bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contemporaneous sample data tracking for the generation of genome edited cell lines
Authors: Plant Anne L. , Halter Michael W. , Stinson Jeffrey R. , Greene Gretchen R. 
Published: December 2022

AbstractIt is difficult to capture the large numbers of steps and details that often characterize research in the biomedical sciences. We present an approach that is based on commercial spreadsheet software so it is easily adaptable by the experimentalist. The approach is designed to be compatible with an experimentalist’s workflow and allows the capture in real time of detailed information associated, in this use case, with laboratory actions involved in the process of editing, enriching and isolating clonal gene-edited pluripotent stem cell (PSC) lines. Intuitive features and flexibility allow an experimentalist without extensive programming knowledge to modify spreadsheets in response to changes in protocols and to perform simple queries. The experimental details are collated in a table format from which they can be exported in open standard formats (e.g., Extensible Markup Language (XML) or Comma Separated Values (CSV) for ingestion into a data repository supporting interoperability with other applications. We demonstrate a sample- and file-naming convention that enables the automated creation of file directory folders with human readable semantic titles within a local file system. These operations facilitate the local organization of documentation and data for each cell line derived from each transfection in designated folder/file locations. This approach is generalizable to experimental applications beyond this use case.
Unsupervised adaptation of an ECoG based brain–computer interface using neural correlates of task performance
Authors: Rouanne Vincent , Costecalde Thomas , Benabid Alim Louis , Aksenova Tetiana 
Published: December 2022

AbstractBrain–computer interfaces (BCIs) translate brain signals into commands to external effectors, and mainly target severely disabled users. The usability of BCIs may be improved by reducing their major constraints, such as the necessity for special training sessions to initially calibrate and later keep up to date the neural signal decoders. In this study, we show that it is possible to train and update BCI decoders during free use of motor BCIs. In addition to the neural signal decoder controlling effectors (control decoder), one more classifier is proposed to detect neural correlates of BCI motor task performances (MTP). MTP decoders reveal whether the actions performed by BCI effectors matched the user’s intentions. The combined outputs of MTP and control decoders allow forming training datasets to update the control decoder online and in real time during free use of BCIs. The usability of the proposed auto-adaptive BCI (aaBCI) is demonstrated for two principle BCIs paradigms: with discrete outputs (4 classes BCI, virtual 4-limb exoskeleton), and with continuous outputs (cursor 2D control). The proof of concept was performed in an online simulation study using an ECoG dataset collected from a tetraplegic during a BCI clinical trial. The control decoder reached a multiclass area under the ROC curve of 0.7404 using aaBCI, compared to a chance level of 0.5173 and to 0.8187 for supervised training for the multiclass BCI, and a cosine similarity of 0.1211 using aaBCI, compared to a chance level of 0.0036 and to 0.2002 for supervised training for the continuous BCI.
The absence of an invasive air sac system in the earliest dinosaurs suggests multiple origins of vertebral pneumaticity
Authors: Aureliano Tito , Ghilardi Aline M. , Müller Rodrigo T. , Kerber Leonardo , Pretto Flávio A. , Fernandes Marcelo A. , Ricardi-Branco Fresia , Wedel Mathew J. 
Published: December 2022

AbstractThe origin of the air sac system present in birds has been an enigma for decades. Skeletal pneumaticity related to an air sac system is present in both derived non-avian dinosaurs and pterosaurs. But the question remained open whether this was a shared trait present in the common avemetatarsalian ancestor. We analyzed three taxa from the Late Triassic of South Brazil, which are some of the oldest representatives of this clade (233.23 ± 0.73 Ma), including two sauropodomorphs and one herrerasaurid. All three taxa present shallow lateral fossae in the centra of their presacral vertebrae. Foramina are present in many of the fossae but at diminutive sizes consistent with neurovascular rather than pneumatic origin. Micro-tomography reveals a chaotic architecture of dense apneumatic bone tissue in all three taxa. The early sauropodomorphs showed more complex vascularity, which possibly served as the framework for the future camerate and camellate pneumatic structures of more derived saurischians. Finally, the evidence of the absence of postcranial skeletal pneumaticity in the oldest dinosaurs contradicts the homology hypothesis for an invasive diverticula system and suggests that this trait evolved independently at least 3 times in pterosaurs, theropods, and sauropodomorphs.
No evidence that gaze anxiety predicts gaze avoidance behavior during face-to-face social interaction
Authors: Tönsing Daniel , Schiller Bastian , Vehlen Antonia , Spenthof Ines , Domes Gregor , Heinrichs Markus 
Published: December 2022

