bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of an AA9 LPMO from Thielavia australiensis, TausLPMO9B, under industrially relevant lignocellulose saccharification conditions
Authors: Calderaro F. , Keser M. , Akeroyd M. , Bevers L. E. , Eijsink V. G. H. , Várnai A. , van den Berg M. A. 
Published: November 2020

AbstractBackgroundThe discovery of lytic polysaccharide monooxygenases (LPMO) has changed our perspective on enzymatic degradation of plant biomass. Through an oxidative mechanism, these enzymes are able to cleave and depolymerize various polysaccharides, acting not only on crystalline substrates such as chitin and cellulose, but also on other polysaccharides, such as xyloglucan, glucomannan and starch. Despite their widespread use, uncertainties related to substrate specificity and stereospecificity, the nature of the co-substrate, in-process stability, and the nature of the optimal reductant challenge their exploitation in biomass processing applications.ResultsIn this work, we studied the properties of a novel fungal LPMO from the thermophilic fungusThielavia australiensis, TausLPMO9B. Heterologous expression ofTausLPMO9B inAspergillus nigeryielded a glycosylated protein with a methylated N-terminal histidine showing LPMO activity. High sequence identity of the AA9 domain to that ofMtLPMO9B (MYCTH_80312) fromMyceliophthora thermophila(84%) indicated strictly C1-oxidizing activity on cellulose, which was confirmed experimentally by the analysis of products released from cellulose using HPAEC. The enzyme was stable and active at a pH ranging from 4 to 6, thus matching the conditions commonly used in industrial biomass processing, where a low pH (between 4 and 5) is used due to the pH-optima of commercial cellulases and a desire to limit microbial contamination.ConclusionWhile the oxidative cleavage of phosphoric acid swollen cellulose (PASC) byTausLPMO9B was boosted by the addition of H2O2as a co-substrate, this effect was not observed during the saccharification of acid pretreated corn stover. This illustrates key differences between the lab-scale tests with artificial, lignin-free substrates and industrial settings with lignocellulosic biomass as substrate.
Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines
Authors: Andrade Juvana Moreira , Gonçalves Leilane Oliveira , Liarte Daniel Barbosa , Lima Davi Alvarenga , Guimarães Frederico Gonçalves , de Melo Resende Daniela , Santi Ana Maria Murta , de Oliveira Luciana Marcia , Velloso João Paulo Linhares , Delfino Renato Guimarães , Pescher Pascale , Späth Gerald F. , Ruiz Jeronimo Conceição , Murta Silvane Maria Fonseca 
Published: November 2020

Abstract
Background
One of the major challenges to leishmaniasis treatment is the emergence of parasites resistant to antimony. To study differentially expressed genes associated with drug resistance, we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing.

Methods
All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search.

Results
The analytical pipeline considering an adjusted p-value < 0.05 and fold change > 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the gene ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host–parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation.

Conclusions
The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with the antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.

Graphical Abstract
Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2
Authors: Nomburg Jason , Meyerson Matthew , DeCaprio James A. 
Published: November 2020

Abstract
Background
SARS-CoV-2, a positive-sense RNA virus in the family Coronaviridae, has caused a worldwide pandemic of coronavirus disease 2019 or COVID-19. Coronaviruses generate a tiered series of subgenomic RNAs (sgRNAs) through a process involving homology between transcriptional regulatory sequences (TRS) located after the leader sequence in the 5′ UTR (the TRS-L) and TRS located near the start of ORFs encoding structural and accessory proteins (TRS-B) near the 3′ end of the genome. In addition to the canonical sgRNAs generated by SARS-CoV-2, non-canonical sgRNAs (nc-sgRNAs) have been reported. However, the consistency of these nc-sgRNAs across viral isolates and infection conditions is unknown. The comprehensive definition of SARS-CoV-2 RNA products is a key step in understanding SARS-CoV-2 pathogenesis.

Methods
Here, we report an integrative analysis of eight independent SARS-CoV-2 transcriptomes generated using three sequencing strategies, five host systems, and seven viral isolates. Read-mapping to the SARS-CoV-2 genome was used to determine the 5′ and 3′ coordinates of all junctions in viral RNAs identified in these samples.

