonstrated significant improvement in symptoms with this approach.
Useful on-site macroscopic quantitative evaluation of EBUS-TBNA samples
Authors: Matias Maria Inês , Caldeira João Nunes , Matos Paulo , de Santis Michele , Fonseca Ana Luísa , Barradas Lurdes
Published: May 2022

Background

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive diagnostic test with a high diagnostic yield. Optimal specimen acquisition is of a key importance; however, rapid on-site cytology examination (ROSE) during EBUS-TBNA has limited access. In an attempt to provide immediate feedback to the operator, the intervention pulmonology team started to classify macroscopically every lymph node sample in terms of abundance. The main objective of this study was to clarify whether this on-site macroscopic evaluation of EBUS sample was related to histology results and therefore any helpful for clinical practice.

Results

From a total of 288 lymph node stations sampled, adequate/diagnostic histological results were present in 11.1% of “insufficient” samples, 40.9% “sufficient” samples, 76.4% “good” samples and 88.1% of “excellent” samples. This was statistically significant with p-value under 0.0001. Also, there was a statistical agreement between samples that were macroscopically “insufficient” or “sufficient” with “inadequate” and “dubious” histological results and also between macroscopically “good” and “excellent” samples and histological results that were adequate/diagnostic. And that statistical agreement was of moderate magnitude according to the “Landis and Koch” classification (k = 0.386).

Conclusions

The positive relationship between the on-site macroscopic evaluation of the EBUS sample as “excellent” and the “adequate/diagnostic” histological result is of high clinical importance since it represents a fast, cheap and easy method that provides immediate feedback to the operator influencing his conduct; by obtaining additional passes to achieve an “excellent” will ensure a higher percentage of samples with a diagnosis, accelerating the patients treatment.
Phase II Study of Lorlatinib in Patients With Anaplastic Lymphoma Kinase–Positive Lung Cancer and CNS-Specific Relapse
Authors: Dagogo-Jack Ibiayi , Oxnard Geoffrey R. , Evangelist Makenzi , Digumarthy Subba R. , Lin Jessica J. , Gainor Justin F. , Murphy John F. , Rabin Michael S. , Heist Rebecca S. , Muzikansky Alona , Shaw Alice T.
Published: May 2022

PURPOSE

The CNS is a recurrent site of progression in anaplastic lymphoma kinase (ALK)–rearranged (ALK+) lung cancer. Lorlatinib is a third-generation ALK inhibitor developed to penetrate the CNS and overcome ALK resistance mutations. We conducted a phase II study to evaluate the intracranial activity of lorlatinib in patients with CNS-only progression on second-generation ALK inhibitors.

METHODS

Patients with ALK+ lung cancer who had intracranial progression on ≥ 1 ALK inhibitor without measurable extracranial disease received lorlatinib 100 mg once daily. The primary end point was intracranial disease control rate at 12 weeks per modified RECIST v1.1. Secondary end points included intracranial progression-free survival, intracranial objective response rate, and safety/tolerability.

RESULTS

Twenty-three patients were enrolled between November 2016 and January 2019. Fifteen (65%) patients had irradiated CNS metastases, with a median of 20.2 months between radiation and lorlatinib. Control of intracranial disease was observed in 21 (95%) evaluable patients at 12 weeks. The intracranial objective response rate was 59% with six complete and seven partial responses. The median intracranial progression-free survival was 24.6 months (95% CI, 20.2 to not reached). With a median follow-up of 16.8 months, nine patients developed disease progression, including four patients with CNS progression. The most common treatment-related adverse events were hypercholesterolemia (96%), hypertriglyceridemia (87%), edema (65%), cognitive effects (52%), and mood effects (43%). Three patients discontinued treatment because of toxicity, including two patients with fatal respiratory events.

