bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular mechanism of glycolytic flux control intrinsic to human phosphoglycerate kinase
Authors: Yagi Hiromasa , Kasai Takuma , Rioual Elisa , Ikeya Teppei , Kigawa Takanori
Published: December 2021

Significance

Control of glycolytic flux plays an important role in energy production and metabolic homeostasis in cells. Phosphoglycerate kinase (PGK), a glycolytic enzyme, catalyzes reversible phosphotransfer to generate 3-phosphoglycerate (3PG) and adenosine triophosphate (ATP) in glycolysis. PGK controls glycolytic flux according to the intracellular [ATP]/[ADP] (adenosine diphosphate) ratio; however, its molecular mechanism remains unknown. Here, we report a protein-level regulation of the human PGK reaction by switching ligand-binding cooperativities between adenine nucleotides and 3PG, which is finely tuned to appropriately respond to changes in the intracellular [ATP]/[ADP] ratio. Our findings reveal a molecular mechanism intrinsic to human PGK that controls glycolytic flux by rapid adaptation to changes in the intracellular environment to avoid critical damage.
P2RY8 variants in lupus patients uncover a role for the receptor in immunological tolerance
Authors: He Yuke , Gallman Antonia E. , Xie Chengmei , Shen Qian , Ma Jianyang , Wolfreys Finn D. , Sandy Moriah , Arsov Todor , Wu Xiaoqian , Qin Yuting , Zhang Pingjing , Jiang Simon , Stanley Maurice , Wu Philip , Tan Jingjing , Ding Huihua , Xue Haiyan , Chen Wei , Xu Jinping , Criswell Lindsey A. , Nititham Joanne , Adamski Marcin , Kitching A. Richard , Cook Matthew C. , Cao Lanfang , Shen Nan , Cyster Jason G. , Vinuesa Carola G.
Published: December 2021

B cell self-tolerance is maintained through multiple checkpoints, including restraints on intracellular signaling and cell trafficking. P2RY8 is a receptor with established roles in germinal center (GC) B cell migration inhibition and growth regulation. Somatic P2RY8 variants are common in GC-derived B cell lymphomas. Here, we identify germline novel or rare P2RY8 missense variants in lupus kindreds or the related antiphospholipid syndrome, including a “de novo” variant in a child with severe nephritis. All variants decreased protein expression, F-actin abundance, and GPCR-RhoA signaling, and those with stronger effects increased AKT and ERK activity and cell migration. Remarkably, P2RY8 was reduced in B cell subsets from some SLE patients lacking P2RY8 gene variants. Low P2RY8 correlated with lupus nephritis and increased age-associated B cells and plasma cells. By contrast, P2RY8 overexpression in cells and mice restrained plasma cell development and reinforced negative selection of DNA-reactive developing B cells. These findings uncover a role of P2RY8 in immunological tolerance and lupus pathogenesis.
Reply to Comment on ‘Do electromagnetic waves always propagate along null geodesics?’
Authors: Asenjo Felipe A , Hojman Sergio A
Published: December 2021

A reply to the previous article commenting on non-geodesical propagation of electromagnetic fields on gravitational backgrounds and the eikonal limit are presented.
Vectorial variational problems in L
∞ constrained by the Navier–Stokes equations*
Authors: Clark Ed , Katzourakis Nikos , Muha Boris
Published: December 2021

We study a minimisation problem in L

p
and L
∞ for certain cost functionals, where the class of admissible mappings is constrained by the Navier–Stokes equations. Problems of this type are motivated by variational data assimilation for atmospheric flows arising in weather forecasting. Herein we establish the existence of PDE-constrained minimisers for all p, and also that L

p
minimisers converge to L
∞ minimisers as p → ∞. We further show that L

p
minimisers solve an Euler–Lagrange system. Finally, all special L
∞ minimisers constructed via approximation by L

p
minimisers are shown to solve a divergence PDE system involving measure coefficients, which is a divergence-form counterpart of the corresponding non-divergence Aronsson–Euler system.
Application of Random Forest Regressions on Stellar Parameters of A-type Stars and Feature Extraction*
Authors: Chen Shu-Xin , Sun Wei-Min , He Ying
Published: December 2021