Results
Using junctional abundances, we show nc-sgRNAs make up as much as 33% of total sgRNAs in cell culture models of infection, are largely consistent in abundance across independent transcriptomes, and increase in abundance over time during infection. By assessing the homology between sequences flanking the 5′ and 3′ junction points, we show that nc-sgRNAs are not associated with TRS-like homology. By incorporating read coverage information, we find strong evidence for subgenomic RNAs that contain only 5′ regions of ORF1a. Finally, we show that non-canonical junctions change the landscape of viral open reading frames.

Conclusions
We identify canonical and non-canonical junctions in SARS-CoV-2 sgRNAs and show that these RNA products are consistently generated by many independent viral isolates and sequencing approaches. These analyses highlight the diverse transcriptional activity of SARS-CoV-2 and offer important insights into SARS-CoV-2 biology.
Feasibility of using a handheld ultrasound device to detect and characterize shunt and deep vein thrombosis in patients with COVID-19: an observational study
Authors: Rajendram Rajkumar , Hussain Arif , Mahmood Naveed , Kharal Mubashar 
Published: November 2020

Abstract
Background
Coronavirus disease 2019 (COVID-19) causes an atypical acute respiratory distress syndrome associated with thromboembolism and high shunt fraction. Shunt may be intrapulmonary, or extrapulmonary. Handheld devices are increasingly being used for point-of-care ultrasound, but their use to characterize shunt has not been reported.

Objectives
Determine the feasibility of using handheld ultrasound to detect and characterize anatomical substrates of hypoxia and deep vein thrombosis (DVT) in patients with COVID-19 suspected to have severe shunt.

Methods
A handheld ultrasound device (iQ, Butterfly, USA) was used to perform lung ultrasound, vascular assessment for DVT, and limited transthoracic echocardiography (TTE) with color Doppler and saline microbubble contrast in patients with COVID-19 suspected to have severe shunt. Images were reassessed by an independent reviewer.

Results
After screening 40 patients, six patients who fulfilled the inclusion criteria were identified. Two were excluded because palliation had been initiated. So, four patients were studied. Interpretable images were obtained in all cases. Interobserver agreement was good. All patients had abnormal lung ultrasound (lung ultrasound score range 17–22). Identified lung pathology included interstitial syndrome with light beams and small peripheral consolidation (4), lobar consolidation (1), and pleural effusion (1). Abnormal echocardiographic findings included interatrial shunt (2), intrapulmonary shunt (1), and dilated right ventricle with tricuspid valve regurgitation (1). Significant DVT was not detected.

Conclusion
Use of handheld ultrasound to perform combined lung ultrasound, DVT ultrasound, and limited TTE with color Doppler and saline microbubble contrast is feasible, and may be able to characterize shunt in critically hypoxic patients. Serial studies could be used to monitor changes in shunt. Further studies are required to determine whether this can guide treatment to improve the outcomes of patients with refractory hypoxia.
An abnormal course of the interazygos vein: a case report
Authors: Shiri Elham , Madadi Soheila 
Published: November 2020

Abstract
Background
The azygos venous system in the posterior mediastinum has a complex developmental pattern.

Case presentation
During the dissection of this region, we encountered a variation in this system. In this case, we observed that the accessory hemiazygos and hemiazygos veins in the left side passed anterior to the aorta and drained to the azygos vein located on the left side of the vertebral column. Other structures were normal in this area.

Conclusions
This variation is important in mediastinal surgery and radiographic interpretation.
A low-area high-efficiency video coding inverse transform core using resource and time sharing architecture
Authors: Chen Yuan-Ho , Liu Chieh-Yang 
Published: November 2020