CONCLUSION

Lorlatinib induced durable intracranial disease control in patients with CNS-only relapse on second-generation ALK inhibitors, suggesting that tumors with CNS-limited progression on brain-penetrant ALK tyrosine kinase inhibitors remain ALK-dependent.
Delta-Aminolevulinic acid dehydratase enzyme activity and susceptibility to lead toxicity in Uganda’s urban children
Authors: mukisa Ambrose , Kasozi Denis , Aguttu Claire , Kyambadde Joseph
Published: May 2022

Background: Rapid industrialization, urbanization, and population explosion in sub-Saharan Africa escalate environmental lead levels and subsequently blood lead levels in children. Its levels in one’s environment account for their blood lead levels. One’s susceptibility to lead toxicity is governed by nutrition status, age and genetics. This study aimed at expounding susceptibility to lead toxicity by relating blood lead levels, delta-aminolevulinic acid dehydratase (ALAD) enzyme activity, and genetic variations of proteins that code for ALAD in urban children of Uganda.

Methods: A total of 198 blood samples were spectrophotometrically analysed for blood lead levels (BLL), hemoglobin (Hb) levels, and ALAD enzyme activity before DNA extraction, polymerase chain reaction, and restriction fragment length digestion for ALAD polymorphism. 

Results: Up to 99.5% of the total samples analyzed coded for ALAD1 allele compared to 0.05% that coded for ALAD2. There was a significant relationship between BLL, Hb status and ALAD enzyme activity in the three isozymes (ALAD1-1, ALAD1-2 and ALAD2-2) in strength of ALAD1-1 (r = 0.42, p -value = 0.02) ˂ ALAD1-2 (r = 0.62, p -value = ˂ 0.001) ˂ ALAD2-2 (r = 0.67, p -value = ˂ 0.001).

Conclusions: Majority of children in Uganda code for the ALAD1 allele, which is important for blood lead ions hoarding during lead toxicity. Hoarding of blood lead not only delays exposure effects but also accumulates its levels in deposit tissues and this poses adverse effects later in their lives
MapOSR - A mapping review dataset of empirical studies on Open Science
Authors: Lasser Jana , Schneider Jürgen , Lösch Thomas , Röwert Ronny , Heck Tamara , Bluemel Clemens , Neufend Maike , Steinhardt Isabel , Skupien Stefan
Published: May 2022

Research that investigates respective researchers’ engagement in Open Science varies widely in the topics addressed, methods employed, and disciplines investigated, which makes it difficult to integrate and compare its results. To investigate current outcomes of Open Science research, and to get a better understanding on well-researched topics and research gaps, we aimed at providing an openly accessible overview of empirical studies that focus on different aspects of Open Science in different scientific disciplines, academic groups and geographical regions. In this paper, we describe a data set of studies about Open Science practices retrieved following a PRISMA approach to compile a literature review. We included studies from the Scopus and Web of Science databases with keywords relating to Open Science between the years 2000 and 2020, as well as a snowball search for relevant articles. Studies that did not investigate any aspect of Open Science, or weren’t peer-reviewed were excluded, resulting in a total of 695 remaining studies. The data set was collaboratively annotated to ensure intercoder reliability of the coded data.
UKB.COVID19: an R package for UK Biobank COVID-19 data processing and analysis
Authors: Wang Longfei , Jackson Victoria E , Fearnley Liam G , Bahlo Melanie
Published: May 2022

COVID-19 caused by SARS-CoV-2 has resulted in a global pandemic with a rapidly developing global health and economic crisis. Variations in the disease have been observed and have been associated with the genomic sequence of either the human host or the pathogen. Worldwide scientists scrambled initially to recruit patient cohorts to try and identify risk factors. A resource that presented itself early on was the UK Biobank (UKBB), which is investigating the respective contributions of genetic predisposition and environmental exposure to the development of disease. To enable COVID-19 studies, UKBB is now receiving COVID-19 test data for their participants every two weeks. In addition, UKBB is delivering more frequent updates of death and hospital inpatient data (including critical care admissions) on the UKBB Data Portal. This frequently changing dataset requires a tool that can rapidly process and analyse up-to-date data. We developed an R package specifically for the UKBB COVID-19 data, which summarises COVID-19 test results, performs association tests between COVID-19 susceptibility/severity and potential risk factors such as age, sex, blood type, comorbidities and generates input files for genome-wide association studies (GWAS). By applying the R package to data released in April 2021, we found that age, body mass index, socioeconomic status and smoking are positively associated with COVID-19 susceptibility, severity, and mortality. Males are at a higher risk of COVID-19 infection than females. People staying in aged care homes have a higher chance of being exposed to SARS-CoV-2. By performing GWAS, we replicated the 3p21.31 genetic finding for COVID-19 susceptibility and severity. The ability to iteratively perform such analyses is highly relevant since the UKBB data is updated frequently. As a caveat, users must arrange their own access to the UKBB data to use the R package.
Prediction of the effects of the top 10 nonsynonymous variants from 30229 SARS-CoV-2 strains on their proteins
Authors: Sia Boon Zhan , Boon Wan Xin , Yap Yoke Yee , Kumar Shalini , Ng Chong Han
Published: May 2022