Measuring the stellar parameters of A-type stars is more difficult than FGK stars because of the sparse features in their spectra and the degeneracy between effective temperature (T
eff) and gravity (log g). Modeling the relationship between fundamental stellar parameters and features through machine learning is possible because we can employ the advantage of big data rather than sparse known features. As soon as the model is successfully trained, it can be an efficient approach for predicting T
eff and log g for A-type stars especially when there is large uncertainty in the continuum caused by flux calibration or extinction. In this paper, A-type stars are selected from LAMOST DR7 with a signal-to-noise ratio greater than 50 and the T
eff ranging within 7000 to 10,000 K. We perform the Random Forest (RF) algorithm, one of the most widely used machine learning algorithms to establish the regression relationship between the flux of all wavelengths and their corresponding stellar parameters (T
eff) and (log g) respectively. The trained RF model not only can regress the stellar parameters but also can obtain the rank of the wavelength based on their sensibility to parameters. According to the rankings, we define line indices by merging adjacent wavelengths. The objectively defined line indices in this work are amendments to Lick indices including some weak lines. We use the Support Vector Regression algorithm based on our new defined line indices to measure the temperature and gravity and use some common stars from Simbad to evaluate our result. In addition, the Gaia Hertzsprung-Russell diagram is used for checking the accuracy of T
eff and log g.
Mining sector in the economic structure of South Kalimantan Province: direct and indirect impacts
Authors: Putri K S , Riswan  , Rahman I
Published: December 2021

Supporting sectors for sustainable economic development in a region can have a direct impact on GRDP and indirectly have an impact through strong backward and forward linkage to other economic sectors. Analysis of backward and forward linkages can be performed using input-output tables that describe the role of each sector in the regional economy. The abundance of coal resources in South Kalimantan Province makes the mining sector the largest contributor to GRDP. Coal is an export commodity that has a very large percentage of the total regional export value. The enormous impact on GRDP, both in terms of business fields and final demand, is not accompanied by strong linkages to other economic sectors. The existence of the mining sector is unable to stimulate production growth in the backward sector and is unable to fulfill the final demand of the forward sector. Restrictions on coal exports to fulfill domestic energy resource needs are able to make the mining sector of South Kalimantan Province a key sector to support sustainable regional economic development.
Antibacterial Activity of Sea Cucumber (Stichopus ocellatus) Against Bacillus cereus and Escherichia coli Bacteria
Authors: Sukmiwati M , Ilza M , Diharmi A , Sherrin S
Published: December 2021

Sea cucumber (Stichopus ocellatus) is one of the bioresources that has not been utilized optimally. Samples were collected in the coastal sea of Lengkang Island, Batam. This study was aimed to determine the bioactive compound and antibacterial activity of sea cucumber extract against Bacillus cereus and Escherichia coli. The research method used was an experiment with a series of experiments, namely the extraction of sea cucumbers with ethanol as a solvent. Parameter analysis were identification of bioactive compound (phytochemical) and antibacterial activity against Bacillus cereus and Escherichia coli using well diffusion method. The treatment for the antibacterial activity test used various extract concentrations consisting of 125, 250, 375, and 500 g/mL with three replications. The results of the identification of the bioactive compounds of sea cucumber extract showed that the ethanolic extract of sea cucumbers contained saponins, alkaloids, and phenolics. The analysis of the antibacterial activity of the sea cucumber extract showed that the diameter of the inhibition zone of the ethanol extract at a solvent ratio of 1: 5 (w/v) and at a concentration of 500µ/mL against B. cereus was 14.66 ± 0.37mm and E. coli was 15.45. ±0.17mm. The results showed that the highest antibacterial activity of sea cucumber extract against E. coli bacteria.
Assessment of Corbicula moltkiana Growth by Different Methods on Variation of Substrates in Lake Maninjau, West Sumatera, Indonesia
Authors: Ibrahim A , Lukman  , Dina R
Published: December 2021