AbstractIn this paper, a very-large-scale integration (VLSI) design that can support high-efficiency video coding inverse discrete cosine transform (IDCT) for multiple transform sizes is proposed. The proposed two-dimensional (2-D) IDCT is implemented at a low area by using a single one-dimensional (1-D) IDCT core with a transpose memory. The proposed 1-D IDCT core decomposes a 32-point transform into 16-, 8-, and 4-point matrix products according to the symmetric property of the transform coefficient. Moreover, we use the shift-and-add unit to share hardware resources between multiple transform dimension matrix products. The 1-D IDCT core can simultaneously calculate the first- and second-dimensional data. The results indicate that the proposed 2-D IDCT core has a throughput rate of 250 MP/s, with only 110 K gate counts when implemented into the Taiwan semiconductor manufacturing (TSMC) 90-nm complementary metal-oxide-semiconductor (CMOS) technology. The results show the proposed circuit has the smallest area supporting the multiple transform sizes.
New generalized Pólya–Szegö and Čebyšev type inequalities with general kernel and measure
Authors: Iqbal S. , Samraiz M. , Abdeljawad Thabet , Nisar Kottakkaran Sooppy , Rahman G. , Adil Khan M. 
Published: November 2020

AbstractIt is always attractive and motivating to acquire the generalizations of known results. In this article, we introduce a new class$\mathfrak{C(h)}$C(h)of functions which can be represented in a form of integral transforms involving general kernel withσ-finite measure. We obtain some new Pólya–Szegö and Čebyšev type inequalities as generalizations to the previously proved ones for different fractional integrals including fractional integral of a function with respect to another function capturing Riemann–Liouville integrals, Hadamard fractional integrals, Katugampola fractional integral operators, and conformable fractional integrals. This new idea shall motivate the researchers to prove the results over a measure space with general kernels instead of special kernels.
Eventual periodicity of the fuzzy max-difference equation $x_{n} = \max \{ C, \frac{x_{n-m-k}}{x_{n-m}}\}$
Authors: Han Caihong , Su Guangwang , Li Lue , Xia Guoen , Sun Taixiang 
Published: November 2020

AbstractIn this paper, we study the eventual periodicity of the fuzzy max-type difference equation$x_{n} =\max \{C , \frac{x_{n-m-k}}{x_{n-m} }\}, n\in \{0,1,\ldots \} $xn=max{C,xn−m−kxn−m},n∈{0,1,…}, wheremandkare positive integers,Cand the initial values are positive fuzzy numbers. Let the support$\operatorname{supp} C=\overline{\{t : C(t) > 0\}}=[C_{1},C_{2}]$suppC={t:C(t)>0}‾=[C1,C2]ofC. We show that: (1) if$C_{1}>1$C1>1, then every positive solution of this equation equalsCeventually; (2) there exists a positive fuzzy numberCwith$C_{1}=1$C1=1such that this equation has a positive solution which is not eventually periodic; (3) if$C_{2}\leq 1$C2≤1, then this equation has a positive solution which is not eventually periodic; (4) if$C_{1}<1<C_{2}$C1<1<C2, then every positive solution of the above equation is not eventually periodic.
Recommendations from the Italian intersociety consensus on Perioperative Anesthesia Care in Thoracic surgery (PACTS) part 1: preadmission and preoperative care
Authors:   on behalf of AIPO, Associazione Italiana Pneumologi Ospedalieri, Piccioni Federico ,   SIAARTI, Società Italiana di Anestesia Analgesia Rianimazione e Terapia Intensiva,   SIC, Società Italiana di Chirurgia,   SICT, Società Italiana di Chirurgia Toracica,   SIET, Società Italiana di Endoscopia Toracica,   SIP, Società Italiana di Pneumologia, Droghetti Andrea , Bertani Alessandro , Coccia Cecilia , Corcione Antonio , Corsico Angelo Guido , Crisci Roberto , Curcio Carlo , Del Naja Carlo , Feltracco Paolo , Fontana Diego , Gonfiotti Alessandro , Lopez Camillo , Massullo Domenico , Nosotti Mario , Ragazzi Riccardo , Rispoli Marco , Romagnoli Stefano , Scala Raffaele , Scudeller Luigia , Taurchini Marco , Tognella Silvia , Umari Marzia , Valenza Franco , Petrini Flavia 
Published: November 2020

Abstract
Introduction
Anesthetic care in patients undergoing thoracic surgery presents specific challenges that necessitate standardized, multidisciplionary, and continuously updated guidelines for perioperative care.