AbstractEye contact is an indispensable social signal, yet for some individuals it is also a source of discomfort they fear and avoid. However, it is still unknown whether gaze anxiety actually produces avoidant gaze behavior in naturalistic, face-to-face interactions. Here, we relied on a novel dual eye-tracking setup that allows us to assess interactive gaze behavior. To investigate the effect of gaze anxiety on gaze behavior, we a priori created groups of participants reporting high or low levels of gaze anxiety. These participants (n = 51) then performed a semi-standardized interaction with a previously unknown individual reporting a medium level of gaze anxiety. The gaze behavior of both groups did not differ in either classical one-way, eye-tracking parameters (e.g. unilateral eye gaze), or interactive, two-way ones (e.g. mutual gaze). Furthermore, the subjective ratings of both participants’ interaction did not differ between groups. Gaze anxious individuals seem to exhibit normal gaze behavior which does not hamper the perceived quality of interactions in a naturalistic face-to-face setup. Our findings point to the existence of cognitive distortions in gaze anxious individuals whose exterior behavior might be less affected than feared by their interior anxiety.
The measuring aerosol spreading during countermeasures (MASC) study presents an automated system to investigate face mask efficacy and other aerosol countermeasures in varying environments
Authors: Schreiber Johannes , Brüggmann Dörthe , Braun Markus , Groneberg David A. 
Published: December 2022

AbstractThe COVID-19 pandemic exemplified the importance of research on personal protective equipment. In specific, understanding how effective surgical masks or particulate filter respirators are at reducing the transmission of infectious diseases has suddenly become one of the most pressing issues for legislators, regulators, and everyday life. However, there was a lack of available scientific platforms to assess this issue. Therefore, we designed and built a system entitled MASC: measuring aerosol spreading during countermeasures. This platform allows the simulation of various everyday situations and evaluation of the efficacy of masks and respirators in reducing the amount of inhaled particulate matter from the air. Furthermore, MASC can be used to investigate how aerosols propagate in closed spaces, such as offices or classrooms. It can be used to generate aerosols on command and control the room temperature, humidity, and wind speed. Up to four laser aerosol spectrometers can be read simultaneously, and a camera can automatically take pictures to evaluate the efficacy of countermeasures to prevent the spread of aerosols. The aerosol generation, measurement periods, and the number of repetitions for an experiment can be configured digitally and are executed by a computer automatically. A website displays the data in real time and allows monitoring of the experiment. Upon completion, statistical values are calculated automatically to accelerate the evaluation of the gathered data. Codes and technical drawings in this present methodology publication are open source and can be used by the scientific community to establish similar systems.
An exopolysaccharide-producing novel Agrobacterium pusense strain JAS1 isolated from snake plant enhances plant growth and soil water retention
Authors: Kaur Jaspreet , Mudgal Gaurav , Chand Kartar , Singh Gajendra B. , Perveen Kahkashan , Bukhari Najat A. , Debnath Sandip , Mohan Thotegowdanapalya C. , Charukesi Rajulu , Singh Gaurav 
Published: December 2022