Corbicula moltkiana is a mussel species in Lake Maninjau and one of the targeted fisheries resources in the lake. This study aimed to determine the feasibility of a controlled growth experiment of mollusk biota in describing their natural growth. The assessment was carried out in areas with different habitats in shore lake, namely sand and gravel-stone substrates. A consecutive 12 month- sampling was carried out from June 2013 to May 2104 using a Surber sampler at a 1-3 m depth were used to assess the wild population growth. Moreover, the growth of the controlled population was observed by rearing various sizes of mussels in artificial substrate namely three small baskets which installed in the shore area with 1-3 m depth at each station for four months. Monthly sampling was carried out to measure the shell length. The growth of C. moltkiana on wild population by VBGF methods show that at the gravel-stone substrate was higher, but the growth a controlled population in artificial substrate seemed in the sand substrate was higher than that in the gravel-stone substrate. The growth of aquatic biota in a controlled system (especially C. moltkiana) does not always reflect similar conditions to their wild growth.
Carapace Length-Weight Relationship and Condition Factors of Macrobrachium rosenbergii in The Rivers of Riau Province, Indonesia
Authors: Fauzi M , Prianto E , Mardalisa M , Hendrizal A , Hermawita A
Published: December 2021

Macrobrachium rosenbergii in Riau Province are almost found in all inland waters, especially in the big rivers, namely Indragiri, Kampar, Siak and Rokan. This species are still the main catch of fishermen even the catch has decreased. Deforestation along the watershed, decreasing water quality and habitat have a very bad impact on Macrobrachium rosenbergii. This study was conducted to determine the relationship of carapace length-weight and the condition factor of Macrobrachium rosenbergii in the rivers of Riau Province. The study used a survey method from May to June 2021. Data collection was carried out in the rivers of Riau Province at the center for giant prawns. Sampling was done randomly from the catches of fishermen. The biological parameters measured were carapace length and weight. The results showed that the relationship between carapace length and weight of giant prawns in the Siak River, Rokan River and Kampar River are 0.0008L2.8473, 0.0049L2.3906 and w = 0.0014L2.643, respectively. The length of the carapace can determine the weight of prawns up to 78.62-96.62%, where the relationship between carapace length and weight is very close. The growth pattern of giant prawns is allometric and the condition factor is 1.03-1.05.
Processing of Gelatin from the Skin of Pangasius hypopthalmus Using Papain Enzyme
Authors: Suparmi S , Edison E , Meivayana M
Published: December 2021

This study aimed to determine the processing of gelatin of catfish skin using the papain enzyme in 3 different concentrations. The method used was an experiment with a factorial Completely Randomized Design (CRD). The experiment consisted of 2 factors, namely papain enzyme concentration and the immersion time of the enzyme with 3 replications. The first factor consisted of 3 levels, namely the use of papain enzymes P1 (2%), P2 (4%) and P3 (6%). The second factor, the immersion time consisted of 3 levels of 25 minutes (W1), 35 minutes (W2) and 45 minutes (W3). The data were analyzed by using CRD. The results showed that the combination of P2W1 showed the best viscosity and gel strength (6.77 CP and 115.17 g bloom).
Enhanced photocatalytic degradation of N-doped TiO2-SiO2composite for degradation of phenol under simulated natural light assisted by S2O82-anions
Authors: Huynh Huu-Tai , Le Minh-Vien , Van Hoang Luan
Published: December 2021

