bluuebunny/crossref_metadata_2025_split huggingface dataset:
Honey contamination from plant protection products approved for cocoa cultivation: a systematic review of existing research and methods
Authors: Boakye Richard G. , Stanley Dara A. , White Blanaid 
Published: December 2022

AbstractCocoa (Theobroma cocoa), which is the key ingredient of chocolate, is an important economic crop plant which supports the livelihoods of an estimated forty to fifty million people directly involved in its cultivation. Many cocoa producing countries, especially those from the developing world, rely on the income from cocoa export to support their economies. The plant is, however, prone to disease and pest attacks and therefore requires the application of large volumes of pesticides to guarantee satisfactory productions. Even though pesticides help protect the cocoa plant from disease and pest attacks, unintended effects of environmental contamination are also a possibility. Honey, a product of nectar collected by honeybees from flowers during foraging, may be a useful proxy for the extent to which landscapes are exposed to pesticides and the degree of pesticide accumulation in the environment. The overreaching question is: to what extent has the effect of pesticides imputed for cocoa production on honey received attention in research? In this present study, we conducted a systematic approach to quantify existing studies on honey contamination from plant protection products approved for cocoa cultivation. We observed that one hundred and sixty-nine different compounds, comprising some recommended and other unapproved compounds for cocoa cultivation, were detected in 81% of the reviewed 104 publications. Our results further point to the neonicotinoids as the most detected class of pesticides, with imidacloprid particularly being the single most detected compound. However, the most remarkable observation made from this study points to disproportionate studies of honey contamination from pesticides conducted in cocoa and non-cocoa producing countries with only 19% of the publications taking place in the latter. To bridge the gap, we suggest prioritising increased research in cocoa growing countries to ameliorate the significant gaps in knowledge owing to limited studies emanating from these geographic regions.
An Activity-Based Nanosensor for Minimally-Invasive Measurement of Protease Activity in Traumatic Brain Injury
Authors: Kudryashev Julia A. , Madias Marianne I. , Kandell Rebecca M. , Lin Queenie X. , Kwon Ester J. 
Published: December 2022

ABSTRACTCurrent screening and diagnostic tools for traumatic brain injury (TBI) have limitations in sensitivity and prognostication. Aberrant protease activity is a central process that drives disease progression in TBI and is associated with worsened prognosis; thus direct measurements of protease activity could provide more diagnostic information. In this study, we engineered a nanosensor that releases a measurable signal into the blood and urine in response to activity from the TBI-associated protease calpain. Readouts from our nanosensor were designed to be compatible with ELISA and lateral flow assays, clinically-relevant assay modalities. In a mouse model of TBI, we demonstrated greater sensitivity of the nanosensor with the addition of targeting ligands to hyaluronic acid. In evaluation of mice with mild or severe injuries, our nanosensor identified mild TBI with a higher sensitivity than the clinical biomarker GFAP. This nanosensor technology allows for measurement of TBI-associated proteases without the need to directly access brain tissue, and has the potential to complement existing TBI diagnostic tools.
Identification of inosine monophosphate dehydrogenase as a potential target for anti-monkeypox virus agents
Authors: Hishiki Takayuki , Morita Takeshi , Akazawa Daisuke , Ohashi Hirofumi , Park Eun-Sil , Kataoka Michiyo , Mifune Junki , Shionoya Kaho , Tsuchimoto Kana , Ojima Shinjiro , Azam Aa Haeruman , Nakajima Shogo , Yoshikawa Tomoki , Shimojima Masayuki , Kiga Kotaro , Maeda Ken , Suzuki Tadaki , Ebihara Hideki , Takahashi Yoshimasa , Watashi Koichi 
Published: December 2022

