bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered functional properties of the codling moth Orco mutagenized in the intracellular loop-3
Authors: Bobkov Yuriy V. , Walker III William B. , Cattaneo Alberto Maria 
Published: February 2021

AbstractAmino acid substitutions within the conserved polypeptide sequence of the insect olfactory receptor co-receptor (Orco) have been demonstrated to influence its pharmacological properties. By sequence analysis and phylogenetic investigation, in the Lepidopteran subgroup Ditrysia we identified a fixed substitution in the intracellular loop-3 (ICL-3) of a conserved histidine to glutamine. By means of HEK293 cells as a heterologous system, we functionally expressed Orco from the Ditrysian model Cydia pomonella (CpomOrco) and compared its functional properties with a site-directed mutagenized version where this ICL-3-glutamine was reverted to histidine (CpomOrcoQ417H). The mutagenized CpomOrcoQ417H displayed decreased responsiveness to VUAA1 and reduced response efficacy to an odorant agonist was observed, when co-transfected with the respective OR subunit. Evidence of reduced responsiveness and sensitivity to ligands for the mutagenized Orco suggest the fixed glutamine substitution to be optimized for functionality of the cation channel within Ditrysia. In addition, contrary to the wild type, the mutagenized CpomOrcoQ417H preserved characteristics of VUAA-binding when physiologic conditions turned to acidic. Taken together, our findings provide further evidence of the importance of ICL-3 in forming basic functional properties of insect Orco- and Orco/OR-channels, and suggest involvement of ICL-3 in the potential functional adaptation of Ditrysian Orcos to acidified extra-/intracellular environment.
Projected plastic waste loss scenarios between 2000 and 2030 into the largest freshwater-lake system in Southeast Asia
Authors: Finnegan Alexander Matthew David , Gouramanis Christos 
Published: February 2021

AbstractFreshwater plastic pollution is critically understudied in Southeast Asia (SEA). Recent modelling studies indicate that SEA rivers contribute vast quantities of plastic to the world’s oceans, however, these fail to capture the complexity of individual systems. We determine the volume of mismanaged plastic waste (MPW) entering Tonle Sap Basin (TSB)—the largest freshwater lake–river system in SEA, between 2000 and 2030. Using economic, population and waste data at provincial and national levels, coupled with high resolution population and flood datasets, we estimate that ca. 221,700 tons of plastic entered between 2000 and 2020, and 282,300 ± 8700 tons will enter between 2021 and 2030. We demonstrate that policy interventions can reduce MPW up to 76% between 2021 and 2030. The most-stringent scenario would prevent 99% of annual MPW losses by 2030, despite substantially higher waste volumes and population. If successfully implemented, Cambodia will prevent significant losses in natural capital, material value and degradation in TSB worth at least US$4.8 billion, with additional benefits for the Mekong River and South China Sea.
Predictors of brain infarction in adult patients on extracorporeal membrane oxygenation: an observational cohort study
Authors: Iacobelli Riccardo , Fletcher-Sandersjöö Alexander , Lindblad Caroline , Keselman Boris , Thelin Eric Peter , Broman Lars Mikael 
Published: February 2021

AbstractNon-hemorrhagic brain infarction (BI) is a recognized complication in adults treated with extracorporeal membrane oxygenation (ECMO) and associated with increased mortality. However, predictors of BI in these patients are poorly understood. The aim of this study was to identify predictors of BI in ECMO-treated adult patients. We conducted an observational cohort study of all adult patients treated with venovenous or venoarterial (VA) ECMO at our center between 2010 and 2018. The primary endpoint was a computed tomography (CT) verified BI. Logistic regression models were employed to identify BI predictors. In total, 275 patients were included, of whom 41 (15%) developed a BI. Pre-ECMO Simplified Acute Physiology Score III, pre-ECMO cardiac arrest, VA ECMO and conversion between ECMO modes were identified as predictors of BI. In the multivariable analysis, VA ECMO demonstrated independent risk association. VA ECMO also remained the independent BI predictor in a sub-group analysis excluding patients who did not undergo a head CT scan during ECMO treatment. The incidence of BI in adult ECMO patients may be higher than previously believed and is independently associated with VA ECMO mode. Larger prospective trials are warranted to validate these findings and ascertain their clinical significance.
Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing
Authors: Ganly Ian , Pei Zhiheng , Hao Yuhan , Ma Yingfei , Rosenthal Matthew , Wu Zhenglin , Migliacci Jocelyn , Huang Bin , Katabi Nora , Tseng Wenzhi , Brown Stuart , Tang Yi-Wei , Yang Liying 
Published: February 2021

