bluuebunny/crossref_metadata_2025_split huggingface dataset:
The computational age‐at‐death estimation from 3D surface models of the adult pubic symphysis using data mining methods
Authors: Kotěrová Anežka , Štepanovský Michal , Buk Zdeněk , Brůžek Jaroslav , Techataweewan Nawaporn , Velemínská Jana 
Published: June 2022

AbstractAge-at-death estimation of adult skeletal remains is a key part of biological profile estimation, yet it remains problematic for several reasons. One of them may be the subjective nature of the evaluation of age-related changes, or the fact that the human eye is unable to detect all the relevant surface changes. We have several aims: (1) to validate already existing computer models for age estimation; (2) to propose our own expert system based on computational approaches to eliminate the factor of subjectivity and to use the full potential of surface changes on an articulation area; and (3) to determine what age range the pubic symphysis is useful for age estimation. A sample of 483 3D representations of the pubic symphyseal surfaces from theossa coxaeof adult individuals coming from four European (two from Portugal, one from Switzerland and Greece) and one Asian (Thailand) identified skeletal collections was used. A validation of published algorithms showed very high error in our dataset—the Mean Absolute Error (MAE) ranged from 16.2 and 25.1 years. Two completely new approaches were proposed in this paper: SASS (Simple Automated Symphyseal Surface-based) and AANNESS (Advanced Automated Neural Network-grounded Extended Symphyseal Surface-based), whose MAE values are 11.7 and 10.6 years, respectively. Lastly, it was demonstrated that our models could estimate the age-at-death using the pubic symphysis over the entire adult age range. The proposed models offer objective age estimates with low estimation error (compared to traditional visual methods) and are able to estimate age using the pubic symphysis across the entire adult age range.
Key role of mitochondrial mutation Leu107Ser (COX1) in deltamethrin resistance in salmon lice (Lepeophtheirus salmonis)
Authors: Tschesche Claudia , Bekaert Michaël , Bassett David I. , Boyd Sally , Bron James E. , Sturm Armin 
Published: June 2022

AbstractThe pyrethroid deltamethrin (DTM) is used to treat Atlantic salmon (Salmo salar) against salmon louse (Lepeophtheirus salmonis) infestations. However, DTM resistance has evolved in L. salmonis and is currently common in the North Atlantic. This study aimed to re-assess the association between DTM resistance and mitochondrial (mtDNA) mutations demonstrated in previous reports. Among 218 L. salmonis collected in Scotland in 2018–2019, 89.4% showed DTM resistance in bioassays, while 93.6% expressed at least one of four mtDNA single nucleotide polymorphisms (SNPs) previously shown to be resistance associated. Genotyping at further 14 SNP loci allowed to define three resistance-associated mtDNA haplotypes, named 2, 3 and 4, occurring in 72.0%, 14.2% and 7.3% of samples, respectively. L. salmonis strains IoA-02 (haplotype 2) and IoA-10 (haplotype 3) both showed high levels (~ 100-fold) of DTM resistance, which was inherited maternally in crossing experiments. MtDNA haplotypes 2 and 3 differed in genotype for 17 of 18 studied SNPs, but shared one mutation that causes an amino acid change (Leu107Ser) in the cytochrome c oxidase subunit 1 (COX1) and was present in all DTM resistant while lacking in all susceptible parasites. We conclude that Leu107Ser (COX1) is a main genetic determinant of DTM resistance in L. salmonis.
Decision-making psychological state and characteristic of proxies of thrombolytic patients: a pilot study
Authors: Yuanli Guo , Yanjin Liu , Lina Guo , Xiaofang Dong , Caixia Yang , Min Wang , Huanhuan Gao , Peihua Lv , Keke Ma 
Published: June 2022