In recent years, TiO2photocatalyst has been studied to increase the overall efficiency in the degradation of organic pollutants in water. Several solutions have been proposed such as non-metal doping to reduce a high band gap energy (3.2 eV) of TiO2to increase absorption in the visible region and synthesis of composite photocatalyst to improve the efficiency of electron-hole separation and the specific surface area. Herein, the N-doped TiO2-SiO2 photocatalysts were investigated. Powder samples with three molar ratios of TiO2/SiO2(95/5-TS5, 85/15-TS15, 75/25-TS25) were successfully synthesized, characterized, and estimated their photocatalytic activity toward the phenol degradation (initial concentration to be 10 ppm) under simulated natural light. N-doped TiO2-SiO2samples were prepared with molar ratios of N to designed TiO2to be 3%, 5%, 7%. The 3N-TS5 photocatalyst (3 mol % N doped TS5) shows the highest phenol efficiency degradation, to be 95% in 4 h, photocatalytic degradation rate constant of 1.02}10−2min−1due to its narrower band gap energy (3.05 eV). Furthermore, the addition of S2O82-anions at a concentration of 1 mM is enhanced degradation efficiency and degradation rate. And phenol is almost completely degraded within 60 min and achieved a degradation rate constant of 7.65*10−2min−1, 7.5 times higher than that without the presence of S2O82-anions. This attractive result is attributed to the generation of sulfate radical (SO4*“) during photolysis. Finally, N-doped TiO2-SiO2photocatalyst assisted by S2O82-anions shows potential to design and improve manufacturing processes to obtain photoreactors for organic degradation from waste-water under natural light degradation.
Use of wheat flour and spent coffee grounds in the production of cookies with high fiber and antioxidant content: Effects of spent coffee grounds ratio on the product quality
Authors: Trà Trấn Thi Thu , Phúc Lê Nguyên , Yến Võ Thi Ngoc , Sang Lê Thánh , Thu Nguyễn Thi Anh , Nguyệt Tôn Nữ Minh , Mẫn Lê Văn Việt
Published: December 2021

Spent coffee ground (SCG) is the main by-product of the instant coffee industry. In this study, wheat flour and dried SCG powder were used in the production of cookies with high fiber and antioxidant content. The objective of the study was to evaluate the effects of SCG ratio in the cookie formulation on nutritional quality, physical properties and sensory overall acceptability of the product. SCG is a rich source of dietary fiber. In 100 g dry weight of SCG, the total fiber and phenolic contents were 76.6 ± 0.58% and 3828±12 mg GAE/100g dry basis, respectively. When the SCG ratio increased from 0 to 0.25 of the composite flour weight, the dough had increased hardness and reduced adhesiveness, cohesiveness and springiness. An increase in the SCG ratio in the cookie formulation also decreased the diameter and thickness of the product but enhanced its hardness. Cookie samples supplemented with SCG had higher dietary fiber and phenolic content as well as a higher antioxidant activity than the control sample. Cookie samples were considered as high fiber food when the SCG ratio was 0.1 or higher. The use of SCG reduced the overall acceptability of cookies. When the ratio of SGC powder varied from 0.1 to 0.2, a sensory score of the obtained cookies was acceptable.
Analysis of rope based mechanism for movement of telescopic conveyor segments
Authors: Hadžikadunić Fuad
Published: December 2021

The subject of analysis in this paper are rope based mechanisms for the movement of the telescopic conveyors substructure. Experimental test of ropes in conjunction with pulleys on 2 telescopic conveyors were performed in order to assess the real cause of damage and cracking of ropes in a full sense, which occurred in the real application of the conveyor at the site. These are examples of two conveyors with the same characteristics on which combinations of ropes with characteristics of construction of cross section 7x19 and construction of cross section 19x7 are placed, as well as combinations of pulleys with two kinds of grooves. Some specific tests are performed that showed the best combination of construction driving system elements.
Optimization of injection parameters from the aspect of dimension accuracy
Authors: Ćoralić Amir
Published: December 2021