Background: SARS-CoV-2 virus is a highly transmissible pathogen that causes COVID-19. The outbreak originated in Wuhan, China in December 2019. A number of nonsynonymous mutations located at different SARS-CoV-2 proteins have been reported by multiple studies. However, there are limited computational studies on the biological impacts of these mutations on the structure and function of the proteins.  

Methods: In our study nonsynonymous mutations of the SARS-CoV-2 genome and their frequencies were identified from 30,229 sequences. Subsequently, the effects of the top 10 highest frequency nonsynonymous mutations of different SARS-CoV-2 proteins were analyzed using bioinformatics tools including co-mutation analysis, prediction of the protein structure stability and flexibility analysis, and prediction of the protein functions.  

Results: A total of 231 nonsynonymous mutations were identified from 30,229 SARS-CoV-2 genome sequences. The top 10 nonsynonymous mutations affecting nine amino acid residues were ORF1a nsp5 P108S, ORF1b nsp12 P323L and A423V, S protein N501Y and D614G, ORF3a Q57H, N protein P151L, R203K and G204R. Many nonsynonymous mutations showed a high concurrence ratio, suggesting these mutations may evolve together and interact functionally. Our result showed that ORF1a nsp5 P108S, ORF3a Q57H and N protein P151L mutations may be deleterious to the function of SARS-CoV-2 proteins. In addition, ORF1a nsp5 P108S and S protein D614G may destabilize the protein structures while S protein D614G may have a more open conformation compared to the wild type.  

Conclusion: The biological consequences of these nonsynonymous mutations of SARS-CoV-2 proteins should be further validated by in vivo and in vitro experimental studies in the future.
Towards personalized medicine by mathematical modeling of tumors
Authors: Drexler Dániel András , Kovács Levente , Moza Gheorghe
Published: May 2022

In this open letter, we give some insights on the potential use of mathematical modeling in understanding cancer research. The article is written in a form that can be understood by a larger public, not only by specialists.
Infectious diseases data observatory (IDDO) visceral leishmaniasis library of clinical therapeutic studies: A protocol for a living systematic review of clinical studies
Authors: Singh-Phulgenda Sauman , Rashan Sumayyah , Harriss Eli , Dahal Prabin , Naylor Caitlin , Brack Matthew , Guérin Philippe J. , Maguire Brittany J.
Published: May 2022

Introduction: Visceral leishmaniasis (VL) is a vector-borne disease caused by protozoan parasites of the genus Leishmania. The disease is endemic in parts of South Asia, East Africa, South America and the Mediterranean region, with an estimated 50,000 to 90,000 cases occurring annually. A living systematic review of existing scientific literature is proposed to identify clinical drug efficacy studies against VL, conducted following the Preferred Reporting Items for Systematic-Reviews and Meta-Analyses (PRISMA) guidelines.

Methods and analysis: The proposed living systematic review builds on a previous systematic review first carried out in 2016, and the current protocol is designed to capture any published or registered VL clinical study from Nov-2021 onwards. The following databases will be searched by a medical librarian: PubMed, Ovid Embase, Scopus, Web of Science Core Collection, Cochrane Central Register of Controlled Trials, clinicaltrials.gov, WHO ICTRP, as well as IMEMR, IMSEAR, and LILACS from the WHO Global Index Medicus. The systematic review will consider both randomised and non-randomised interventional studies, including single-armed studies.