AbstractA peculiar bacterial growth was very often noticed in leaf-initiated tissue cultures of Sansevieriatrifasciata, a succulent belonging to the Asparagaceae family. The isolate left trails of some highly viscous material on the walls of the suspension vessels or developed a thick overlay on semisolid media without adversities in plant growth. FTIR identified this substance to be an extracellular polysaccharide. Various morphological, biochemical tests, and molecular analyses using 16S rRNA, atpD, and recA genes characterized this isolate JAS1 as a novel strain of Agrobacteriumpusense. Its mucoidal growth over Murashige and Skoog media yielded enormous exopolysaccharide (7252 mg l−1), while in nutrient agar it only developed fast-growing swarms. As a qualifying plant growth-promoting bacteria, it produces significant indole-3-acetic acid (86.95 mg l−1), gibberellic acid (172.98 mg l−1), ammonia (42.66 µmol ml−1). Besides, it produces siderophores, 1-aminocyclopropane-1-carboxylicaciddeaminase, fixes nitrogen, forms biofilms, and productively solubilizes soil inorganic phosphates, and zinc. Under various treatments with JAS1, wheat and chickpea resulted in significantly enhanced shoot and root growth parameters. PGP effects of JAS1 positively enhanced plants’ physiological growth parameters reflecting significant increments in overall chlorophyll, carotenoids, proline, phenols, flavonoids, and sugar contents. In addition, the isolated strain maintained both plant and soil health under an intermittent soil drying regime, probably by both its PGP and EPS production attributes, respectively.
Uptrend in global managed honey bee colonies and production based on a six-decade viewpoint, 1961–2017
Authors: Phiri Bernard J. , Fèvre Damien , Hidano Arata 
Published: December 2022

AbstractWe conducted a retrospective study to examine the long-term trends for the global honey bee population and its two main products: honey and beeswax. Our analysis was based on the data collected by the Food and Agriculture Organization of the United Nations from 1961 to 2017. During this period, there were increases in the number of managed honey bee colonies (85.0%), honey production (181.0%) and beeswax production (116.0%). The amount of honey produced per colony increased by 45.0%, signifying improvements in the efficiency for producing honey. Concurrently, the human population grew by 144.0%. Whilst the absolute number of managed colonies increased globally, the number per capita declined by 19.9% from 13.6 colonies per 1000 population in 1961 to 10.9 colonies per 1000 population in 2017. Beeswax had a similar trend as the global production per capita reduced by 8.5% from 8.2 to 7.5 kg per 1000 population. In contrast, the global honey production per capita increased by 42.9% at the global level. The global human population growth outpaced that of managed honey bee colonies. Continuation of this trend raises the possibility of having a shortfall of pollinators to meet the increasing consumer demand for pollinated crops. To mitigate these challenges locally driven solutions will be key as influencing factors differed geographically.
Urinary neopterin reflects immunological variation associated with age, helminth parasitism, and the microbiome in a wild primate
Authors: Schneider-Crease India A. , Feder Jacob A. , Baniel Alice , McCann Colleen , Haile Abebaw Azanaw , Abebe Belayneh , Fitzgerald Lauren , Gomery Megan A. , Simberloff Ruth A. , Petrie Zack L. , Gabriel Sarah , Dorny Pierre , Fashing Peter J. , Nguyen Nga , Bergman Thore J. , Beehner Jacinta C. , Snyder-Mackler Noah , Lu Amy 
Published: December 2022

AbstractNeopterin, a product of activated white blood cells, is a marker of nonspecific inflammation that can capture variation in immune investment or disease-related immune activity and can be collected noninvasively in urine. Mounting studies in wildlife point to lifetime patterns in neopterin related to immune development, aging, and certain diseases, but rarely are studies able to assess whether neopterin can capture multiple concurrent dimensions of health and disease in a single system. We assessed the relationship between urinary neopterin stored on filter paper and multiple metrics of health and disease in wild geladas (Theropithecus gelada), primates endemic to the Ethiopian highlands. We tested whether neopterin captures age-related variation in inflammation arising from developing immunity in infancy and chronic inflammation in old age, inflammation related to intramuscular tapeworm infection, helminth-induced anti-inflammatory immunomodulation, and perturbations in the gastrointestinal microbiome. We found that neopterin had a U-shaped relationship with age, no association with larval tapeworm infection, a negative relationship with metrics related to gastrointestinal helminth infection, and a negative relationship with microbial diversity. Together with growing research on neopterin and specific diseases, our results demonstrate that urinary neopterin can be a powerful tool for assessing multiple dimensions of health and disease in wildlife.
Engineered human organ-specific urethra as a functional substitute
Authors: Caneparo Christophe , Chabaud Stéphane , Fradette Julie , Bolduc Stéphane 
Published: December 2022