Methods
A multidisciplinary expert group, the Perioperative Anesthesia in Thoracic Surgery (PACTS) group, comprising 24 members from 19 Italian centers, was established to develop recommendations for anesthesia practice in patients undergoing thoracic surgery (specifically lung resection for cancer). The project focused on preoperative patient assessment and preparation, intraoperative management (surgical and anesthesiologic care), and postoperative care and discharge. A series of clinical questions was developed, and PubMed and Embase literature searches were performed to inform discussions around these areas, leading to the development of 69 recommendations. The quality of evidence and strength of recommendations were graded using the United States Preventative Services Task Force criteria.

Results
Recommendations for preoperative care focus on risk assessment, patient preparation (prehabilitation), and the choice of procedure (open thoracotomy vs. video-assisted thoracic surgery).

Conclusions
These recommendations should help pulmonologists to improve preoperative management in thoracic surgery patients. Further refinement of the recommendations can be anticipated as the literature continues to evolve.
Standard reference values of weight and maximum pressure distribution in healthy adults aged 18–65 years in Germany
Authors: Ohlendorf D. , Kerth K. , Osiander W. , Holzgreve F. , Fraeulin L. , Ackermann H. , Groneberg D. A. 
Published: November 2020

AbstractBackgroundThe aim of this study was to collect standard reference values of the weight and the maximum pressure distribution in healthy adults aged 18–65 years and to investigate the influence of constitutional parameters on it.MethodsA total of 416 healthy subjects (208 male / 208 female) aged between 18 and 65 years (Ø 38.3 ± 14.1 years) participated in this study, conducted 2015–2019 in Heidelberg. The age-specific evaluation is based on 4 age groups (G1, 18–30 years; G2, 31–40 years; G3, 41–50 years; G4, 51–65 years). A pressure measuring plate FDM-S (Zebris/Isny/Germany) was used to collect body weight distribution and maximum pressure distribution of the right and left foot and left and right forefoot/rearfoot, respectively.ResultsBody weight distribution of the left (50.07%) and right (50.12%) foot was balanced. There was higher load on the rearfoot (left 54.14%; right 55.09%) than on the forefoot (left 45.49%; right 44.26%). The pressure in the rearfoot was higher than in the forefoot (rearfoot left 9.60 N/cm2, rearfoot right 9.51 N/cm2/forefoot left 8.23 N/cm2, forefoot right 8.59 N/cm2). With increasing age, the load in the left foot shifted from the rearfoot to the forefoot as well as the maximum pressure (p≤ 0.02 and 0.03; poor effect size). With increasing BMI, the body weight shifted to the left and right rearfoot (p≤ 0.001, poor effect size). As BMI increased, so did the maximum pressure in all areas (p≤ 0.001 and 0.03, weak to moderate effect size). There were significant differences in weight and maximum pressure distribution in the forefoot and rearfoot in the different age groups, especially between younger (18–40 years) and older (41–65 years) subjects.DiscussionHealthy individuals aged from 18 to 65 years were found to have a balanced weight distribution in an aspect ratio, with a 20% greater load of the rearfoot. Age and BMI were found to be influencing factors of the weight and maximum pressure distribution, especially between younger and elder subjects. The collected standard reference values allow comparisons with other studies and can serve as a guideline in clinical practice and scientific studies.
Induction of amyloid-β deposits from serially transmitted, histologically silent, Aβ seeds issued from human brains
Authors:   The Brainbank Neuro-CEB Neuropathology Network, Hérard Anne-Sophie , Petit Fanny , Gary Charlotte , Guillermier Martine , Boluda Susana , Garin Clément M. , Lam Suzanne , Dhenain Marc 
Published: November 2020