Ethics and dissemination: A database of eligible studies, including study characteristics, is openly available (https://www.iddo.org/tool/vl-surveyor) and will be continually updated every six months. All findings will be published in a peer-reviewed journal.

PROSPERO registration: CRD42021284622 (29/11/2021)
Competencia digital del alumnado universitario y rendimiento académico en tiempos de COVID-19
Authors: García Prieto Francisco Javier
Published: May 2022

La situación de pandemia mundial provocada por la COVID-19 ha tenido consecuencias en las diferentes esferas de la sociedad. La educación superior ha tenido que adaptar las metodologías de enseñanza hacia unos entornos de aprendizaje virtuales o semipresenciales, mientras que los estudiantes también han visto condicionado su proceso de aprendizaje por la necesidad de disponer de recursos digitales con los que sustituir a las herramientas y procesos tradicionalmente utilizados. Este estudio pretende analizar la incidencia que tiene la competencia digital del alumnado universitario sobre su rendimiento académico en tiempos de COVID-19. A través de una metodología cuantitativa descriptiva-inferencial, se aplicó una escala validada a una muestra de 603 estudiantes de grado y posgrado durante el curso 2020/2021. Los resultados obtenidos reflejan, por una parte, altos valores en las dimensiones relativas al manejo de la información y la comunicación digital, así como en los aspectos de organización para los que utilizan las herramientas digitales y, por otra parte, valores bajos en lo que se refiere a habilidades relativas al manejo técnico de la tecnología. Las conclusiones confirman la hipótesis que sostiene que el alumnado con mayores niveles de competencia digital es aquel que obtiene un mejor rendimiento académico en la enseñanza universitaria. Los hallazgos alcanzados coinciden con trabajos previos realizados.
Propósitos de uso de tecnologías digitales en estudiantes de pedagogía chilenos: Construcción de una escala basada en competencias digitales
Authors: Cerda González Cristian , León Herrera . Miriam , Saiz Vidallet José Luis , Villegas Medrano Lorena
Published: May 2022

La adquisición de competencias digitales permite el desarrollo de las personas en diversas áreas de la sociedad. En el caso de muchos jóvenes, y en especial de los futuros docentes, dicha adquisición es obtenida a través del uso cotidiano de tecnologías digitales. Disponer de instrumentos para medir competencias digitales, considerando diversos propósitos de uso, puede contribuir a retroalimentar la adquisición de estas competencias en procesos de formación inicial docente. Esta investigación tuvo como objetivo construir y analizar psicométricamente la Escala de Propósitos de Uso y Competencias Digitales (EPUCD). Una muestra de 618 estudiantes de pedagogía de dos universidades chilenas contestó un cuestionario que mide frecuencia de uso académico, recreativo, social y económico, utilizando DigComp como marco de competencias digitales. Los procedimientos estadísticos realizados (AFE, AFC y cálculo coeficiente de fiabilidad compuesta y varianza extraída media) permitieron obtener evidencias adecuadas de validez estructural y discriminante y de consistencia interna de este instrumento. Las aceptables propiedades psicométricas de la EPUCD permiten que se ponga a disposición de la comunidad académica un instrumento que contribuya a develar cómo los futuros docentes hacen uso de las tecnologías digitales, permitiendo de esta forma retroalimentar el proceso de formación inicial docente.
Osobiście w zdaniu i w strukturze tematyczno-rematycznej wypowiedzenia
Authors: Danielewiczowa Magdalena
Published: May 2022