AbstractThe aim of this study was to carry out a case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma (OC-SCC) to normal patients using metagenomic shotgun sequencing. We recruited 50 OC-SCC cases which were then matched with a control patient by age, gender, race, smoking status and alcohol status. DNA was extracted from oral wash samples from all patients and whole genome shotgun sequencing performed. The raw sequence data was cleaned, reads aligned with the human genome (GRCH38), nonhuman reads identified and then HPV genotypes identified using HPViewer. In the 50 patients with OC-SCC, the most common subsite was tongue in 26 (52%). All patients were treated with primary resection and neck dissection. All but 2 tumors were negative on p16 immunohistochemistry. There were no statistically significant differences between the cases and controls in terms of gender, age, race/ethnicity, alcohol drinking, and cigarette smoking. There was no statistically significant difference between the cancer samples and control samples in the nonhuman DNA reads (medians 4,228,072 vs. 5,719,715, P value = 0.324). HPV was detected in 5 cases (10%) of OC-SCC (genotypes 10, 16, 98) but only 1 tumor sample (genotype 16) yielded a high number of reads to suggest a role in the etiology of OC-SCC. HPV was detected in 4 control patients (genotypes 16, 22, 76, 200) but all had only 1–2 HPV reads per human genome. Genotypes of HPV are rarely found in patients with oral cancer.
Transient prenatal ruxolitinib treatment suppresses astrogenesis during development and improves learning and memory in adult mice
Authors: Lee Han-Chung , Hamzah Hamizun , Leong Melody Pui-Yee , Md Yusof Hadri , Habib Omar , Zainal Abidin Shahidee , Seth Eryse Amira , Lim Siong-Meng , Vidyadaran Sharmili , Mohd Moklas Mohamad Aris , Abdullah Maizaton Atmadini , Nordin Norshariza , Hassan Zurina , Cheah Pike-See , Ling King-Hwa 
Published: February 2021

AbstractRuxolitinib is the first janus kinase 1 (JAK1) and JAK2 inhibitor that was approved by the United States Food and Drug Administration (FDA) agency for the treatment of myeloproliferative neoplasms. The drug targets the JAK/STAT signalling pathway, which is critical in regulating the gliogenesis process during nervous system development. In the study, we assessed the effect of non-maternal toxic dosages of ruxolitinib (0–30 mg/kg/day between E7.5-E20.5) on the brain of the developing mouse embryos. While the pregnant mice did not show any apparent adverse effects, the Gfap protein marker for glial cells and S100β mRNA marker for astrocytes were reduced in the postnatal day (P) 1.5 pups' brains. Gfap expression and Gfap+ cells were also suppressed in the differentiating neurospheres culture treated with ruxolitinib. Compared to the control group, adult mice treated with ruxolitinib prenatally showed no changes in motor coordination, locomotor function, and recognition memory. However, increased explorative behaviour within an open field and improved spatial learning and long-term memory retention were observed in the treated group. We demonstrated transplacental effects of ruxolitinib on astrogenesis, suggesting the potential use of ruxolitinib to revert pathological conditions caused by gliogenic-shift in early brain development such as Down and Noonan syndromes.
Molecular communication of the membrane insertase YidC with translocase SecYEG affects client proteins
Authors: Steudle Anja , Spann Dirk , Pross Eva , Shanmugam Sri Karthika , Dalbey Ross E. , Kuhn Andreas 
Published: February 2021