AbstractMonkeypox virus (MPXV) is a neglected zoonotic pathogen that caused a worldwide outbreak in May 2022. Given the lack of an established therapy, the development of an anti-MPXV strategy is of vital importance. To identify drug targets for the development of anti-MPXV agents, we screened a chemical library using an MPXV infection cell assay and found that gemcitabine, trifluridine, and mycophenolic acid (MPA) inhibited MPXV propagation. These compounds showed broad-spectrum anti-orthopoxvirus activities and presented lower 90% inhibitory concentrations (0.032-1.40 μM) than brincidofovir, an approved anti-smallpox agent. These three compounds have been suggested to target the post-entry step to reduce the intracellular production of virions. Knockdown of inosine monophosphate dehydrogenase (IMPDH), the rate-limiting enzyme of guanosine biosynthesis and a target of MPA, dramatically reduced MPXV DNA production. Moreover, supplementation with guanosine recovered the anti-MPXV effect of MPA, suggesting that IMPDH and its guanosine biosynthetic pathway regulate MPXV replication. By targeting IMPDH, we identified a series of compounds with stronger anti-MPXV activity than MPA. These evidences propose that IMPDH is a potential target for the development of anti-MPXV agents.ImportanceMonkeypox is a zoonotic disease caused by infection with the monkeypox virus, and a worldwide outbreak occurred in May 2022. The smallpox vaccine has recently been approved for clinical use against monkeypox in the United States. Although brincidofovir and tecovirimat are drugs approved for the treatment of smallpox by the U.S. Food and Drug Administration, their efficacy against monkeypox has not been established. Moreover, these drugs may present negative side effects. Therefore, new anti-monkeypox virus agents are needed. This study revealed that gemcitabine, trifluridine, and mycophenolic acid inhibited monkeypox virus propagation, exhibited broad-spectrum anti-orthopoxvirus activities. We also suggested inosine monophosphate dehydrogenase as a potential target for the development of anti-monkeypox virus agents. By targeting this molecule, we identified a series of compounds with stronger anti-monkeypox virus activity than mycophenolic acid.
Study protocol: Medium throughput, deep proteomic characterization of children with PIMS-TS, and identification of candidate diagnostic biomarkers
Authors: Roarty Cathal , Mills Clare , Tonry Claire , Cosgrove Peter , Norman-Bruce Hannah , Groves Helen , Watson Chris , Waterfield Tom 
Published: December 2022

AbstractSARS-CoV-2 infection in children results in a wide range of clinical outcomes. Paediatric Multisystem Inflammatory syndrome temporally associated with COVID-19(PIMS-TS) occurs weeks after a SARS-CoV-2 infection, and results in severe illness. This protocol describes a study to fully characterize the circulating proteome of children who have PIMS-TS, the proteome of healthy children who have previously been infected with SARS-CoV-2 and the proteome of febrile children with a confirmed invasive infection. Orthogonal proteomic techniques will be utilized to provide a deep proteomic characterization.
The Effects of the Timing of Diuretic Administration and Other Covariates on Urine Volume in Hospitalized Patients
Authors: Abbaspour Sara , Aguirre Aaron D. , Westover M. Brandon , Klerman Elizabeth B. 
Published: December 2022

Abstract“What time should I take my medicine?” is an increasingly important question. Current knowledge of time-of-day effects for specific medications in hospitalized patients with cardiovascular disease is very limited. In such patients, increased medication efficiency could potentially reduce dose use and/or the length of time in the Intensive Care Unit (ICU) and/or hospital – potentially improving patient outcomes and patient and family quality of life, and reducing financial costs. We studied whether the time of day or night a patient is given a diuretic affects urine volume response. In this observational study, data were from 7,704 patients (63% male, 18 to 98 years old) admitted to one hospital’s acute care cardiac units, cardiac ICUs, cardiac surgery ICUs, and/or non-cardiac ICUs, who received intravenous furosemide (a diuretic), had measurements of urine volume, were hospitalized for ≥ 3 days between January 2016 to July 2021 and were older than 18 years. We used machine learning (ML) techniques to analyze the data. The ML technique identified factors that were expected to predict urine volume response to the diuretic: sex, age, medication dose and time, creatinine concentration, diagnosis, and hospital unit. The ML technique also identified medication administration time 00:00–06:00 as a predictor of higher urine volume response. Randomized controlled trials should be conducted to quantify the relative effect of modifiable factors, such as time of medication administration.
A machine learning based image classification method to estimate fish sizes from images without a specified reference object
Authors: Silva Catarina NS , Dainys Justas , Simmons Sean , Audzijonyte Asta 
Published: December 2022

