bluuebunny/crossref_metadata_2025_split huggingface dataset:
Massively parallel, computationally-guided design of a pro-enzyme
Authors: Yachnin Brahm J. , Azouz Laura R. , White Ralph E. , Minetti Conceição A. S. A. , Remeta David P. , Tan Victor M. , Drake Justin M. , Khare Sagar D. 
Published: March 2021

AbstractConfining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to re-design any chosen enzyme to be similarly stimulus-responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for pro-enzyme design. As a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of the most effective designed variants shows that they are inhibited by approximately 80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro-and catalytic domains based on the design models increases the degree of inhibition to 98%, but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing pro-enzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the pro-domain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of pro-proteins with precise spatial regulation.SignificanceProteins have shown promise as therapeutics and diagnostics, but their effectiveness is limited by our inability to spatially target their activity. To overcome this limitation, we developed a computationally-guided method to design inactive “pro-enzymes” or “zymogens,” which are activated through cleavage by a protease. Since proteases are differentially expressed in various tissues and disease states, including cancer, these pro-enzymes could be targeted to the desired microenvironment. We tested our method on the therapeutically-relevant protein, carboxypeptidase G2 (CPG2). We designed Pro-CPG2s that are inhibited by 80-98% and are partially to fully re-activatable following protease treatment. The developed methodology, with further refinements, could pave the way for routinely designing protease-activated protein-based therapeutics and diagnostics that act in a spatially controlled manner.
Shank3mutations impair electrical synapse scaffolding and transmission in mouse brain
Authors: Lautz Jonathan , Zhu Zhiyi , Speed Haley E. , Smith Stephen E. P. , Welsh John P. 
Published: March 2021

SUMMARYShank3mutations contribute to intellectual disability. Because SHANK3 is a protein scaffold that helps organize the multiprotein network of the glutamatergic postsynaptic density (PSD), alterations in chemical synaptic transmission are implicated. Electrical synaptic transmission is a second form of synaptic transmission, enabled by intercellular channels comprised of connexin36 that support direct electrical communication among neurons, electrical brain rhythms, and neurocognitive states. Using multiplex proteomics, we report that two autism-related mutations of mouseShank3disrupt the glutamatergic PSD differently, but have in common the disruption of an association between NMDA-type glutamate-receptors (NMDARs) and connexin36. Mutation ofShank3exons 13-16 most robustly dissociated connexin36 from NMDARs while impairing electrical synaptic transmission and the synchrony of an electrical rhythm in mouse inferior olive. We suggest that electrical synapses are a component of an “extended PSD” sensitive toShank3mutations that produce intellectual disability, at least in part, by impairing electrical synaptic transmission.
Cinnamon bark extract suppresses metastatic dissemination of cancer cells through inhibition of glycolytic metabolism
Authors: Konno Yuki , Maruyama Ami , Tomita Masaru , Makinoshima Hideki , Nakayama Joji 
Published: March 2021

AbstractMetastasis, a leading contributor to the morbidity of cancer patients, occurs through multiple steps. As each of these steps is promoted by different molecular mechanisms, blocking metastasis needs to target each of these steps. Here we report that cinnamon bark extract (CBE) has a suppressor effect on metastatic dissemination of cancer cells. Though a zebrafish embryo screen which utilizes conserved mechanisms between metastasis and zebrafish gastrulation for identifying anti-metastasis drugs, CBE was identified to interfere with gastrulation progression of zebrafish. A zebrafish xenotransplantation model of metastasis validated that CBE suppressed metastatic dissemination of human cancer cells (MDA-MB-231). Interestingly, quantitative metabolome analyses revealed that CBE-treated MDA-MB-231 cells disrupted the production of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P), which are intermediate metabolites of glycolytic metabolism. CBE decreased the expression of hexokinase 2 (HK2), which catalyzes G6P production, and pharmacological inhibition of HK2 suppressed cell invasion and migration of MDA-MB-231 cells. Taken together, CBE suppressed metastatic dissemination of human cancer cells by inhibiting glycolytic metabolism.
Evolutionary differences in the ACE2 reveals the molecular origins of
COVID-19 susceptibility
Authors: Cheng Ryan R. , Dodero-Rojas Esteban , Di Pierro Michele , Onuchic José N. 
Published: March 2021

Abstract
We explore the energetic frustration patterns associated with the binding
between the SARS-CoV-2 spike protein and the ACE2 receptor protein in a broad
selection of animals. Using energy landscape theory and the concept of energy
frustration—theoretical tools originally developed to study protein folding—we
are able to identify interactions among residues of the spike protein and ACE2
that result in COVID-19 resistance. This allows us to identify whether or not a
particular animal is susceptible to COVID-19 from the protein sequence of ACE2
alone. Our analysis predicts a number of experimental observations regarding
COVID-19 susceptibility, demonstrating that this feature can be explained, at
least partially, on the basis of theoretical means.
Severely burned wood from wildfires has low functional potential in streams
Authors: Vaz Pedro Gonçalves , Merten Eric C. , Robinson Christopher T. , Pinto Paulo 
Published: March 2021

Abstract

More frequent and more severe forest fires mean more severely burned wood in streams. Instream wood provides habitat complexity, alters geomorphology, retains organic and inorganic material, promotes hyporheic flow and acts as substrate for biofilm and invertebrates. However, little is known about instream wood functions in fire‐prone biomes and how they combine with wood burning levels to guide postfire management efforts.