During the injection molding process, the polymers are subject to shrinkage and bending, which causes an unwanted change in geometry. These deficiencies can be caused by many factors: injection pressure, overpressure, overpressure time, cooling, etc. Within this work, the influence of overpressure and overpressure time on the accuracy of product dimensions is presented. Dimension control was performed by measuring on a 3D coordinate machine. The products are injected in 2 different combinations of parameters. For each combination of parameters, measurements were performed in five injection cycles.
Determination of the bending strength of corner joint – metal corner brace, for corps furniture made of refined panels of particleboards
Authors: Antovska Ivana , Krstev Marija , Jevtoska Elena , Gruevski Gjorgi
Published: December 2021

This paper presents data about the bending strength of outside corner joint – metal corner brace, for corps furniture made of refined panels of particleboard with a width of 25 mm. The research was conducted on two kinds of samples. The two kinds of sample objects are divided in two groups according to the way of composition as follows:

group 1: the first are obtained by extraction i.e. cutting up an already constructed element – bedside table which was subjected to a test method for determining strength, durability and stability-furniture for indoor use EN 1730: 2000;

group 2: the second sample objects were not subjected to any tests and were composed of two parts of particle board with given dimensions in accordance with the normative and are connected with the chosen connective object.
A web application for remote control of ROS robot based on WebSocket protocol and Django development environment
Authors: Kapić Zinaid , Crnkić Aladin , Mujčić Edin , Hamzabegović Jasna
Published: December 2021

The development of teleoperation systems, robots, or any physical part of the system can be costly and if something goes wrong it can lead to development overdue. Precisely for these reasons, engineers and scientists today resort to the development of simulated systems before the construction of a real system. Robot Operating System (ROS) is one of the most popular solutions for robot development, manipulation, and simulation. In this paper, we present a web application for remote control of a ROS robot. The robot is controlled via a web application that is used as a virtual Joystick. Also, in this paper, an experimental work analysis of the projected system is performed. Further research possibilities include upgrading the presented web interface, adding certain motion autonomy sensors, or integrating some path planning algorithms.
Challenges and opportunities for semiconductor and electronic design automation industry in post-Covid-19 years
Authors: Marinova Galia I , Bitri Aida K
Published: December 2021

The coronavirus pandemic found the semiconductor industry and the chip production supply chain ecosystem unprepared. Companies and main actors in the sector could not read the signs. The decision-makers suffered to deal with the challenges in time and take the right actions. The bullwhip effect caused by the COVID-19 destabilized the operations and some of the experts say that these problems might last and on the other side, this might open doors to innovative solutions that might change the game. The global shutdowns, the misread of the demand for electronics, underestimating customers’ demand for the automotive sector, and the Internet of Things in general, were some of the main problems causing chaos in the industry. The paper studies the state-of-the-art and the solutions offered by the semiconductor industry and by the initiatives that Europe, the USA, and especially China, took to make companies and their countries take the most out of this situation.
Numerical modelling of the bearing capacity of a beam cross-section
Authors: Demirović Besim , Hadžović Rašid , Osmić Nedim
Published: December 2021

The paper presents a procedure for numerical modelling of the rod cross-section bearing capacity. Equilibrium between cross sectional forces and cross-sectional stresses is determined by iterative procedures. According to the described procedure, the load-bearing capacity of the cross-section is determined according to the isotropic linear and nonlinear behavior of the material, for homogeneous and inhomogeneous cross-sections. The nonlinear behavior of the material reduces the stiffness of the cross section of the rod EA and EI, with a significant increase in the deformation values ε and κ. The applicability of the calculation and analysis of obtained results is presented using numerical examples.
Assessment of masonry structure “Radnički dom” in Mostar
Authors: Šarančić-Logo Amra , Ćećez Marko , Šahinagić-Isović Merima
Published: December 2021

