bluuebunny/crossref_metadata_2025 huggingface dataset:
Visualizing the transiently populated closed-state of human HSP90 ATP binding domain
Authors: Henot Faustine , Rioual Elisa , Favier Adrien , Macek Pavel , Crublet Elodie , Josso Pierre , Brutscher Bernhard , Frech Matthias , Gans Pierre , Loison Claire , Boisbouvier Jerome
Published: December 2022

HSP90 are abundant molecular chaperones, assisting the folding of several hundred client proteins, including substrates involved in tumor growth or neurodegenerative diseases. A complex set of large ATP-driven structural changes occurs during HSP90 functional cycle. However, the existence of such structural rearrangements in apo HSP90 has remained unclear. Here, we identify a metastable excited state in the isolated human HSP90α ATP binding domain. We use solution NMR and mutagenesis to characterize structures of both ground and excited states. We demonstrate that in solution the HSP90α ATP binding domain transiently samples a functionally relevant ATP-lid closed state, distant by more than 30 Å from the ground state. NMR relaxation enables to derive information on the kinetics and thermodynamics of this interconversion, while molecular dynamics simulations establish that the ATP-lid in closed conformation is a metastable exited state. The precise description of the dynamics and structures sampled by human HSP90α ATP binding domain provides information for the future design of new therapeutic ligands.
Engineering antiviral immune-like systems for autonomous virus detection and inhibition in mice
Authors: Wang Yidan , Xu Ying , Tan Chee Wah , Qiao Longliang , Chia Wan Ni , Zhang Hongyi , Huang Qin , Deng Zhenqiang , Wang Ziwei , Wang Xi , Shen Xurui , Liu Canyu , Pei Rongjuan , Liu Yuanxiao , Xue Shuai , Kong Deqiang , Anderson Danielle E. , Cai Fengfeng , Zhou Peng , Wang Lin-Fa , Ye Haifeng
Published: December 2022

The ongoing COVID-19 pandemic has demonstrated that viral diseases represent an enormous public health and economic threat to mankind and that individuals with compromised immune systems are at greater risk of complications and death from viral diseases. The development of broad-spectrum antivirals is an important part of pandemic preparedness. Here, we have engineer a series of designer cells which we term autonomous, intelligent, virus-inducible immune-like (ALICE) cells as sense-and-destroy antiviral system. After developing a destabilized STING-based sensor to detect viruses from seven different genera, we have used a synthetic signal transduction system to link viral detection to the expression of multiple antiviral effector molecules, including antiviral cytokines, a CRISPR-Cas9 module for viral degradation and the secretion of a neutralizing antibody. We perform a proof-of-concept study using multiple iterations of our ALICE system in vitro, followed by in vivo functionality testing in mice. We show that dual output ALICESaCas9+Ab system delivered by an AAV-vector inhibited viral infection in herpetic simplex keratitis (HSK) mouse model. Our work demonstrates that viral detection and antiviral countermeasures can be paired for intelligent sense-and-destroy applications as a flexible and innovative method against virus infection.
An ionic vinylene-linked three-dimensional covalent organic framework for selective and efficient trapping of ReO4− or 99TcO4−
Authors: Zhang Cheng-Rong , Cui Wei-Rong , Yi Shun-Mo , Niu Cheng-Peng , Liang Ru-Ping , Qi Jia-Xin , Chen Xiao-Juan , Jiang Wei , Liu Xin , Luo Qiu-Xia , Qiu Jian-Ding
Published: December 2022

The synthesis of ionic olefin linked three-dimensional covalent organic frameworks (3D COFs) is greatly challenging given the hardness of the formation of stable carbon-carbon double bonds (–C = C–). Herein, we report a general strategy for designing porous positively charged sp2carbon-linked 3D COFs through the Aldol condensation promoted by quaternization. The obtained 3D COFs, namely TFPM-PZI and TAPM-PZI, showed impressive chemical stability. Furthermore, the positively charged frameworks with regular porosity endow 3D ionic COFs with selective capture radioactive ReO4−/TcO4−and great removal efficiency in simulated Hanford waste. This research not only broadens the category of 3D COFs but also promotes the application of COFs as efficient functional materials.
Biofilms preserve the transmissibility of a multi-drug resistance plasmid
Authors: Metzger Genevieve A. , Ridenhour Benjamin J. , France Michael , Gliniewicz Karol , Millstein Jack , Settles Matthew L. , Forney Larry J. , Stalder Thibault , Top Eva M.
Published: December 2022