Over 3 years, we tracked instream wood following forest fires in central Portugal. We examined for the first time the influence of burning level, season and a large suite of driving factors on the likelihood of four different functions having primary ecological consequences—retention of organic matter, serving as substrate for aquatic biota, being key pieces forming wood jams and deflecting flow including pool habitat formation.

One of the main ecological functions of wood in rivers is to provide substrate for vegetation, periphyton, biofilm and oviposition. Our results show that this can be negatively affected when the wood is severely burned.

Except for jam formation, the probability of each stream wood function changed markedly with season and the probability of non‐function was nearly twice as high in the Euro‐Mediterranean dry season than in the wet season.

More anchored and decayed wood increased the probability of all functions, whereas the effect of submergence depended on the function. Challenging the ‘size paradigm’ that larger sized pieces provide more function, our data suggest that the effect of size is function‐specific.

Synthesis and applications. We show how postfire stream restoration success can be maximized by selecting the most appropriate wood and taking advantage of attribute‐function relationships. We urge managers to refrain from removing wood or to selectively remove the most severely carbonized only, allowing the persistence of great potential to provide substrate for stream biota. The non‐attraction of severely burned wood as substrate can be compensated for by other wood with attributes enhancing this function, such as wood deeper within the bankfull area, and with large diameters. These results will help to inform successful management, as is increasingly asked from restoration ecology.
What is better for animal conservation translocation programmes: Soft‐ or hard‐release? A phylogenetic meta‐analytical approach
Authors: Resende Paloma S. , Viana‐Junior Arleu B. , Young Robert John , Azevedo Cristiano S. 
Published: March 2021

Abstract

Animal conservation translocation is an important tool available to conservation biologists to address problems of isolated, declining or endangered populations. This approach includes both captive‐bred and free‐ranging origin animals, which are used to rescue genetically limited populations and re‐establish extirpated populations. Both soft‐ and hard‐release protocols (the release of animals with or without acclimatization, respectively) are used in animal conservation translocation programmes; however, there is no consensus on whether one has better conservation outcomes than the other.

Here, we analysed data from 17 studies to measure the efficiency of both techniques for fauna conservation. Using phylogenetic meta‐analysis, we compared results from articles that used soft‐ and hard‐release protocols to determine the overall effect size. In addition, we examined if the success metrics, type of environment, taxonomic group and animal's origin affected the outcomes of each type of translocation programmes.

We calculated 61 effect sizes for 17 species. We found that the soft‐release protocol is approximate 40% better than the hard‐release protocol (Estimates = 0.44, CI 95: 0.11–0.76). Soft‐release programme increased success by 77% (Estimates = 0.78, CI 95: 0.37–1.19) when movement metrics were used (as compared to hard‐release) and were 41% more successful with terrestrial species.

In general, soft‐releases showed better outcomes by reducing movements away from the release site, but this was driven mostly by terrestrial reptile translocations (77% chance of success); when birds and mammals or the other success metrics were evaluated, both release techniques had similar effects. Lastly, the origin (i.e. captive or wild) of the released animals did not influence the success rate of soft‐ versus hard‐releases.

Synthesis and applications. We conducted a meta‐analysis to evaluate which is the best release protocol for success in animal conservation: soft‐ or hard‐release. Our results showed that soft‐releases are in general better than hard‐releases, especially for reptiles. Protocol outcomes were similar for birds and mammals and were not linked to the origin of the released animals. We recommend that the decision of which protocol to use needs also to consider the financial costs of the used protocol.
Low‐cost tools mitigate climate change during reproduction in an endangered marine ectotherm
Authors: Clarke Leo J. , Elliot Rebecca L. , Abella‐Perez Elena , Jenkins Stuart R. , Marco Adolfo , Martins Samir , Hawkes Lucy A. 
Published: March 2021

Abstract

The impacts of anthropogenic climate change will be most dramatic for species that live in narrow thermal niches, such as reptiles. Given the imminent threat to biodiversity, and that actions to reduce carbon emissions are not yet sufficient, it is important that a sound evidence base of potential mitigation options is available for conservation managers.