AbstractIntravenous thrombolysis is the preferred treatment modality for acute ischemic stroke. In China, written informed consent from patients or proxies must be obtained before intravenous thrombolysis is performed, which always leads to in-hospital delay of thrombolysis. To explore the relationship between characteristics of thrombolysis decision-making and psychological states of proxies of AIS patients. This was a pilot study. 231 proxies of AIS patients were recruited, including 147 males and 84 females. STAI, WFPTS, CAOT, CPS, C-DCS and time-consuming of decision-making were collected by trained nurses during the period from signing informed consent to thrombolysis finished. The general information was collected within 24 h after admission. Pearson correlation analysis and the Ridge regression analysis were used to explore the correlation and causality between psychological indicators (STAI, WFPTS, CAOT, CPS) and decision-making characteristics (C-DCS, Time consuming). Structural equation modeling was used to explore the direct and indirect effect of psychological factors on decision-making characteristics. The mean of anxiety, trust in physicians, and decision conflict were 49.20 ± 9.50, 37.83 ± 6.63 and 30.60 ± 14.77, respectively. The CAOT was associated with C-DCS through the mediation of STAI and WFPTS (p < 0.001). The CAOT was associated with time-consuming through the mediation of STAI, WFPTS and CPS (p < 0.05). The CAOT, STAI and WFPTS were associated with C-DCS (p < 0.05), and STAI, WFPTS and CPS were associated with time-consuming (p < 0.01). The proxy of patients with acute ischemic stroke had severe decision conflict in thrombolysis decision-making. The psychological state was associated with decision conflict and the time-consuming. Medical staff should explore methods to release the anxiety and increase the trust in physicians to reduce the decision-making conflict and time-consuming, which could promote the smooth progress of the informed consent.
Predictive blood biomarkers of sheep pregnancy and litter size
Authors: Goldansaz Seyed Ali , Markus Susan , Plastow Graham , Wishart David S. 
Published: June 2022

AbstractEarly detection of sheep pregnancy and the prediction of how many lambs a pregnant ewe delivers affects sheep farmers in a number of ways, most notably with regard to feed management, lambing rate, and sheep/lamb health. The standard practice for direct detection of sheep pregnancy and litter size (PLS) is ultrasonography. However, this approach has a number of limitations. Indirect measurement of PLS using blood biomarkers could offer a simpler, faster and earlier route to PLS detection. Therefore, we undertook a large-scale metabolomics study to identify and validate predictive serum biomarkers of sheep PLS. We conducted a longitudinal experiment that analyzed 131 serum samples over five timepoints (from seven days pre-conception to 70 days post-conception) from six commercial flocks in Alberta and Ontario, Canada. Using LC–MS/MS and NMR, we identified and quantified 107 metabolites in each sample. We also identified three panels of serum metabolite biomarkers that can predict ewe PLS as early as 50 days after breeding. These biomarkers were then validated in separate flocks consisting of 243 animals yielding areas-under-the-receiver-operating-characteristic-curve (AU-ROC) of 0.81–0.93. The identified biomarkers could lead to the development of a simple, low-cost blood test to measure PLS at an early stage of pregnancy, which could help optimize reproductive management on sheep farms.
Alterations in metal homeostasis occur prior to canonical markers in Huntington disease
Authors: Pfalzer Anna C. , Yan Yan , Kang Hakmook , Totten Melissa , Silverman James , Bowman Aaron B. , Erikson Keith , Claassen Daniel O. 
Published: June 2022

AbstractThe importance of metal biology in neurodegenerative diseases such as Huntingtin Disease is well documented with evidence of direct interactions between metals such as copper, zinc, iron and manganese and mutant Huntingtin pathobiology. To date, it is unclear whether these interactions are observed in humans, how this impacts other metals, and how mutant Huntington alters homeostatic mechanisms governing levels of copper, zinc, iron and manganese in cerebrospinal fluid and blood in HD patients. Plasma and cerebrospinal fluid from control, pre-manifest, manifest and late manifest HD participants were collected as part of HD-Clarity. Levels of cerebrospinal fluid and plasma copper, zinc, iron and manganese were measured as well as levels of mutant Huntingtin and neurofilament in a sub-set of cerebrospinal fluid samples. We find that elevations in cerebrospinal fluid copper, manganese and zinc levels are altered early in disease prior to alterations in canonical biomarkers of HD although these changes are not present in plasma. We also evidence that CSF iron is elevated in manifest patients. The relationships between plasma and cerebrospinal fluid metal are altered based on disease stage. These findings demonstrate that there are alterations in metal biology selectively in the CSF which occur prior to changes in known canonical biomarkers of disease. Our work indicates that there are pathological changes related to alterations in metal biology in individuals without elevations in neurofilament and mutant Huntingtin.
Novel smart window using photonic crystal for energy saving
Authors: Zaky Zaky A. , Aly Arafa H. 
Published: June 2022