Self-transmissible multidrug resistance (MDR) plasmids are a major health concern because they can spread antibiotic resistance to pathogens. Even though most pathogens form biofilms, little is known about how MDR plasmids persist and evolve in biofilms. We hypothesize that (i) biofilms act as refugia of MDR plasmids by retaining them in the absence of antibiotics longer than well-mixed planktonic populations and that (ii) the evolutionary trajectories that account for the improvement of plasmid persistence over time differ between biofilms and planktonic populations. In this study, we evolvedAcinetobacter baumanniiwith an MDR plasmid in biofilm and planktonic populations with and without antibiotic selection. In the absence of selection, biofilm populations were better able to maintain the MDR plasmid than planktonic populations. In planktonic populations, plasmid persistence improved rapidly but was accompanied by a loss of genes required for the horizontal transfer of plasmids. In contrast, in biofilms, most plasmids retained their transfer genes, but on average, plasmid, persistence improved less over time. Our results showed that biofilms can act as refugia of MDR plasmids and favor the horizontal mode of plasmid transfer, which has important implications for the spread of MDR.
Bulk RNA sequencing analysis of developing human induced pluripotent cell-derived retinal organoids
Authors: Agarwal Devansh , Kuhns Rian , Dimitriou Christos N. , Barlow Emmalyn , Wahlin Karl J. , Enke Ray A.
Published: December 2022

Retinogenesis involves the transformation of the anterior developing brain into organized retinal lamellae coordinated by intricate gene signalling networks. This complex process has been investigated in several model organisms such as birds, fish, mammals and amphibians, yet many facets of retinal development are different in humans and remain unexplored. In this regard, human pluripotent stem cell (hPSC)-derived 3D retinal organoids and Next Generation Sequencing (NGS) have emerged as key technologies that have facilitated the discovery of previously unknown details about cell fate specification and gene regulation in the retina. Here we utilized hPSCs integrated with fluorescent reporter genes (SIX6-p2A-eGFP/CRX-p2A-h2b-mRuby3) to generate retinal organoids and carry out bulk RNA sequencing of samples encompassing the majority of retinogenesis (D0-D280). This data set will serve as a valuable reference for the vision research community to characterize differentially expressed genes in the developing human eye.
Filamentation in low pressure conditions
Authors: Peña Jessica , Reyes Danielle , Richardson Martin
Published: December 2022

Filamentation is favorable for many long-range outdoor laser applications, some of which require propagation to or at high altitudes. Understanding how the filamentation process and filament properties are impacted by the low pressure conditions present at high altitudes is essential in designing effective applications. The scaling of filament preconditions with pressure is considered. An increase in critical power and decrease in transition numerical aperture (NA) is predicted to occur with a drop in pressure, indicating that nonlinear pulse propagation and filamentation at high altitudes requires higher energy and a longer assisted focal length than sea level filamentation. A summary of pressure-scaled filament properties is also presented. New simulations demonstrate filamentation at pressures as low as 0.0035 atm (38.5 km altitude) is possible.
Obesity is associated with myelin oligodendrocyte glycoprotein antibody-associated disease in acute optic neuritis
Authors: Stiebel-Kalish Hadas , Rubarth Kerstin , Shouchane-Blum Karny , Tiosano Alon , Lotan Itay , Hellmann Mark A. , Wilf-Yarkoni Adi , Bialer Omer , Flanagan Eoin P. , Pittock Sean J. , Bhatti M. Tariq , Schmitz-Hübsch Tanja , Paul Friedemann , Asseyer Susanna , Chen John J.
Published: December 2022

Optic neuritis (ON) is a frequent presentation at onset of multiple sclerosis (MS), neuromyelitis optica spectrum disorder (NMOSD), and myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD). The pathophysiology underlying these diseases, especially MOGAD, is still being elucidated. While obesity has been reported to potentially be a risk factor for MS, this has not been explored in NMOSD or MOGAD. We aimed to investigate a possible association between obesity (body mass index [BMI] > 30 kg/m2) in patients with MOGAD, aquaporin 4-IgG positive NMOSD (AQP4-IgG+ NMOSD) or MS. In this multicenter non-interventional retrospective study, data was collected from patients with a first ever demyelinating attack of ON subsequently diagnosed with MOGAD (n = 44), AQP4-IgG+ NMOSD (n = 49) or MS (n = 90) between 2005 and 2020. The following data was collected: age, sex, ethnicity, BMI (documented before corticosteroid treatment), and the ON etiology after diagnostic work-up. A mixed model analysis was performed to assess the potential of obesity or BMI to predict MOGAD-ON, and to distinguish MOGAD-ON from AQP4-IgG+ NMOSD-ON and MS-ON. Main outcome measures included BMI in patients with acute ON and subsequent diagnosis of MOGAD, AQP4-IgG+ NMOSD or MS. A higher BMI was significantly associated with a diagnosis of MOGAD-ON (p < 0.001); in MOGAD patients the mean BMI was 31.6 kg/m2 (standard deviation (SD) 7.2), while the mean BMI was 24.7 kg/m2 (SD 5.3) in AQP4-IgG+ NMOSD patients, and 26.9 kg/m2 (SD 6.2) in MS patients. Mixed-effects multinomial logistic regression, adjusted for age and sex, with obesity as a binary variable, revealed that obesity was associated with a higher odds ratio (OR) of a subsequent MOGAD diagnosis (OR 5.466, 95% CI [2.039, 14.650], p = 0.001) in contradistinction with AQP4-IgG+ NMOSD. This study suggests an association between obesity and MOGAD. Our findings require further exploration, but could have significant pathophysiologic implications if confirmed in larger prospective studies.
Mask images on Twitter increase during COVID-19 mandates, especially in Republican counties
Authors: Lin Xiaofeng , Kernell Georgia , Groeling Tim , Joo Jungseock , Luo Jun , Steinert-Threlkeld Zachary C.
Published: December 2022