AbstractMost fish populations around the world are unassessed and their status is unknown. Size based methods could provide fast and transparent assessments, but they require information on fish sizes. Citizen science programs, social media and smart phone applications generate millions of georeferenced fish images globally. Machine learning based fish species and size identification could help turn these images into valuable data for population status assessments. We present a machine learning, image classification based method to identify fish size classes from photos of anglers holding fish. To train the model we group images into ten 5-10 cm size classes, similar to classes used in underwater visual fish surveys. The model was trained using 2602 images from angler citizen science platforms MyCatch and FishSizeProject. Although the number of images was limited, the model achieved an overall accuracy of ~50%. Importantly, the misidentification of size classes was consistent across 20 separate model training rounds, each conducted with an independent, random allocation of images for training and test datasets. Our method suggests that photo based fish size class identification is feasible, and that prediction uncertainty should be incorporated into subsequent analysis, as it is done with fish ageing errors in fisheries stock assessments.
Patterns and drivers of the diving behavior of large pelagic predators
Authors: Nuno Amy , Guiet Jérome , Baranek Brooke , Bianchi Daniele 
Published: December 2022

AbstractMany large pelagic predators, including shark, tuna, and billfish, periodically dive to deep oceanic layers, connecting the surface and mesopelagic ecosystems. However, the patterns and drivers of deep dives across species remain poorly understood. To close this gap, we conduct a meta-analysis of the diving behavior of 24 pelagic predator species from the global ocean, resulting in 671 independent diving depth estimates from 87 tagging studies. Our analysis reveals consistent large-scale patterns in diving depths, with predators diving deeper offshore and during the day, and shallower closer to the coast and during the night. Deep diving species show similar diving depths during the night, with deeper dives for sharks, and shallower dives for tuna and swordfish. These patterns are reversed during the day, widening the gap between day and night vertical ranges for these groups. In contrast, shallow diving species show smaller variations between day and night dives, with sharks diving slightly deeper on average, followed by tuna and billfish. Correlations with co-located environmental variables suggest an important predictive role for proxies of prey abundance and light availability, as well as variables that influence physiology, such as oxygen and temperature. These relationships are more robust for deep divers during the day, and shallow divers at night. Our analysis highlights the value of tagging observations for the development of a mechanistic, quantitative characterization of vertical habitat use of large marine predators and its environmental constraints.
Early excitatory and inhibitory modifications in the motor cortex following skill learning support motor memory consolidation and cortical plasticity overnight
Authors: Eisenstein Tamir , Furman-Haran Edna , Tal Assaf 
Published: December 2022