AbstractSmart windows are emerging as an effective way of minimizing energy consumption in buildings. They attracted the major relevance for minimizing energy consumption in buildings. More research studies are needed to design smart windows with operating wide range and don’t require additional energy to operate. We suggest a novel smart window structure using photonic crystal to regulate the solar radiation intensity by preventing it from penetrating the buildings in summer. For the first time, the suggested smart window photonic crystal at room temperature is proposed. The suggested smart window can block about 400 nm of near-infrared. This smart window model doesn’t require additional heat or electric input to operate.
An interpretable machine learning approach to identify mechanism of action of antibiotics
Authors: Mongia Mihir , Guler Mustafa , Mohimani Hosein 
Published: June 2022

AbstractAs antibiotic resistance is becoming a major public health problem worldwide, one of the approaches for novel antibiotic discovery is re-purposing drugs available on the market for treating antibiotic resistant bacteria. The main economic advantage of this approach is that since these drugs have already passed all the safety tests, it vastly reduces the overall cost of clinical trials. Recently, several machine learning approaches have been developed for predicting promising antibiotics by training on bioactivity data collected on a set of small molecules. However, these methods report hundreds/thousands of bioactive molecules, and it remains unclear which of these molecules possess a novel mechanism of action. While the cost of high-throughput bioactivity testing has dropped dramatically in recent years, determining the mechanism of action of small molecules remains a costly and time-consuming step, and therefore computational methods for prioritizing molecules with novel mechanisms of action are needed. The existing approaches for predicting bioactivity of small molecules are based on uninterpretable machine learning, and therefore are not capable of determining known mechanism of action of small molecules and prioritizing novel mechanisms. We introduce InterPred, an interpretable technique for predicting bioactivity of small molecules and their mechanism of action. InterPred has the same accuracy as the state of the art in bioactivity prediction, and it enables assigning chemical moieties that are responsible for bioactivity. After analyzing bioactivity data of several thousand molecules against bacterial and fungal pathogens available from Community for Open Antimicrobial Drug Discovery and a US Food and Drug Association-approved drug library, InterPred identified five known links between moieties and mechanism of action.
Transcriptomic and proteomic profiling of peptidase expression in Fasciola hepatica eggs developing at host’s body temperature
Authors: Ilgová Jana , Vorel Jiří , Roudnický Pavel , Škorpíková Lucie , Horn Martin , Kašný Martin 
Published: June 2022

AbstractFasciola hepatica is a global parasite of livestock which also causes a neglected zoonosis in humans. The parasite’s communication with the host during its complicated lifecycle is based on an ingenious enzymatic apparatus which includes a variety of peptidases. These enzymes are implicated in parasite migration, pathogenesis of the disease, and modification of host immune response. Although the dynamics of proteolytic machinery produced by intra-mammalian F. hepatica life stages has been previously investigated in great detail, peptidases of the eggs so far received little scientific attention. In this study, we performed a comparative RNA-seq analysis aimed at identification of peptidases expressed in F. hepatica eggs, cultured at 37 °C to represent gall bladder retained eggs, for different time periods and employed mass spectrometry in order to identify and quantify peptidases translated in F. hepatica egg lysates. We demonstrated that F. hepatica eggs undergo significant molecular changes when cultured at the physiological temperature of the definitive host. Egg transcriptome is subject to numerous subtle changes while their proteome is even more variable. The peptidase profile is considerably modified on both transcriptome and proteome level. Finally, we measured and classified proteolytic activities in extracts from F. hepatica eggs using a library of fluorogenic substrates and peptidase class-selective inhibitors. Activities of threonine peptidases were detected constantly, while the cysteine peptidases prevailing in freshly laid eggs are substituted by aspartic peptidase and metallopeptidase activities in the later stages of egg development.
A colorimetric method to measure in vitro nitrogenase functionality for engineering nitrogen fixation
Authors: Payá-Tormo Lucía , Coroian Diana , Martín-Muñoz Silvia , Badalyan Artavazd , Green Robert T. , Veldhuizen Marcel , Jiang Xi , López-Torrejón Gema , Balk Janneke , Seefeldt Lance C. , Burén Stefan , Rubio Luis M. 
Published: June 2022