AbstractThe membrane insertase YidC inserts newly synthesized proteins by its hydrophobic slide consisting of the two transmembrane (TM) segments TM3 and TM5. Mutations in this part of the protein affect the insertion of the client proteins. We show here that a quintuple mutation, termed YidC-5S, inhibits the insertion of the subunit a of the FoF1 ATP synthase but has no effect on the insertion of the Sec-independent M13 procoat protein and the C-tail protein SciP. Further investigations show that the interaction of YidC-5S with SecY is inhibited. The purified and fluorescently labeled YidC-5S did not approach SecYEG when both were co-reconstituted in proteoliposomes in contrast to the co-reconstituted YidC wild type. These results suggest that TM3 and TM5 are involved in the formation of a common YidC-SecYEG complex that is required for the insertion of Sec/YidC-dependent client proteins.
Structural design principles for specific ultra-high affinity interactions between colicins/pyocins and immunity proteins
Authors: Shushan Avital , Kosloff Mickey 
Published: February 2021

AbstractThe interactions of the antibiotic proteins colicins/pyocins with immunity proteins is a seminal model system for studying protein–protein interactions and specificity. Yet, a precise and quantitative determination of which structural elements and residues determine their binding affinity and specificity is still lacking. Here, we used comparative structure-based energy calculations to map residues that substantially contribute to interactions across native and engineered complexes of colicins/pyocins and immunity proteins. We show that the immunity protein α1–α2 motif is a unique structurally-dissimilar element that restricts interaction specificity towards all colicins/pyocins, in both engineered and native complexes. This motif combines with a diverse and extensive array of electrostatic/polar interactions that enable the exquisite specificity that characterizes these interactions while achieving ultra-high affinity. Surprisingly, the divergence of these contributing colicin residues is reciprocal to residue conservation in immunity proteins. The structurally-dissimilar immunity protein α1–α2 motif is recognized by divergent colicins similarly, while the conserved immunity protein α3 helix interacts with diverse colicin residues. Electrostatics thus plays a key role in setting interaction specificity across all colicins and immunity proteins. Our analysis and resulting residue-level maps illuminate the molecular basis for these protein–protein interactions, with implications for drug development and rational engineering of these interfaces.
Identification of sarcomatoid differentiation in renal cell carcinoma by machine learning on multiparametric MRI
Authors: Mazin Asim , Hawkins Samuel H. , Stringfield Olya , Dhillon Jasreman , Manley Brandon J. , Jeong Daniel K. , Raghunand Natarajan 
Published: February 2021

AbstractSarcomatoid differentiation in RCC (sRCC) is associated with a poor prognosis, necessitating more aggressive management than RCC without sarcomatoid components (nsRCC). Since suspected renal cell carcinoma (RCC) tumors are not routinely biopsied for histologic evaluation, there is a clinical need for a non-invasive method to detect sarcomatoid differentiation pre-operatively. We utilized unsupervised self-organizing map (SOM) and supervised Learning Vector Quantizer (LVQ) machine learning to classify RCC tumors on T2-weighted, non-contrast T1-weighted fat-saturated, contrast-enhanced arterial-phase T1-weighted fat-saturated, and contrast-enhanced venous-phase T1-weighted fat-saturated MRI images. The SOM was trained on 8 nsRCC and 8 sRCC tumors, and used to compute Activation Maps for each training, validation (3 nsRCC and 3 sRCC), and test (5 nsRCC and 5 sRCC) tumor. The LVQ classifier was trained and optimized on Activation Maps from the 22 training and validation cohort tumors, and tested on Activation Maps of the 10 unseen test tumors. In this preliminary study, the SOM-LVQ model achieved a hold-out testing accuracy of 70% in the task of identifying sarcomatoid differentiation in RCC on standard multiparameter MRI (mpMRI) images. We have demonstrated a combined SOM-LVQ machine learning approach that is suitable for analysis of limited mpMRI datasets for the task of differential diagnosis.
Extraction of short chain chitooligosaccharides from fungal biomass and their use as promoters of arbuscular mycorrhizal symbiosis
Authors: Crosino Andrea , Moscato Elisa , Blangetti Marco , Carotenuto Gennaro , Spina Federica , Bordignon Simone , Puech-Pagès Virginie , Anfossi Laura , Volpe Veronica , Prandi Cristina , Gobetto Roberto , Varese Giovanna Cristina , Genre Andrea 
Published: February 2021