Successful incubation and production of male sea turtle hatchlings is threatened by increased global temperatures (sex is determined by the temperature at which eggs incubate). Here we test two conservation tools to reduce incubation temperatures: clutch splitting and clutch shading, on a nesting loggerhead turtle Caretta caretta population in the Eastern Atlantic Ocean.

During the thermosensitive period of incubation, split and shaded clutches were both 1.00°C cooler than control nests. Clutch splitting (mean: 45 eggs) reduced nest temperatures by reducing metabolic heating during incubation compared to controls (mean: 92 eggs). Modelled primary sex ratios differed between nest treatments, with 1.50% (±6% SE) females produced in shaded nests, 45.00% (±7% SE) females in split nests and 69.00% (±6% SE) females in controls. Neither treatment affected hatchling size, success, mass or vigour. When clutch splitting was repeated 2 years later, hatch success was higher in split clutches compared to controls.

Synthesis and applications. Clutch splitting and clutch shading successfully altered the thermal profile of incubating turtle nests. When there is sufficient knowledge to better understand the effects of intervention on fundamental population demographics, they will be useful for reducing incubation temperatures in sea turtle nests, potentially increasing nest survival and male hatchling production. The effect of clutch splitting in reducing nest temperature was lower relative to clutch shading, but requires significantly less funding, materials and specialist skill, key factors for management of turtle rookeries that are often in remote, resource‐limited areas.
Walking the Dark Side: Evading Parliamentary Scrutiny
Authors: Judge David 
Published: March 2021

AbstractParliamentary scrutiny assumes a dual willingness—a willingness of government to be scrutinised and a willingness of Parliament to scrutinise, alongside a singular capacity: the ability of Parliament to scrutinise. In the official Westminster view of scrutiny these principles and practicalities are aligned and serve to illuminate the processes and actions of government. There is, however, also a ‘dark side’: where the principles and practicalities of scrutiny are not aligned. While an aversion to parliamentary scrutiny has been hard‐wired into the ‘executive mentality’, the ‘ministerial mindset’, and the ‘instincts of secrecy’ shared by all contemporary UK governments, an examination of the first eighteen months of Boris Johnson's premiership—in the exceptionally turbulent times of ‘getting Brexit done’ and ‘beating coronavirus’—reveals a distinct propensity of his Conservative government to walk on the dark side of parliamentary scrutiny in this period.
The effect of sample hemolysis on blood ethanol analysis using headspace gas chromatography
Authors: Kosecki Patrick Allan , Brooke Phillip , Abbott Lori , Canonico Erika 
Published: March 2021

AbstractHemolysis, a common occurrence in blood collected for chemical analysis, has been reported to affect analytical test results for some analytes depending upon the material tested and the analytical technique employed. The potential for hemolysis to impact blood ethanol determinations using headspace gas chromatography of samples diluted with an internal standard was investigated. A sample of non‐hemolyzed blood and a matched sample of hemolyzed blood were both analyzed thirty times for ethanol concentration using headspace gas chromatography. The mean ethanol concentration measured for the non‐hemolyzed samples was 0.0639 g/dl. The mean ethanol concentration measured for the hemolyzed samples was 0.0642 g/dl. The calculated t value, 1.897, was less than the critical t value, 2.002, at a 0.05 level of significance. There was no measured statistical difference detected between the mean blood ethanol concentration determined for a hemolyzed whole blood sample and a non‐hemolyzed whole blood sample.
Impact of patient race/ethnicity on emergency department management of pediatric gastroenteritis in the setting of a clinical pathway
Authors: Congdon Morgan , Schnell Stephanie A. , Londoño Gentile Tatiana , Faerber Jennifer A. , Bonafide Christopher P. , Blackstone Mercedes M. , Johnson Tiffani J. 
Published: March 2021