AbstractBiological nitrogen fixation (BNF) is the reduction of N2 into NH3 in a group of prokaryotes by an extremely O2-sensitive protein complex called nitrogenase. Transfer of the BNF pathway directly into plants, rather than by association with microorganisms, could generate crops that are less dependent on synthetic nitrogen fertilizers and increase agricultural productivity and sustainability. In the laboratory, nitrogenase activity is commonly determined by measuring ethylene produced from the nitrogenase-dependent reduction of acetylene (ARA) using a gas chromatograph. The ARA is not well suited for analysis of large sample sets nor easily adapted to automated robotic determination of nitrogenase activities. Here, we show that a reduced sulfonated viologen derivative (S2Vred) assay can replace the ARA for simultaneous analysis of isolated nitrogenase proteins using a microplate reader. We used the S2Vred to screen a library of NifH nitrogenase components targeted to mitochondria in yeast. Two NifH proteins presented properties of great interest for engineering of nitrogen fixation in plants, namely NifM independency, to reduce the number of genes to be transferred to the eukaryotic host; and O2 resistance, to expand the half-life of NifH iron-sulfur cluster in a eukaryotic cell. This study established that NifH from Dehalococcoides ethenogenes did not require NifM for solubility, [Fe-S] cluster occupancy or functionality, and that NifH from Geobacter sulfurreducens was more resistant to O2 exposure than the other NifH proteins tested. It demonstrates that nitrogenase components with specific biochemical properties such as a wider range of O2 tolerance exist in Nature, and that their identification should be an area of focus for the engineering of nitrogen-fixing crops.
Population dynamics of synanthropic rodents after a chemical and infrastructural intervention in an urban low-income community
Authors: Awoniyi Adedayo Michael , Venegas-Vargas Cristina , Souza Fabio Neves , Zeppelini Caio Graco , Hacker Kathryn P. , Carvalho-Pereira Ticiana , Marins Catarina Lobo , de Santana Mayara Carvalho , Pertile Arsinoê Cristina , Begon Michael , Ko Albert I. , Diggle Peter J. , Reis Mitermayer G. , Childs James E. , da Silva Eduardo Mendes , Costa Federico , Khalil Hussein 
Published: June 2022

AbstractSynanthropic rodents are ubiquitous in low-income communities and pose risks for human health, as they are generally resistant to control programs. However, few or no studies have evaluated the long-term effect of chemical and infrastructural interventions on rodent population dynamics, especially in urban low-income communities, or evaluated the potential recovery of their population following interventions. We conducted a longitudinal study in a low-income community in the city of Salvador (BA, Brazil) to characterize the effect of interventions (chemical and infrastructural) on the dynamics of rodent population, and documented the post-intervention recovery of their population. We evaluated the degree of rodent infestation in 117 households/sampling points over three years (2014–2017), using tracking plates, a proxy for rodent abundance/activity. We reported a significant lower rodent activity/abundance after the chemical and infrastructural interventions (Z = −4.691 (p < 0.001)), with track plate positivity decreasing to 28% from 70% after and before interventions respectively. Therefore, the combination of chemical and infrastructural interventions significantly decreased the degree of rodent infestation in the study area. In addition, no rodent population rebound was recorded until almost a year post-intervention, and the post-intervention infestation level did not attain the pre-intervention level all through the study. Moreover, among pre-treatment conditions, access to sewer rather than the availability of food was the variable most closely associated with household rodent infestation. Our study indicates that Integrated Pest Management (IPM)-approaches are more effective in reducing rodent infestation than the use of a single method. Our findings will be useful in providing guidance for long-term rodent control programs, especially in urban low-income communities.
A comprehensive bioinformatics analysis to identify potential prognostic biomarkers among CC and CXC chemokines in breast cancer
Authors: Hozhabri Hossein , Moghaddam Marziyeh Mazaheri , Moghaddam Madiheh Mazaheri , Mohammadian Ali 
Published: June 2022