AbstractShort chain chitooligosaccharides (COs) are chitin derivative molecules involved in plant-fungus signaling during arbuscular mycorrhizal (AM) interactions. In host plants, COs activate a symbiotic signalling pathway that regulates AM-related gene expression. Furthermore, exogenous CO application was shown to promote AM establishment, with a major interest for agricultural applications of AM fungi as biofertilizers. Currently, the main source of commercial COs is from the shrimp processing industry, but purification costs and environmental concerns limit the convenience of this approach. In an attempt to find a low cost and low impact alternative, this work aimed to isolate, characterize and test the bioactivity of COs from selected strains of phylogenetically distant filamentous fungi: Pleurotus ostreatus, Cunninghamella bertholletiae and Trichoderma viride. Our optimized protocol successfully isolated short chain COs from lyophilized fungal biomass. Fungal COs were more acetylated and displayed a higher biological activity compared to shrimp-derived COs, a feature that—alongside low production costs—opens promising perspectives for the large scale use of COs in agriculture.
Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber
Authors: Adedze Yawo Mawunyo Nevame , Lu Xia , Xia Yingchun , Sun Qiuyue , Nchongboh Chofong G. , Alam Md. Amirul , Liu Menghua , Yang Xue , Zhang Wenting , Deng Zhijun , Li Wenhu , Si Longting 
Published: February 2021

AbstractInsertion and Deletion (InDel) are common features in genomes and are associated with genetic variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber (Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis. Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market type inbred line ‘9930’ and gaps conforming to InDel were pinpointed. Further, the level of cross-parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48 cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these, 385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis. It is worth noting that 16 of these markers were predominately associated to enzymatic activities in cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds purity testing, germplasm classification and marker-assisted breeding in cucumber.
Molecular detection and whole genome characterization of Canine Parainfluenza type 5 in Thailand
Authors: Charoenkul Kamonpan , Nasamran Chanakarn , Janetanakit Taveesak , Chaiyawong Supassama , Bunpapong Napawan , Boonyapisitsopa Supanat , Tangwangvivat Ratanaporn , Amonsin Alongkorn 
Published: February 2021

AbstractParainfluenza virus type 5 (PIV-5) causes respiratory infection in several animal species and humans. Canine parainfluenza virus type 5 (CPIV-5) causes respiratory disease in domestic dogs worldwide. In this study, we conducted a cross-sectional survey of CPIV-5 in dogs with respiratory symptoms from small animal hospitals in Thailand from November 2015 to December 2018. Our results showed that 32 out of 571 nasal swab samples (5.6%) were positive for CPIV-5 by RT-PCR specific to the NP gene. To characterize the viruses, three representative CPIV-5 were subjected to whole genome sequencing, and an additional ten CPIV-5 were subjected to HN, F, SH and V/P gene sequencing. Pairwise sequence comparison and phylogenetic analysis showed that Thai CPIV-5 was closely related to the CPIV-5 isolated from China and Korea. In conclusion, this study constitutes a whole genome characterization of CPIV-5 from dogs in Thailand. The surveillance of CPIV-5 should be further investigated at a larger scale to determine the dynamics, distribution and potential zoonotic transmission of CPIV-5.
A summary of eye-related visits to a tertiary emergency department
Authors: Rai Ravneet S. , Mehta Nitish , Larochelle Ryan , Rathi Siddarth , Schuman Joel S. 
Published: February 2021