The paper presents the assessment of the building “Radnički dom” (Workers’ Home) in Mostar, which was built in the Austro-Hungarian period, and represents one of the buildings of cultural and historical significance, located in the area of the historic urban core of the city. The paper explains the steps in assessing the condition of the existing structure, which include the collection of existing documentation, structural inspections, tests and calculations, and the assessment and decision on further action. The paper presents the drafts and gives descriptions of the performed visual inspection and the performed static calculation of the existing structure. At the end of the paper, recommendations are given for the rehabilitation and consolidation of the walls of the building: classical methods (injection and grouting) as well as modern methods (carbon strips). The paper points out the complexity of the procedure for the restoration of cultural and historical heritage buildings, the need for valid expertise of the condition and causes of building degradation, the importance of designing details of new structural elements and their corresponding and adequate connections with the original structure of the object.
Study on the effect of temperature and strain rate on Ni2FeCrCuAl high entropy alloy: a molecular dynamics study
Authors: Gowthaman S , Jagadeesha T
Published: December 2021

High entropy alloy has offered significant attention in various material science applications, due to its excellent material features. In this investigation, the mechanical characteristics of Ni2FeCrCuAl High Entropy Alloy (HEA) have been examined under variable temperature and strain rates to analyze its influence over the material features of high entropy alloy through Molecular Dynamics (MD) simulation and it is stated that the formation of various point defects and dislocations are the major cause for the augmentation of tensile deformation which impacts the tensile behavior of high entropy alloy. Moreover, the Radial Distribution Function (RDF) has been examined throughout tensile deformation, to investigate the impact of applied stress over the de-bonding of various atoms and it is found that the strain rate has a greater beneficial impact over the material feature trailed by the temperature outcome, owed to its superior impact on the formation of point defects and shear strain during tensile characterization.
Assessing Cognitive Decline in High-Functioning Spanish-Speaking Patients: High Score Base Rates on the Spanish-Language NIH Toolbox Cognition Battery
Authors: Karr Justin E , Mindt Monica Rivera , Iverson Grant L
Published: December 2021

Objective

Prior research has focused on the normal frequency of obtaining low scores on a neuropsychological test battery, but few studies have examined the normal frequency of obtaining high scores. This study involved the preparation of high score multivariate base rates for the Spanish-language National Institutes of Health (NIH) Toolbox Cognition Battery (NIHTB-CB).

Method

Participants included 250 healthy Latinx adults (age range: 19–80) from the Spanish-language NIHTB-CB normative sample who completed the full battery (two crystallized and four fluid cognition tests). Multivariate base rates, stratified by education, crystallized ability, and sociocultural characteristics, quantified the frequency at which participants obtained one or more “high” fluid test scores (i.e., ≥50th, ≥63rd, ≥75th, ≥84th, ≥91st, ≥95th, and ≥ 98th percentile).

Results

It was common for participants to obtain one or more high scores (i.e., 50.8% obtained one or more scores ≥84th percentile) and uncommon for participants to obtain “no” high scores, especially when using non-conventional thresholds for defining a high score (i.e., 10.8% obtained no scores ≥50th percentile). High scores were more commonly obtained by participants with greater education and higher crystallized ability, who were bilingual, born and educated within the United States, and from higher income households.

Conclusions

This study demonstrated that participants administered multiple neuropsychological tests commonly obtain high scores, and that the frequency of high scores varies by education, crystallized ability, and sociocultural characteristics. The absence of high scores may be indicative of cognitive impairment among examinees who are higher functioning, have greater education, and have specific sociocultural characteristics (e.g., bilingualism, higher socioeconomic status).
BRCC36 promotes intestinal mucosal barrier injury caused by BMP2 after ischemia reperfusion via inhibiting PPARγ signaling
Authors: Zhang Jin-Ming , Wang Kun-Nan , Zhang Yun , Zhang Jun-Ze , Yuan Xin-Pu , Zou Gui-Jun , Cao Zhen , Zhang Chao-Jun
Published: December 2021