AbstractThe learning of new motor skills constitutes an inseparable part of our lives. Motor consolidation refers to the offline processing of motor memories following the acquisition of new motor skills. The animal literature suggests that the primary motor cortex (M1) plays a key role in motor memory consolidation, and structural and functional plasticity in M1 following motor consolidation have been demonstrated. However, the mechanisms supporting motor memory consolidation and plasticity in the human M1 are not well understood. Initial human neuroimaging studies show that the initial stages of motor learning in humans are accompanied by short-term temporal dynamics of the brain’s main excitatory and inhibitory neurotransmitters – Glutamate (Glu) and GABA – in M1, but it remains unclear how these relate to the question of motor memory consolidation.Here, we show that early Glu and GABA modifications in M1 following motor skill learning may play vital roles in supporting motor memory consolidation and neural plasticity that take place over longer time scales. Using a multimodal magnetic resonance approach implemented on ultra-high field 7T scanner in healthy young adults (n=36), we found increased Glu and decreased GABA in M1 during the initial offline period following learning to support consolidation-related local and inter-regional functions of M1, such as motor memory reactivation and increased functional connectivity with the striatum. These neurochemical changes also correlated with overnight structural and functional plasticity expressed as increased M1 grey matter volume and functional connectivity, while Glu modifications also correlated with adaptive behavior, as reflected by improvements in skill performance.Our results provide intriguing microscale mechanistic evidence to the potential distinctive roles of Glu and GABA in promoting motor memory consolidation and plasticity in the human M1. They also highlight a role for early neurochemical modifications to memory consolidation and plasticity in the human brain and may hold important clinical implications in rehabilitative settings such as in stroke and brain injury.
A 3D Clinical Face Phenotype Space of Genetic Syndromes using a Triplet-Based Singular Geometric Autoencoder
Authors: Mahdi Soha S. , Caldeira Eduarda , Matthews Harold , Vanneste Michiel , Nauwelaers Nele , Yuan Meng , Gong Shunwang , Bouritsas Giorgos , Baynam Gareth S , Hammond Peter , Spritz Richard , Klein Ophir D , Bronstein Michael , Hallgrimsson Benedikt , Peeters Hilde , Claes Peter 
Published: December 2022

AbstractClinical diagnosis of syndromes benefits strongly from objective facial phenotyping. This study introduces a novel approach to enhance clinical diagnosis through the development and exploration of a low-dimensional metric space referred to as the clinical face phenotypic space (CFPS). As a facial matching tool for clinical genetics, such CFPS can enhance clinical diagnosis. It helps to interpret facial dysmorphisms of a subject by placing them within the space of known dysmorphisms. In this paper, a triplet loss-based autoencoder developed by geometric deep learning (GDL) is trained using multi-task learning, which combines supervised and unsupervised learning approaches. Experiments are designed to illustrate the following properties of CFPSs that can aid clinicians in narrowing down their search space: a CFPS can 1) classify syndromes accurately, 2) generalize to novel syndromes, and 3) preserve the relatedness of genetic diseases, meaning that clusters of phenotypically similar disorders reflect functional relationships between genes. The proposed model consists of three main components: an encoder based on GDL optimizing distances between groups of individuals in the CFPS, a decoder enhancing classification by reconstructing faces, and a singular value decomposition layer maintaining orthogonality and optimal variance distribution across dimensions. This allows for the selection of an optimal number of CFPS dimensions as well as improving the classification capacity of the CFPS.
Comparative genetic study of the colony structure and colony spatial distribution between the higher termiteAmitermes parvulusand the lower, subterranean termiteReticulitermes flavipesin an urban environment
Authors: Eyer Pierre-André , Moran Megan N. , Richardson Steven , Shults Phillip T. , Liu Kuan-Ling Kelly , Blumenfeld Alexander J. , Davis Robert , Vargo Edward L. 
Published: December 2022

In insects, ecological competition has often resulted in phenotypic changes and modifications to foraging areas. In termites - and social insects as a whole - colonies cannot easily escape competition through the relocation of their colony. In these species, the outcomes of inter and intra-specific competition are influenced by different life history traits, such as colony size, breeding system (number and types of reproductives), food preference, tunneling patterns, nest site selection, and antagonism between colonies.Here, we investigated variation in breeding system and spatial distribution among colonies of a higher termiteAmitermes parvulusand a subterranean termiteReticulitermes flavipeswithin an urban landscape. We first developed microsatellite markers as a tool to study these life history traits inA. parvulus. Second, we assessed competitive exclusion or tolerance ofA. parvulusandR. flavipescolonies by determining their fine-scale distribution using monitoring stations on a grid site, and their large-scale distribution across an urban landscape. Third, we investigated the breeding system ofA. parvuluscolonies. We showed that the numerous colonies ofR. flavipesinhabiting a restricted area contrast with the few, but spatially expansive colonies ofA. parvulus, suggesting these species face different degrees of intra-specific competition. We showed that colonies ofA. parvulusfrequently merged together, and all of them were headed by inbred neotenic reproductives, two characteristics rarely observed in higher termites. Overall, our study revealed drastic differences in colony structure, breeding systems and foraging ranges between the two species. These differences may reflect differences in food preference and food availability between the two species allowing their co-existence within the same urban environment.
Computational and structural insights into the pre- and post-hydrolysis states of bovine multidrug resistance associated protein 1 (MRP1)
Authors: Tóth Ágota , Crespi Veronica , Janaszkiewicz Angelika , Di Meo Florent 
Published: December 2022