AbstractBackgroundAcute gastroenteritis (AGE) is a common pediatric diagnosis in emergency medicine, accounting for 1.7 million visits annually. Little is known about racial/ethnic differences in care in the setting of standardized care models.MethodsWe used quality improvement data for children 6 months to 18 years presenting to a large, urban pediatric emergency department (ED) treated via a clinical pathway for AGE/dehydration between 2011 and 2018. Race/ethnicity was evaluated as a single variable (non‐Hispanic [NH]‐White, NH‐Black, Hispanic, and NH‐other) related to ondansetron and intravenous fluid (IVF) administration, ED length of stay (LOS), hospital admission, and ED revisits using multivariable regression.ResultsOf 30,849 ED visits for AGE/dehydration, 18.0% were NH‐White, 57.2% NH‐Black, 12.5% Hispanic, and 12.3% NH‐other. Multivariable mixed‐effects generalized linear regression controlling for age, sex, triage acuity, payer, and language revealed that, compared to NH‐White patients, NH‐other patients were more likely to receive ondansetron (adjusted odds ratio [95% CI] = 1.30 [1.17 to 1.43]). NH‐Black, Hispanic, and NH‐other patients were significantly less likely to receive IVF (0.59 [0.53 to 0.65]; 0.74 [0.64 to 0.84]; 0.74 [0.65 to 0.85]) or be admitted to the hospital (0.54 [0.45 to 0.64]; 0.62 [0.49 to 0.78]; 0.76 [0.61 to 0.94]), respectively. NH‐Black and Hispanic patients had shorter LOS (median = 245 minutes for NH‐White, 176 NH‐Black, 199 Hispanic, and 203 NH‐other patients) without significant differences in ED revisits.ConclusionsDespite the presence of a clinical pathway to guide care, NH‐Black, Hispanic, and NH‐other children presenting to the ED with AGE/dehydration were less likely to receive IVF or hospital admission and had shorter LOS compared to NH‐White counterparts. There was no difference in patient revisits, which suggests discretionary overtreatment of NH‐White patients, even with clinical guidelines in place. Further research is needed to understand the drivers of differences in care to develop interventions promoting equity in pediatric emergency care.
Impact of early life geohelminths on wheeze, asthma and atopy in Ecuadorian children at 8 years
Authors: Cooper Philip J. , Chis Ster Irina , Chico Martha E. , Vaca Maritza , Oviedo Yisela , Maldonado Augusto , Barreto Mauricio L. , Platts‐Mills Thomas A. E. , Strachan David P. 
Published: March 2021

AbstractBackgroundEarly‐life exposures to geohelminths may protect against development of wheeze/asthma and atopy.ObjectiveTo study the effect of maternal geohelminths and infections in children during the first 5 years on atopy, wheeze/asthma and airways reactivity/inflammation at 8 years.MethodsBirth cohort of 2404 neonates followed to 8 years in rural Ecuador. Data on wheeze/asthma were collected by questionnaire and atopy by skin prick test (SPT) reactivity to 9 allergens. We measured airways reactivity to bronchodilator, fractional exhaled nitric oxide (FeNO) and nasal eosinophilia. Stool samples were examined for geohelminths by microscopy.Results1933 (80.4%) children were evaluated at 8 years. Geohelminths were detected in 45.8% of mothers and 45.5% of children to 5 years. Frequencies of outcomes at 8 years were as follows: wheeze (6.6%), asthma between 5 and 8 years (7.9%), SPT (14.7%), airways reactivity (10%) and elevated FeNO (10.3%) and nasal eosinophilia (9.2%). Any maternal geohelminth was associated with reduced SPT prevalence (OR 0.72). Childhood Trichuris trichiura infections during the first 5 years were associated with reduced wheeze (OR 0.57) but greater parasite burdens with Ascaris lumbricoides at 5 years were associated with increased wheeze (OR 2.83) and asthma (OR 2.60). Associations between maternal geohelminths and wheeze/asthma were modified by atopy. Parasite‐specific effects on wheeze/asthma and airways reactivity and inflammation were observed in non‐atopic children.ConclusionsOur data provide novel evidence for persistent effects of in utero geohelminth exposures on childhood atopy but highlight the complex nature of the relationship between geohelminths and the airways. Registered as an observational study (ISRCTN41239086).
Biallelic RFC1 pentanucleotide repeat expansions in Greek patients with late‐onset ataxia
Authors: Kontogeorgiou Zoi , Kartanou Chrisoula , Tsirligkani Chrysanthi , Anagnostou Evangelos , Rentzos Michail , Stefanis Leonidas , Karadima Georgia , Koutsis Georgios 
Published: March 2021

AbstractCerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) has been recently linked to biallelic expansions of a pentanucleotide repeat in the replication factor C subunit 1 (RFC1) gene. Herein, we sought to investigate the presence of pathological RFC1 expansions in selected Greek patients with late‐onset ataxia and delineate the phenotypic spectrum of genetically confirmed CANVAS in the Greek population. We screened genetically a total of 77 selected index patients, 67 originating from a cerebellar ataxia cohort and 10 from a hereditary neuropathy cohort. We identified five index cases (6.5%) with biallelic pathological RFC1 expansions, two in the cerebellar ataxia cohort (3%) and three in the neuropathy cohort (30%). Overall, four out of five of cases with full‐blown CANVAS and one case with sensory ataxic neuropathy had biallelic pathological expansions. The phenotypic spectrum of positive cases (including two affected siblings) was consistent with previous reports and implied that the sensory neuropathy may be the earliest feature in genetically confirmed CANVAS. Screening for biallelic RFC1 expansions is recommended in all cases with late‐onset ataxia of unknown cause, particularly when a sensory neuropathy is present.