AbstractBreast cancer (BC) is a major human health problem due to its increasing incidence and mortality rate. CC and CXC chemokines are associated with tumorigenesis and the progression of many cancers. Since the prognostic values of CC and CXC families' expression in various types of cancers are becoming increasingly evident, we aimed to conduct a comprehensive bioinformatics analysis elucidating the prognostic values of the CC and CXC families in BC. Therefore, TCGA, UALCAN, Kaplan–Meier plotter, bc-GenExMiner, cBioPortal, STRING, Enrichr, and TIMER were utilized for analysis. We found that high levels of CCL4/5/14/19/21/22 were associated with better OS and RFS, while elevated expression of CCL24 was correlated with shorter OS in BC patients. Also, high levels of CXCL9/13 indicated longer OS, and enhanced expression of CXCL12/14 was linked with better OS and RFS in BC patients. Meanwhile, increased transcription levels of CXCL8 were associated with worse OS and RFS in BC patients. In addition, our results showed that CCL5, CCL8, CCL14, CCL20, CCL27, CXCL4, and CXCL14 were notably correlated with the clinical outcomes of BC patients. Our findings provide a new point of view that may help the clinical application of CC and CXC chemokines as prognostic biomarkers in BC.
Mechanistic interaction studies of synthesized ZIF-8 nanoparticles with bovine serum albumin using spectroscopic and molecular docking approaches
Authors: Mittal Ashi , Gandhi Sona , Roy Indrajit 
Published: June 2022

AbstractNumerous studies have shown that nanosized zeolitic imidazolate framework particles (ZIF-8 NPs) serve as promising vehicles for pH-responsive drug delivery. An understanding of their interaction with serum proteins present in physiological systems will thus be of critical importance. In this work, monodisperse ZIF-8 NPs with an average size of 60 nm were synthesized at room temperature and characterized for their various physicochemical properties. Bovine serum albumin (BSA) was used as model serum protein for various interaction studies with ZIF-8 NPs. Spectroscopic techniques such as UV–visible and fluorescence spectroscopy indicated the formation of a ground-state complex with a binding constant of the order 103 M−1and a single binding site. Steady-state and time-resolved fluorescence spectroscopy confirmed the mechanism of quenching to be static. Conformational changes in the secondary structure of BSA were observed using CD and FT-IR spectroscopies. Binding sites were explored using molecular docking studies.
The safety and efficacy of laparoscopic gastrectomy for patients with locally advanced gastric cancer following neoadjuvant chemotherapy
Authors: Liu Lihang , Wang Chuandong , Li Feng , Zhang Xiaojuan , Cheng Xuefei , Lin Shengtao , Liu Yi , Yang Changshun , Li Weihua 
Published: June 2022

AbstractLimited researches focused on the application of laparoscopic gastrectomy (LG) in locally advanced gastric cancer (LAGC) patients following neoadjuvant chemotherapy (NACT). In this study, we aimed at illustrating the surgical and survival outcome of LG in LAGC patients following NACT. We performed a retrospective study of patients with LAGC who received either LG following NACT or upfront LG at Fujian Provincial Hospital between March 2013 and October 2018. Perioperative parameters, short-term and long-term outcomes were compared. The Kaplan–Meier estimator was used to describe the survival curves, and the differences were examined by the log-rank test. In total, 76 consecutive patients were enrolled into the NACT-LG (41 patients) and LG (35 patients) group. The postoperative hospital stay was significantly longer for LG than for NACT-LG (11.0 vs. 12.0 day, P = 0.031). Significant difference was found in Grade ≥ III severe postoperative complications in two groups (0 vs. 17.1%, P = 0.001). No patient died of postoperative complications in the NACT-LG group, and one patient (1/35, 2.9%) died of postoperative complications in the LG group. A forest plot revealed that most subgroups of LG group were at great risks of postoperative complications. Compared with the LG group, the NACT-LG group had a significantly better DFS (14.4% vs. 5.7%, P = 0.0299) and better OS (34.1% vs. 8.6%, P = 0.0061) at 3 years. NACT increased the safety of LG for patients with LAGC and offer better disease-free and overall survival. For patients with LAGC, LG following NACT should be the priority treatment.