Wearing masks reduces the spread of COVID-19, but compliance with mask mandates varies across individuals, time, and space. Accurate and continuous measures of mask wearing, as well as other health-related behaviors, are important for public health policies. This article presents a novel approach to estimate mask wearing using geotagged Twitter image data from March through September, 2020 in the United States. We validate our measure using public opinion survey data and extend the analysis to investigate county-level differences in mask wearing. We find a strong association between mask mandates and mask wearing—an average increase of 20%. Moreover, this association is greatest in Republican-leaning counties. The findings have important implications for understanding how governmental policies shape and monitor citizen responses to public health crises.
A comparison of node vaccination strategies to halt SIR epidemic spreading in real-world complex networks
Authors: Sartori F. , Turchetto M. , Bellingeri M. , Scotognella F. , Alfieri R. , Nguyen N.-K.-K. , Le T.-T. , Nguyen Q. , Cassi D.
Published: December 2022

We compared seven node vaccination strategies in twelve real-world complex networks. The node vaccination strategies are modeled as node removal on networks. We performed node vaccination strategies both removing nodes according to the initial network structure, i.e., non-adaptive approach, and performing partial node rank recalculation after node removal, i.e., semi-adaptive approach. To quantify the efficacy of each vaccination strategy, we used three epidemic spread indicators: the size of the largest connected component, the total number of infected at the end of the epidemic, and the maximum number of simultaneously infected individuals. We show that the best vaccination strategies in the non-adaptive and semi-adaptive approaches are different and that the best strategy also depends on the number of available vaccines. Furthermore, a partial recalculation of the node centrality increases the efficacy of the vaccination strategies by up to 80%.
Identification and characterization of proteins that form the inner core Ixodes scapularis tick attachment cement layer
Authors: Mulenga Albert , Radulovic Zeljko , Porter Lindsay , Britten Taylor Hollman , Kim Tae Kwon , Tirloni Lucas , Gaithuma Alex Kiarie , Adeniyi-Ipadeola Grace O. , Dietrich Jolene K. , Moresco James J. , Yates John R.
Published: December 2022

Ixodes scapularis long-term blood feeding behavior is facilitated by a tick secreted bio adhesive (tick cement) that attaches tick mouthparts to skin tissue and prevents the host from dislodging the attached tick. Understanding tick cement formation is highly sought after as its disruption will prevent tick feeding. This study describes proteins that form the inner core layer of I. scapularis tick cement as disrupting these proteins will likely stop formation of the outer cortical layer. The inner core cement layer completes formation by 24 h of tick attachment. Thus, we used laser-capture microdissection to isolate cement from cryosections of 6 h and 24 h tick attachment sites and to distinguish between early and late inner core cement proteins. LC–MS/MS analysis identified 138 tick cement proteins (TCPs) of which 37 and 35 were unique in cement of 6 and 24 h attached ticks respectively. We grouped TCPs in 14 functional categories: cuticular protein (16%), tick specific proteins of unknown function, cytoskeletal proteins, and enzymes (13% each), enzymes (10%), antioxidant, glycine rich, scaffolding, heat shock, histone, histamine binding, proteases and protease inhibitors, and miscellaneous (3–6% each). Gene ontology analysis confirm that TCPs are enriched for bio adhesive properties. Our data offer insights into tick cement bonding patterns and set the foundation for understanding the molecular basis of I. scapularis tick cement formation.
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