As one of the most common pathological changes in trauma and surgery practice, intestinal ischemia-reperfusion (I/R) injury is regarded as a major precipitating factor in the occurrence and development of fatal diseases. BRCA1–BRCA2-containing complex subunit 36 (BRCC36), a deubiquitinase, has been proved important in a variety of pathophysiological processes such as DNA repair, cell cycle regulation, tumorigenesis, and inflammatory response. However, the effect of BRCC36 on intestinal mucosal barrier injury after I/R has not been fully elucidated. Our research found that BRCC36 aggravated intestinal mucosal barrier injury caused by bone morphogenetic protein 2 after I/R by downregulating peroxisome proliferator-activated receptor-γ (PPARγ) signaling. These results suggested that BRCC36/PPARγ axis might serve as a potential therapeutic target for preventing intestinal mucosal barrier injury after I/R.
swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution
Authors: Chen Lulu , Wu Chiung-Ting , Lin Chia-Hsiang , Dai Rujia , Liu Chunyu , Clarke Robert , Yu Guoqiang , Van Eyk Jennifer E , Herrington David M , Wang Yue
Published: December 2021

Motivation

Complex biological tissues are often a heterogeneous mixture of several molecularly distinct cell subtypes. Both subtype compositions and subtype-specific (STS) expressions can vary across biological conditions. Computational deconvolution aims to dissect patterns of bulk tissue data into subtype compositions and STS expressions. Existing deconvolution methods can only estimate averaged STS expressions in a population, while many downstream analyses such as inferring co-expression networks in particular subtypes require subtype expression estimates in individual samples. However, individual-level deconvolution is a mathematically underdetermined problem because there are more variables than observations.

Results

We report a sample-wise Convex Analysis of Mixtures (swCAM) method that can estimate subtype proportions and STS expressions in individual samples from bulk tissue transcriptomes. We extend our previous CAM framework to include a new term accounting for between-sample variations and formulate swCAM as a nuclear-norm and ℓ2,1-norm regularized matrix factorization problem. We determine hyperparameter values using cross-validation with random entry exclusion and obtain a swCAM solution using an efficient alternating direction method of multipliers. Experimental results on realistic simulation data show that swCAM can accurately estimate STS expressions in individual samples and successfully extract co-expression networks in particular subtypes that are otherwise unobtainable using bulk data. In two real-world applications, swCAM analysis of bulk RNASeq data from brain tissue of cases and controls with bipolar disorder or Alzheimer’s disease identified significant changes in cell proportion, expression pattern and co-expression module in patient neurons. Comparative evaluation of swCAM versus peer methods is also provided.

Availability and implementation

The R Scripts of swCAM are freely available at https://github.com/Lululuella/swCAM. A user’s guide and a vignette are provided.

Supplementary information

Supplementary data are available at Bioinformatics online.
Niche conservatism, divergence and polyploidy inSennaseriesAphyllae(Fabaceae: Caesalpinioideae) from arid zones of South America
Authors: Robbiati Federico O , Moro Cordobés Fernando , Fortunato Renée H , Anton Ana M , Urdampilleta Juan D
Published: December 2021

This paper aims to integrate cytogenetic and ecological approaches into a phylogenetic framework to better understand the evolution and systematics of Senna series Aphyllae, an endemic group of arid and semi-arid regions of South America. We counted the chromosome numbers at the population level in three species of series Aphyllae using a conventional technique (GIEMSA) and in situ hybridization (FISH). Phylogenetic reconstructions and inference of chromosome evolution were based on four plastid DNA regions and one nuclear marker. A principal component analysis was carried out using environmental data. Finally, ecological niche models (ENM) were implemented: (1) to identify the abiotic factors that constraint the potential geographical distribution of series Aphyllae and (2) to understand the ecological drivers for species diversification. The basic chromosome number is x = 12. Senna aphylla showed three cytotypes with (2n = 24, 48 and 60) and S. pachyrrhiza has two cytotypes (2n = 24 and 48). Senna crassiramea appeared to be polyploid with 2n = 48. In diploid S. pachyrrhiza, two 45S and three 5S rDNA sites were reported. In tetraploid S. crassiramea, four 45S and four 5S rDNA sites were detected. The ENM and ecological speciation tests suggest that in series Aphyllae speciation was sometimes associated with conservatism and sometimes with niche divergence. Our results contribute to the evolutionary knowledge of Neotropical legumes and understanding of drivers of diversification in arid regions in South America.
Exploring dysconnectivity of the large-scale neurocognitive network across psychiatric disorders using spatiotemporal constrained nonnegative matrix factorization method
Authors: Li Ying , Zeng Weiming , Deng Jin , Shi Yuhu , Nie Weifang , Luo Sizhe , Zhang Hua
Published: December 2021