AbstractUrologic patients may be affected by pathologies requiring surgical reconstruction to re-establish a normal function. The lack of autologous tissues to reconstruct the urethra led clinicians toward new solutions, such as tissue engineering. Tridimensional tissues were produced and characterized from a clinical perspective. The balance was optimized between increasing the mechanical resistance of urethral-engineered tissue and preserving the urothelium’s barrier function, essential to avoid urine extravasation and subsequent inflammation and fibrosis. The substitutes produced using a mix of vesical (VF) and dermal fibroblasts (DF) in either 90%:10% or 80%:20% showed mechanical resistance values comparable to human native bladder tissue while maintaining functionality. The presence of mature urothelium markers such as uroplakins and tight junctions were documented. All substitutes showed similar histological features except for the noticeable decrease in polysaccharide globules for the substitutes made with a higher proportion of DF. The degree of maturation evaluated with electron microscopy was positively correlated with the increased concentration of VF in the stroma. Substitutes produced with VF and at least 10% of DF showed sufficient mechanical resistance to withstand surgeon manipulation and high functionality, which may improve long-term patients’ quality of life, representing a great future alternative to current treatments.
Biological properties of Staphylococcus virus ΦSA012 for phage therapy
Authors: Fujiki Jumpei , Nakamura Tomohiro , Nakamura Keisuke , Nishida Keita , Amano Yurika , Watanabe Yusaku , Gondaira Satoshi , Usui Masaru , Shimizu Masaru , Miyanaga Kazuhiko , Watanabe Shinya , Iwasaki Tomohito , Kiga Kotaro , Hanawa Tomoko , Higuchi Hidetoshi , Sawa Teiji , Tanji Yasunori , Tamura Yutaka , Cui Longzhu , Iwano Hidetomo 
Published: December 2022

AbstractStaphylococcus virus ΦSA012 has a wide host range and efficient lytic activity. Here, we assessed the biological stability of ΦSA012 against temperature, freeze-thawing, and pH to clinically apply the phage. In addition, inoculation of ΦSA012 through i.p. and i.v. injections into mice revealed that phages were reached the limit of detection in serum and accumulated notably spleens without inflammation at 48 h post-inoculation. Furthermore, inoculation of ΦSA012 through s.c. injections in mice significantly induced IgG, which possesses neutralizing activity against ΦSA012 and other Staphylococcus viruses, ΦSA039 and ΦMR003, but not Pseudomonas viruses ΦS12-3 and ΦR18 or Escherichia viruses T1, T4, and T7 in vitro. Immunoelectron microscopic analysis showed that purified anti-phage IgG recognizes the long-tail fiber of staphylococcus viruses. Although S. aureus inoculation resulted in a 25% survival rate in a mouse i.p. model, ΦSA012 inoculation (i.p.) improved the survival rate to 75%; however, the survival rate of ΦSA012-immunized mice decreased to less than non-immunized mice with phage i.v. injection at a MOI of 100. These results indicated that ΦSA012 possesses promise for use against staphylococcal infections but we should carefully address the appropriate dose and periods of phage administration. Our findings facilitate understandings of staphylococcus viruses for phage therapy.
Acute and chronic blood serum proteome changes in patients with methanol poisoning
Authors: Cejnar Pavel , Smirnova Tatiana Anatolievna , Kuckova Stepanka , Prochazka Ales , Zak Ivan , Harant Karel , Zakharov Sergey 
Published: December 2022