It 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

Brain–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

The 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

Eye 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

The 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

A 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

We 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

Neopterin, 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

Urologic 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

Staphylococcus 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

Twenty-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

Wastewaters 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

Bancha 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.
Expert pianists make specific exaggerations for teaching
Authors: Tominaga Atsuko , Knoblich Günther , Sebanz Natalie
Published: December 2022

Experts modulate their performance of actions for teaching purposes, performing slower and exaggerated movements when demonstrating novel actions to novices. The present study asked whether such modulations also occur during teaching performance of a music instrument, where subtle movement modulations are crucial for achieving artistic expression. While exaggerating performances of goal-directed actions outside of artistic contexts may be straightforward, it is an open question whether and how exaggeration for the purpose of teaching operates for actions that are expressive even when performed outside of a teaching context. Pianists were asked to demonstrate to students the techniques required for implementing notated expressions, compared to performing the piece without didactic intentions. Expressions in the piece concerned either articulation (i.e., legato and staccato) or dynamics (i.e., forte and piano). The pianists played either with the goal to perform the piece to an audience or with the goal to teach the respective techniques to novices. When intending to teach articulation, skilled pianists produced more exaggerated staccato. When intending to teach dynamics, they created a larger contrast between forte and piano. We found consistent results across a simple musical scale (Experiment 1) and a more naturalistic piece of music (Experiment 2). These findings show that teaching-specific action modulations generalise to expressive actions and suggest that action modulations serve to highlight the most relevant aspects of the actions to be learnt.
Hypoxia-associated prognostic markers and competing endogenous RNA coexpression networks in lung adenocarcinoma
Authors: Xiong Lecai , He Xueyu , Wang Le , Dai Peng , Zhao Jinping , Zhou Xuefeng , Tang Hexiao
Published: December 2022

Lung adenocarcinoma (LUAD) is the most common form of non-small cell lung cancer (NSCLC). Hypoxia has been found in 50–60% of locally advanced solid tumors and is associated with poor prognosis in various tumors, including NSCLC. This study focused on hypoxia-associated molecular hallmarks in LUAD. Fifteen hypoxia-related genes were selected to define the hypoxia status of LUAD by ConsensusClusterPlus based on data from The Cancer Genome Atlas (TCGA). Then, we investigated the immune status under different hypoxia statuses. Subsequently, we constructed prognostic models based on hypoxia-related differentially expressed genes (DEGs), identified hypoxia-related microRNAs, lncRNAs and mRNAs, and built a network based on the competing endogenous RNA (ceRNA) theory. Two clusters (Cluster 1 and Cluster 2) were identified with different hypoxia statuses. Cluster 1 was defined as the hypoxia subgroup, in which all 15 hypoxia-associated genes were upregulated. The infiltration of CD4+ T cells and Tfh cells was lower, while the infiltration of regulatory T (Treg) cells, the expression of PD-1/PD-L1 and TMB scores were higher in Cluster 1, indicating an immunosuppressive status. Based on the DEGs, a risk signature containing 7 genes was established. Furthermore, three differentially expressed microRNAs (hsa-miR-9, hsa-miR-31, hsa-miR-196b) associated with prognosis under different hypoxia clusters and their related mRNAs and lncRNAs were identified, and a ceRNA network was built. This study showed that hypoxia was associated with poor prognosis in LUAD and explored the potential mechanism from the perspective of the gene signature and ceRNA theory.
Resting state functional connectivity as a marker of internalizing disorder onset in high-risk youth
Authors: Pawlak McKinley , Bray Signe , Kopala-Sibley Daniel C.
Published: December 2022

While research has linked alterations in functional connectivity of the default mode (DMN), cognitive control (CCN), and salience networks (SN) to depression and anxiety, little research has examined whether these alterations may be premorbid vulnerabilities. This study examined resting state functional connectivity (RSFC) of the CCN, DMN, and SN as markers of risk for developing an onset of a depressive or anxiety disorder in adolescents at high familial risk for these disorders. At baseline, 135 participants aged 11–17 completed resting-state functional magnetic resonance imaging, measures of internalizing symptoms, and diagnostic interviews to assess history of depressive and anxiety disorders. Diagnostic assessments were completed again at 9- or 18-month follow-up for 112 participants. At baseline, increased CCN connectivity to areas of the visual network, and decreased connectivity between the left SN and the precentral gyrus, predicted an increased likelihood of a new onset at follow-up. Increased connectivity between the right SN and postcentral gyrus at baseline predicted first episode onsets at follow-up. Altered connectivity between these regions may represent a risk factor for developing a clinically significant onset of an internalizing disorder. Results may have implications for understanding the neural bases of internalizing disorders for early identification and prevention efforts.
Distribution of controlled unitary quantum gates towards factoring large numbers on today’s small-register devices
Authors: Tănăsescu Andrei , Constantinescu David , Popescu Pantelimon George
Published: December 2022