UNITS WITH THE FORM OSOBIŚCIE IN SENTENCES AND IN THE THEMATIC-RHEMATIC STRUCTURE OF UTTERANCES The author of this article claims that in Polish there are three independent language units containing the form osobiście. They differ both functionally and formally. Only one of these units (osobiście1 ‘in a personal manner’) is an ordinary adverb operating on the syntactic level, that is, entering into syntactic and semantic relations with other components of a given sentence. The other two units are operators of the thematic-rhematic structure. They organize the content of utterances they participate in and comment on it. Osobiście2 (‘personally’) is inherently thematic; it can function as the main theme of a given utterance or stands next to the theme making this element easier to identify. The unit osobiście3 (‘in person’) is, in turn, primarily rhematic or precedes the rheme as its thematized exponent. Osobiście2 and osobiście3 are two types of dictum, on the one hand – thematic comment and on the other – rhematic. These expressions have much in common with the units of the form sam. Besides osobiście1, osobiście2 and osobiście3, there is also in Polish the idiom znać / poznać [kogoś] osobiście ‘know / get to know someone personally’.
Czy (i jak) warto jeszcze badać staropolskie latynizmy i grecyzmy?
Authors: German Jan
Published: May 2022

IS IT STILL WORTH RESEARCHING GREEK AND LATIN LOANWORDS IN OLD POLISH? (AND HOW SHOULD WE DO IT?)
The paper focuses on Greek and Latin loanwords in Old Polish language. It attempts to show what has already been done and what still needs to be done in this important issue. Three main aspects are discussed: (1) definitions of the terms loanword, Latinism, Hellenism, and the problem of direct and indirect borrowing; (2) the current state of investigation of Greek and Latin loanwords in Old Polish; (3) the Old Polish Christian terminology – the problem of chronology and borrowing channels of Greek and Latin Christian words to Old Polish. The final part of the paper contains a brief research history i.e. it describes the most important works in chronological order.
PEMBERDAYAAN EKONOMI MASYARAKAT MELALUI PENGOLAHAN HASIL BUMI LOKAL UNTUK MENINGKATKAN MINAT BERWIRAUSAHA
Authors: Fahmi Syariful , Shinta Faizah Sarah
Published: May 2022

Artikel ini bertujuan untuk (1) memberikan wawasaanÂ  dalam rangka memaksimalkan potensi sumber daya alam lokal yang ada di Dusun Ketos, (2) menciptakan peluang usaha serta meningkatkan minat berwirausaha warga Dusun Ketos, (3) memberikan strategi pemasaran yang kreatif guna mendorong pemasaran dan daya saing produk lokal Dusun Ketos. Adapun artikel ini juga diharapkan dapat memberi manfaat untuk (1) masyarakat dalam rangka meningkatkan perekonomian melalui strategi pengolahan hasil bumi dan pemasaran yang kreatif, (2) untuk pemerintah diharapkan bisa berpartisipasi dalam memberikan dorongan dan stimulan dalam rangka pengembangan ekonomi kreatif bagi masyarakat, (3) Untuk Dinas Pertanian diharapkan memberikan pendampingan dalam peningkatan sumber daya lokal yang menjadi hasil panen pokok masyarakat agar lebih baik, (4) Dinas Perpustakaan dan Arsip Daerah diharapakan dapat menyediakan literatur yang mampu menunjangÂ  peningkatan wawasanbagi masyarakat, (5) Dinas Koperasi diharapkan dapat memberikan pengarahan serta pendampingan untuk warga dari hasil pengolahan hingga pemasaran produk.
PELATIHAN PENGOLAHAN MINYAK JELANTAH MENJADI SABUN DAN STRATEGI PEMASARAN DI DESA KEMIRI
Authors: Erviana Vera Yuli
Published: May 2022

Limbah minyak jelantah di Desa Kemiri cukup banyak. Hal tersebut dikarenakan banyaknya warga yang berprofesi sebagai penjual kuliner (sejenis gorengan yang dibuat dari tepung pati) ditambah lagi minyak jelantah yang dihasilkan dari rumahan. Berdasarkan permasalahan tersebut tujuan pengabdian pada masyarakat ini mengolah limbah minyak jelantah untuk menjadi sabun cuci tangan dengan berbagai modivikasi. Metode yang digunakan yaitu sistem pengolahan limbah berbasis zero waste industry. Konsep zero waste industry terdiri dari reduce (mengurangi), reuse (menggunakan kembali) dan recycle (mendaur ulang). Kegiatan tersebut terdiri dari: 1) penyuluhan limbah minyak jelantah bagi lingkungan, 2) pelatihan penjernihan minyak jelantah, 3) pelatihan pengolahan limbah minyak jelantah menjadi sabun mandi, dan 4) pelatihan strategi pemasaran. Luaran yang dihasilkan berupa teknik pengelolaan limbah minyak jelantah berbasis Zero Waste Industry, produk sabun cuci tangan, dan strategi pemasaran.
APLIKASI PAKAN PELET BUATAN UNTUK PENINGKATAN PRODUKTIVITAS BUDIDAYA IKAN AIR TAWAR
Authors: Yunaidi Yunaidi , Rahmanta Anugrah Perdana , Wibowo Ari
Published: May 2022