AbstractIn humans, iatrogenic transmission of cerebral amyloid-β (Aβ)-amyloidosis is suspected following inoculation of pituitary-derived hormones or dural grafts presumably contaminated with Aβ proteins as well as after cerebral surgeries. Experimentally, intracerebral inoculation of brain homogenate extracts containing misfolded Aβ can seed Aβ deposition in transgenic mouse models of amyloidosis or in non-human primates. The transmission of cerebral Aβ is governed by the host and by the inoculated samples. It is critical to better characterize the propensities of different hosts to develop Aβ deposition after contamination by an Aβ-positive sample as well as to better assess which biological samples can transmit this lesion. Aβ precursor protein (huAPPwt) mice express humanized non-mutated forms of Aβ precursor protein and do not spontaneously develop Aβ or amyloid deposits. We found that inoculation of Aβ-positive brain extracts from Alzheimer patients in these mice leads to a sparse Aβ deposition close to the alveus 18 months post-inoculation. However, it does not induce cortical or hippocampal Aβ deposition. Secondary inoculation of apparently amyloid deposit-free hippocampal extracts from these huAPPwt mice to APPswe/PS1dE9 mouse models of amyloidosis enhanced Aβ deposition in the alveus 9 months post-inoculation. This suggests that Aβ seeds issued from human brain samples can persist in furtive forms in brain tissues while maintaining their ability to foster Aβ deposition in receptive hosts that overexpress endogenous Aβ. This work emphasizes the need for high-level preventive measures, especially in the context of neurosurgery, to prevent the risk of iatrogenic transmission of Aβ lesions from samples with sparse amyloid markers.
Initial survey of PLA2G6 missense variant causing neuroaxonal dystrophy in Papillon dogs in North America and Europe
Authors: Raj Karthik , Giger Urs 
Published: November 2020

Abstract
Background
An autosomal recessive, rapidly progressive degenerative neuropathy known as infantile neuroaxonal dystrophy (NAD) was originally reported in Papillion puppies in 1995. In 2015, a causative missense variant in the PLA2G6 gene was identified in three affected puppies. Archived samples from Papillons clinically diagnosed with NAD prior to 2015 as well as samples obtained from 660 Papillons from North America and Europe between 2015 and 2017 were screened for the presence of this PLA2G6 gene variant (XM_022424454.1:c.1579G > A) using a TaqMan assay.

Results
Archived samples from affected puppies diagnosed prior to 2015 and three more recently acquired samples from Papillons clinically affected with NAD were all homozygous for the variant. SIFT analysis predicts that the PLA2G6 missense substitution (XP_022280162.1:p.Ala527Thr) will not be tolerated in the iPLA2β protein. Notably, 17.5% of the 660 tested Papillons were heterozygotes, resulting in a variant allele frequency of 0.092 in this initial survey. Since then, screening for NAD in Papillons by at least 10 other laboratories and data from the Health Committee of Papillon Club of America gathered between 2017 and 2019 reveal a variant allele frequency of 0.047.

Conclusions
This survey and data from other laboratories documents the widespread presence of the PLA2G6 variant in the Papillon population in North America and Europe. Despite the apparent declining prevalence of the PLA2G6 variant, screening of Papillons intended for breeding is still recommended to avoid inadvertent production of puppies with infantile NAD.
Ultrasound-guided arthroscopic communication enlargement surgery may be an ideal treatment option for popliteal cysts – indications and technique
Authors: Goto Kazumi , Saku Isaku 
Published: November 2020

AbstractPurposeSeveral studies have shown an excellent success rate of communication enlargement surgery for popliteal cysts (Baker’s cysts). Ultrasound-guided surgery can improve the accuracy of this procedure and may lead to better outcomes. This study describes a simple ultrasound-guided arthroscopic technique to manage popliteal cysts and reduce postoperative pain.MethodsAfter routine arthroscopic observation with a standard 2-portal approach, the arthroscope is redirected toward the posteromedial compartment from the anterolateral portal through the intercondylar notch. A posteromedial portal is then placed at this view. Subsequently, a contrast dye (indigo carmine) is injected into the popliteal cyst percutaneously using ultrasonography. This procedure makes it easier to find a capsular fold or valvular opening. The valvular opening between the semimembranosus and medial gastrocnemius is enlarged with a shaver and radiofrequency ablation. Cystectomy is not performed in any case. Finally, the irrigation fluid is suctioned, and the reduced cyst is visualized by ultrasound. Additionally, a periarticular multimodal drug injection is administered into the septum and inner wall of the cyst under ultrasound guidance.ConclusionsUltrasound-guided arthroscopic surgery for popliteal cysts can ensure reproducibility and be effective for postoperative pain relief. Thus, this combined procedure may be an optimal treatment option.