AbstractTimely ophthalmologic consultation is important to ensure patients receive high quality ophthalmologic care in the Emergency Department (ED). Tele-ophthalmology may prove useful in safely and efficiently managing ED eye-related complaints. Prior to implementing such a solution, current consultation patterns must be understood. We aimed to assess case-mix acuity and consultation workflow patterns in the ophthalmology consult service at a tertiary emergency department in New York City. The medical records of patients with eye-related complaints who presented to the ED between January 1, 2015 and December 31, 2015 were reviewed. Visits were retrospectively assigned acuities and the ophthalmologic subspecialty involved in the case was recorded. The number of ophthalmologic consultations ordered and consultant response times were analyzed. Patients who were transferred to the ED for eye-related complaints were included. The ED received 1090 eye-related complaints in this period. 60% were retrospectively assigned low acuity, 27% were assigned medium acuity, and 13% were assigned high acuity. Ophthalmology was consulted on 19% of low, 18% of medium, and 48% of high acuity cases. 44% of complaints involved the anterior segment and 30% involved oculoplastics. 2/3 of transfer patients initially assigned high acuity were downgraded to low acuity upon examination. On average, the consult note was created and signed within 109 and 153 min, respectively, after consult order. ED consults are heavily weighted towards pathology of low-to-medium acuity affecting the anterior segment and ocular adnexa. Currently available tele-ophthalmology technology can potentially address a large volume of eye-related visits.
Social signals mediate oviposition site selection in Drosophila suzukii
Authors: Elsensohn Johanna E. , Aly Marwa F. K. , Schal Coby , Burrack Hannah J. 
Published: February 2021

AbstractThe information that female insects perceive and use during oviposition site selection is complex and varies by species and ecological niche. Even in relatively unexploited niches, females interact directly and indirectly with conspecifics at oviposition sites. These interactions can take the form of host marking and re-assessment of prior oviposition sites during the decision-making process. Considerable research has focused on the niche breadth and host preference of the polyphagous invasive pest Drosophila suzukii Matsumura (Diptera: Drosophilidae), but little information exists on how conspecific signals modulate oviposition behavior. We investigated three layers of social information that female D. suzukii may use in oviposition site selection—(1) pre-existing egg density, (2) pre-existing larval occupation, and (3) host marking by adults. We found that the presence of larvae and host marking, but not egg density, influenced oviposition behavior and that the two factors interacted over time. Adult marking appeared to deter oviposition only in the presence of an unmarked substrate. These results are the first behavioral evidence for a host marking pheromone in a species of Drosophila. These findings may also help elucidate D. suzukii infestation and preference patterns within crop fields and natural areas.
Purification and characterization of bacteriocins-like inhibitory substances from food isolated Enterococcus faecalis OS13 with activity against nosocomial enterococci
Authors: El-Gendy Ahmed O. , Brede Dag A. , Essam Tamer M. , Amin Magdy A. , Ahmed Shaban H. , Holo Helge , Nes Ingolf F. , Shamikh Yara I. 
Published: February 2021

AbstractNosocomial infections caused by enterococci are an ongoing global threat. Thus, finding therapeutic agents for the treatment of such infections are crucial. Some Enterococcus faecalis strains are able to produce antimicrobial peptides called bacteriocins. We analyzed 65 E. faecalis isolates from 43 food samples and 22 clinical samples in Egypt for 17 common bacteriocin-encoding genes of Enterococcus spp. These genes were absent in 11 isolates that showed antimicrobial activity putatively due to bacteriocins (three from food, including isolate OS13, and eight from clinical isolates). The food-isolated E. faecalis OS13 produced bacteriocin-like inhibitory substances (BLIS) named enterocin OS13, which comprised two peptides (enterocin OS13α OS13β) that inhibited the growth of antibiotic-resistant nosocomial E. faecalis and E. faecium isolates. The molecular weights of enterocin OS13α and OS13β were determined as 8079 Da and 7859 Da, respectively, and both were heat-labile. Enterocin OS13α was sensitive to proteinase K, while enterocin OS13β was resistant. Characterization of E. faecalis OS13 isolate revealed that it belonged to sequence type 116. It was non-hemolytic, bile salt hydrolase-negative, gelatinase-positive, and sensitive to ampicillin, penicillin, vancomycin, erythromycin, kanamycin, and gentamicin. In conclusion, BLIS as enterocin OS13α and OS13β represent antimicrobial agents with activities against antibiotic-resistant enterococcal isolates.