This activity aims to provide guidance, training, and mentoring to help resolve problems faced by partners, including high operational costs of fish farming because of the high cost of factory-made pellets, limited understanding and knowledge of fish farming techniques, and limited access to business capital in groups of freshwater fish farming in village of Jerukagung Srumbung Magelang. In this activity, the use of semi-intensive farming technology was introduced and the introduction of mixer and fish pellet feed making machines technology were able to produce pellets independently for groups of fish farmers. Semi-intensive system farming techniques are proven to be able to increase productivity at a low cost to replace the conventional methods that have been done so far. The service program was completed in eight months, divided into three stages consisting of competency enhancement, technology development, and partnership development. The use of semi-intensive farming technology by applying good pond water maintenance techniques, selecting the right seeds, and optimal feeding techniques has been shown to increase fish production. High feed costs during the enlargement process which can reach 75% of the total cost can be replaced using pellet feed has made by group using local raw materials that are easily available in the surrounding area or environment, so as to reduce feed costs by up to 25%.
PEMBERDAYAAN MASYARAKAT DALAM PENINGKATAN EKONOMI DENGAN MEMANFAATKAN KEARIFAN LOKAL
Authors: Sukesi Tri Wahyuni , Irjayanti Azizah , Hapsari Sekarsih Dyah , Efendi Ariko
Published: May 2022

Usaha home industry sebagai usaha yang berbasis rumah tangga selain dapat menyerap tenaga kerja, secara sosial ekonomi juga dapat membantu meningkatkan kesejahteraan terhadap bukan saja kepada pelaku namun juda pada masyarakat sekitarnya. Hal ini disebabkan karena dengan mengelola usaha home industry akan melibatkan masyarakat sekitar untuk proses produksinya dan pemasarannya. Pemanfaatan sumber daya alam lokal sangat penting dilakukan terutama diwilayah Gedangsari, Gunungkidul banyak ditemukan ubi-ubian, jati dan pohon pisang.Metode yang digunakan adalah dengan pelatihan pembuatan makanan dan kerajinan yang berbasis pada bahan alam (ubi, pisang dan daun jati) dn bahan bekas (limbah kayu jati) secara langsung kepada warga sekitar. Memberikan sumbangan peralatan yang digunakan dalam pelatihan tersebut. Hasil yang diperoleh adalah kegiatan pelatihan berjalan dengan baik dan peserta aktif bertanya dan mengikuti kegiatan pelatihan sampai selesai. Pelatihan dilakukan dengan interaktif antara narasumber dengan peserta pelatihan.
Assessing and ameliorating acute pain in rabbits
Authors: Benato Livia
Published: May 2022

Pain management in rabbits has improved greatly during the last 20 years. At present, rabbits are commonly treated for acute pain caused by a variety of medical and surgical conditions. When not treated adequately, pain can be a very debilitating experience for the animal. The ability to properly qualify and quantify pain can improve not only the rabbit's general health and welfare but it also reduces the risks under general anaesthesia and helps the animal to recover more quickly.
Ein Modell zur systematischen Erfassung genuenischer Phraseme in Wörterbüchern, illustriert am Beispiel der Forschungsprojekte GEPHRAS und GEPHRAS2
Authors: Autelli Erica
Published: May 2022