AbstractTwenty-four blood serum samples from patients with acute methanol poisoning (M) from the mass methanol poisoning outbreak in the Czech Republic in 2012 were compared with 46 patient samples taken four years after poisoning (S) (overlap of 10 people with group M) and with a control group (C) of 24 samples of patients with a similar proportion of chronic alcohol abuse. When comparing any two groups, tens to hundreds of proteins with a significant change in concentration were identified. Fifteen proteins showed significant changes when compared between any two groups. The group with acute methanol poisoning showed significant changes in protein concentrations for at least 64 proteins compared to the other groups. Among the most important identified proteins closely related to intoxication are mainly those involved in blood coagulation, metabolism of vitamin A (increased retinol-binding protein), immune response (e.g., increased complement factor I, complement factors C3 and C5), and lipid transport (increased apolipoprotein A I, apolipoprotein A II, adiponectin). For blood coagulation, the most affected proteins with significant changes in the methanol poisoning group were von Willebrand factor, carboxypeptidase N, alpha-2-antiplasmin (all increased), inter-alpha-trypsin inhibitor heavy chain H4, kininogen-1, plasma serine protease inhibitor, plasminogen (all decreased). However, heparin administration used for the methanol poisoning group could have interfered with some of the changes in their concentrations. Data are available via ProteomeXchange with the identifier PXD035726.
Kinetic studies of dexamethasone degradation in aqueous solution via a photocatalytic UV/H2O2/MgO process
Authors: Asgari Ghorban , Salari Mehdi , Molla Mahmoudi Mohammad , Jamshidi Reza , Dehdar Ali , Faraji Hossein , Zabihollahi Solmaz , Alizadeh Saber 
Published: December 2022

AbstractWastewaters discharged from different industries and hospitals may contain pharmaceuticals, especially dexamethasone (DEX). Thus, we applied the UV/H2O2 photocatalytic method in the presence of the MgO nanoparticles to remove dexamethasone from synthetic wastewater. Moreover, the effects of parameters such as pH (3–11), hydrogen peroxide concentration (1–8 mM), initial DEX concentration (5–30 mg/L), and catalyst dosage (0.01–0.2 g/L) during the reaction times (0–30 min) were investigated. Furthermore, the efficiency of UV/H2O2 in the presence and absence of catalysts was investigated. The photocatalyst is characterized by X-ray diffraction (XRD), field emission scanning electron microscope (FE-SEM), and Fourier-transform infrared spectroscopy (FTIR) techniques. It was found that the removal rate was enhanced by decreasing pH and the initial dexamethasone concentration. The removal rate was enhanced somewhat with concentrations of hydrogen peroxide and MgO. In the case of UV/H2O2/MgO, 87% removal efficiency was achieved, under the optimal conditions: pH 3, contact time of 30 min, dexamethasone concentration of 20 mg/L, H2O2 of 0.5 mM, and UV radiation of 55 watts. The kinetic data indicated that the reaction followed the second-order kinetic model. The results showed that the UV/H2O2 photochemical process can efficiently remove dexamethasone from aqueous in the presence of a MgO catalyst, and the mineralization efficiency was reached at about 98%.
Multiple response optimizations on the leached-spray-dried bancha green tea towards healthy ageing
Authors: Paramita Vita , Masruchin Nanang , Wirohadidjojo Yohanes Widodo , Puruhito Buwono , Ariyanto Hermawan Dwi , Yulianto Mohamad Endy , Hartati Indah , Yohana Eflita , Hidayatulloh Furqon , Sutrisno Tris , Wijayanto Bagus 
Published: December 2022

AbstractBancha is a popular type of green tea in Japan, rich in tea polyphenols (TPs) and has a more astringent aroma with a less aromatic and strong character that complements functional foods. The blanching process is used to extract TPs and remove unwanted microorganisms, as well as inhibit phenolic oxidation. This study proposed a green tea blanching process followed by spray drying the extracts with maltodextrin. Furthermore, it is focused on maximizing the major chemical components of green tea (i.e., catechins, caffeine, and phenolic contents) based on powder particle size obtained through Multiple Response Surface Methodology optimizations. The results show that the proposed model accurately predicts leached-spray dried green tea’s total catechin and caffeine content, with a coefficient of 0.9475 and 0.8692, respectively. This process yielded composite desirability of 0.9751, while individual desirability yielded excellent results of 1.0000, 0.9188, 1.0000, and 0.9839 for catechin, caffeine, phenol content, and powder. The settings appear to yield functional results for entire responses. Due to the concerns in tropical skin nutrition applications, smaller particle size green tea can promote better adsorption than larger sizes.