AbstractATP-binding cassette C-family drug membrane transporters play an important role in local pharmacokinetics,i.e., drug concentration in cellular compartments. From the structural point of view, only the bovine ortholog of the multidrug-resistance associated protein 1 (bMRP1) has been resolved. We here used μs-scaled molecular dynamics simulations to investigate the structure and dynamics ofbMRP1 in pre- and post-hydrolysis functional states. The present work aims to examine the slight but likely relevant structural differences between pre- and post-hydrolysis states of outward-facing conformations as well as the interactions between MRP1 and the surrounding lipid bilayer. Global conformational dynamics show unfavourable extracellular opening associated with nucleotide binding domain dimerization indicating that the post-hydrolysis state adopts a close-cleft conformation rather than an outward-open conformation. Our present simulations also highlight persistent interactions with annular cholesterol molecules and the expected active role of lipid bilayer in the allosteric communication between distant domains of MRP1 transporter.
Lumped Parameter Liver Simulation to Predict Acute Hemodynamic Alterations Following Partial Resections
Authors: Tithof Jeffrey , Pruett Timothy L. , Rao Joseph Sushil 
Published: December 2022

AbstractPartial liver resections are routinely performed in living donor liver transplantation and to debulk tumors in liver malignancies, but surgical decisions on vessel reconstruction for adequate inflow and outflow are challenging. Pre-operative evaluation is often limited to radiological imaging, which fails to account for post-resection hemodynamic alterations. Substantial evidence suggests post-surgical increase in local volume flow rate enhances shear stress, signaling hepatic regeneration, but excessive shear stress has been postulated to result in small for size syndrome and liver failure. Predicting hemodynamic alterations throughout the liver is particularly challenging due to the dendritic architecture the vasculature, spanning several orders of magnitude in diameter. Therefore, we developed a mathematical lumped parameter model with realistic heterogeneities capturing inflow/outflow of the human liver to simulate acute perfusion alterations following surgical resection. Our model is parameterized using clinical measurements, relies on a single free parameter, and accurately captures established perfusion characteristics. We quantify acute changes in volume flow rate, flow speed, and wall shear stress following variable, realistic liver resections and make comparisons to the intact liver. Our numerical model runs in minutes and can be adapted to patient-specific anatomy, providing a novel computational tool aimed at assisting pre- and intra-operative surgical decisions for liver resections.
Preservation of Mitochondrial Membrane Potential is Necessary for Lifespan Extension from Dietary Restriction
Authors: Berry Brandon J. , Mjelde Evan , Carreno Fatima , Gilham Kathryn , Hanson Emily J. , Na Emily , Kaeberlein Matt 
Published: December 2022

ABSTRACTDietary restriction (DR) increases lifespan in many organisms, but its underlying mechanisms are not fully understood. Mitochondria play a central role in metabolic regulation and are known to undergo changes in structure and function in response to DR. Mitochondrial membrane potential (Δψm) is the driving force for ATP production and mitochondrial outputs that integrate many cellular signals. One such signal regulated by Δψmis nutrient-status sensing. Here, we tested the hypothesis that DR promotes longevity through preserved Δψmduring adulthood. Using the nematodeCaenorhabditis elegans, we find that Δψmdeclines with age relatively early in the lifespan, and this decline is attenuated by DR. Pharmacologic depletion of Δψmblocked the longevity and health benefits of DR. Genetic perturbation of Δψmand mitochondrial ATP availability similarly prevented lifespan extension from DR. Taken together, this study provides further evidence that appropriate regulation of Δψmis a critical factor for health and longevity in response to DR.