Factoring a 2048-bit number using Shor’s algorithm, when accounting for error correction, reportedly requires 400,000 qubits. However, it is well known that there is yet much time before we will have this many qubits in the same local system. This is why we propose a protocol for distributed quantum computation applicable to small register devices, specifically for the distribution of controlled unitary gates, the key element in the construction of every quantum computation algorithm. We leverage quantum sharing of partial results to obtain a parallel processing scheme, allowing for the first time the quantum distribution of very large gates with thousands of inputs using only small register devices with tens of qubits. In this way, we improve all previous controlled unitary gate distribution approaches, obtaining surprising results. The impact is quantified for recent milestone hardware realizations of quantum processors.
Dual-energy CT iodine map in predicting the efficacy of neoadjuvant chemotherapy for hypopharyngeal carcinoma: a preliminary study
Authors: Wei Xianfeng , Cao Rui , Li Han , Long Miaomiao , Sun Peipei , Zheng Yongzhe , Li Li , Yin Jianzhong
Published: December 2022

Neoadjuvant chemotherapy has become one of the important means for advanced hypopharyngeal carcinoma. So far, there is no effective index to predict the curative effect. To investigate the value of iodine map of dual-energy computed tomography (CT) in predicting the efficacy of neoadjuvant chemotherapy for hypopharyngeal carcinoma. A total of 54 hypopharyngeal carcinomapatients who underwent two courses of TPF neoadjuvant chemotherapy were recruited in this study. Three cases had a complete response (CR), thirty-six cases had a partial response (PR), eleven cases had stable disease (SD), and four cases had a progressive disease (PD) after the chemotherapy. All patients underwent a dual-source CT scan before chemotherapy and rescanned after chemotherapy. The normalized iodine-related attenuation (NIRA) of the mean of maximum slice and most enhanced region of lesion at arterial and parenchymal phase were measured: NIRAmean-A, NIRAmax-A, NIRAmean-P, and NIRAmax-P, respectively. Correlation analysis was conducted between different metrics of NIRA and the diameter change rate of lesions, and the curative effect was evaluated based on the receiver operating characteristic (ROC) curve. There were a significant correlation between NIRAmean-A, NIRAmax-A, NIRAmean-P, NIRAmax-P and the change rate of lesion’s maximum diameter (ΔD%) (all P < 0.01). The NIRAmax-A, NIRAmean-P, NIRAmax-P had significant differences between CR, PR, SD, PD groups, but NIRAmean-A did not reach a significant difference. All NIRAmean-A, NIRAmax-A, NIRAmean-P, NIRAmax-P had significant differences between effective (CR + PR) and ineffective (SD + PD) groups. The ROC analysis revealed that NIRAmean-P had the largest AUC and prediction efficacy (AUC = 0.809). Dual-energy CT iodine map could predict the efficacy of neoadjuvant chemotherapy and provides imaging evidence to assist in treatment decisions for hypopharyngeal carcinoma patients.
Floquet engineering of tilted and gapped Dirac bandstructure in 1T$$^\prime$$-MoS$$_2$$
Authors: Iurov Andrii , Zhemchuzhna Liubov , Gumbs Godfrey , Huang Danhong , Tse Wang-Kong , Blaise Kathy , Ejiogu Chinedu
Published: December 2022

We have developed a rigorous theoretical formalism for Floquet engineering, investigating, and subsequently tailoring most crucial electronic properties of 1T$$^\prime$$

′

-MoS$$_2$$

2

by applying an external high-frequency dressing field within the off-resonance regime. It was recently demonstrated that monolayer semiconducting 1T$$^\prime$$

′

-MoS$$_2$$

2

exhibits tunable and gapped spin- and valley-polarized tilted Dirac bands. The electron-photon dressed states depend strongly on the polarization of the applied irradiation and reflect a full complexity of the low-energy Hamiltonian for non-irradiated material. We have calculated and analyzed the properties of the electron dressed states corresponding to linear and circular polarization of a dressing field by focusing on their symmetry, anisotropy, tilting, direct and indirect band gaps. Circularly polarized dressing field is known for transition into a new electronic state with broken time-reversal symmetry and a non-zero Chern number, and therefore, the combination of these topologically non-trivial phases and transitions between them could reveal some truly unique and previously unknown phenomena and applications. We have also computed and discussed the density of states for various types of 1T$$^\prime$$

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-MoS$$_2$$

2

materials and its modification in the presence of a dressing field.