This paper aims at describing the innovations brought in the digital phraseography of Genoese thanks to the recent FWF projects GEPHRAS and GEPHRAS2. First, an overview on dialectal phraseography will be given, then the focus will be postponed on the Genoese one. The projects will be described, explaining the main choices that had to be made and that contribute to the innovative character of the Genoese-Italian phraseological dictionary.
Ultra-fast detail enhancement for a short-wave infrared image
Authors: Chen Yaohong , Zhang Hui , Zhao Zehao , Wang Zhen , Wang Hao , Kwan Chiman
Published: May 2022

Image detail enhancement is critical to the performance of short-wave infrared (SWIR) imaging systems, especially to the long-range systems. However, the existing high-performance infrared (IR) image enhancement methods typically have difficulty in meeting the requirements of the imaging system with high resolution and high frame rate. In this paper, we propose an ultra-fast and simple SWIR image detail enhancement method based on the difference of Gaussian (DoG) filter and plateau equalization. Our method consists of efficient edge detail information extraction and histogram equalization. The experimental results demonstrated that the proposed method achieves outstanding enhancement performance with a frame rate around 50 fps for

1280

×

1024

SWIR images.
Analysis of the smoothing characteristics and shape-retaining ability of conformal vibration polishing and suppression strategy for full-spatial frequency errors of optics
Authors: Liu Shiwei , Wang Hongxiang , Hou Jing , Zhang Qinghua , Chen Xianhua , Zhong Bo , Zhang Mingzhuang
Published: May 2022

Conformal vibration polishing (CVP) employing flexible polishing tools is expected to be an efficient means of optical processing, and all current research on it is limited to planar components. Hence, the smoothing characteristics of the middle spatial frequency (MSF) errors and the ability to maintain the surface shape of different types of optics in CVP are analyzed. A combined processing method based on magnetorheological finishing and CVP for full-spatial frequency errors is proposed and verified by experiment. The peak-to-valley value, MSF errors, and surface roughness of the large-diameter component can reach 75 nm, 1.1 nm, and 0.37 nm after 9 h of processing. The research not only demonstrates the excellent removal characteristics of CVP and the effectiveness of the proposed method but also provides an additional choice for the high-precision manufacturing of optics.
Deep learning for denoising in a Mueller matrix microscope
Authors: Yang Xiongjie , Zhao Qianhao , Huang Tongyu , Hu Zheng , Bu Tongjun , He Honghui , Hou Anli , Li Migao , Xiao Yucheng , Ma Hui
Published: May 2022

The Mueller matrix microscope is a powerful tool for characterizing the microstructural features of a complex biological sample. Performance of a Mueller matrix microscope usually relies on two major specifications: measurement accuracy and acquisition time, which may conflict with each other but both contribute to the complexity and expenses of the apparatus. In this paper, we report a learning-based method to improve both specifications of a Mueller matrix microscope using a rotating polarizer and a rotating waveplate polarization state generator. Low noise data from long acquisition time are used as the ground truth. A modified U-Net structured network incorporating channel attention effectively reduces the noise in lower quality Mueller matrix images obtained with much shorter acquisition time. The experimental results show that using high quality Mueller matrix data as ground truth, such a learning-based method can achieve both high measurement accuracy and short acquisition time in polarization imaging.
Multifunctional metasurfaces for switchable polarization selectivity and absorption
Authors: Zhang Hui , Peng Kangzhun , Jiang Huan , Li Wenhua , Zhao Weiren
Published: May 2022

A multifunctional metasurface capable of dynamic control for polarization selectivity and absorption is proposed by controlling the phase of Ge2Sb2Te5 (GST) in the near-infrared region. At amorphous state of GST (a-GST), the proposed GST strip array realized polarization selectivity in transmission-reflection integrated modes. The high-efficiency asymmetric transmission (AT = 0.92) and asymmetric reflection (AR = -0.82) are both obtained by selectively exciting Mie multipole resonances. With the transition from a-GST to crystalline (c-GST) state, the giant polarization selectivity almost disappeared, and the absorptions climb from < 0.1 to > 0.9. The maximum modulation depth reaches 94%. The mechanism of the dynamic switching between polarization selectivity and absorption is quantitively analyzed via multipole expansion. The GST based metasurfaces simultaneously possess excellent switchable capability for AT, AR, and absorption without refabricating structures, which is promising to the applications for next generation optical devices.