Psychiatric disorders usually have similar clinical and neurobiological features. Nevertheless, previous research on functional dysconnectivity has mainly focused on a single disorder and the transdiagnostic alterations in brain networks remain poorly understood. Hence, this study proposed a spatiotemporal constrained nonnegative matrix factorization (STCNMF) method based on real reference signals to extract large-scale brain networks to identify transdiagnostic changes in neurocognitive networks associated with multiple diseases. Available temporal prior information and spatial prior information were first mined from the functional magnetic resonance imaging (fMRI) data of group participants, and then these prior constraints were incorporated into the nonnegative matrix factorization objective functions to improve their efficiency. The algorithm successfully obtained 10 resting-state functional brain networks in fMRI data of schizophrenia, bipolar disorder, attention deficit/hyperactivity disorder, and healthy controls, and further found transdiagnostic changes in these large-scale networks, including enhanced connectivity between right frontoparietal network and default mode network, reduced connectivity between medial visual network and default mode network, and the presence of a few hyper-integrated network nodes. Besides, each type of psychiatric disorder had its specific connectivity characteristics. These findings provide new insights into transdiagnostic and diagnosis-specific neurobiological mechanisms for understanding multiple psychiatric disorders from the perspective of brain networks.
Risk for subsequent hypertension and cardiovascular disease after living kidney donation: is it clinically relevant?
Authors: Ferro Charles J , Townend Jonathan N
Published: December 2021

The first successful live donor kidney transplant was performed in 1954. Receiving a kidney transplant from a live kidney donor remains the best option for increasing both life expectancy and quality of life in patients with end-stage kidney disease. However, ever since 1954, there have been multiple questions raised on the ethics of live kidney donation in terms of negative impacts on donor life expectancy. Given the close relationship between reduced kidney function in patients with chronic kidney disease (CKD) and hypertension, cardiovascular disease and cardiovascular mortality, information on the impact of kidney donation on these is particularly relevant. In this article, we review the existing evidence, focusing on the more recent studies on the impact of kidney donation on all-cause mortality, cardiovascular mortality, cardiovascular disease and hypertension, as well as markers of cardiovascular damage including arterial stiffness and uraemic cardiomyopathy. We also discuss the similarities and differences between the pathological reduction in renal function that occurs in CKD, and the reduction in renal function that occurs because of a donor nephrectomy. Kidney donors perform an altruistic act that benefits individual patients as well as the wider society. They deserve to have high-quality evidence on which to make informed decisions.
Association between four-dimensional echocardiographic left atrial measures and left atrial fibrosis assessed by left atrial late gadolinium enhancement
Authors: Olsen Flemming Javier , Bertelsen Litten , Vejlstrup Niels , Diederichsen Søren Zöga , Bjerregaard Caroline Løkke , Graff Claus , Brandes Axel , Krieger Derk , Haugan Ketil , Køber Lars , Højberg Søren , Svendsen Jesper Hastrup , Biering-Sørensen Tor
Published: December 2021

Aims

Left atrial (LA) fibrosis is a hallmark of atrial cardiomyopathy, and non-invasive surrogate measures of LA fibrosis are therefore needed. We investigated the association between four-dimensional (4D) echocardiographic LA measures and LA fibrosis.

Methods and results

A multimodality imaging substudy was performed in a randomized clinical trial (LOOP study), recruiting elderly participants with cardiovascular risk factors. LA late gadolinium enhancement (LGE) by cardiac magnetic resonance imaging was used as a surrogate for LA fibrosis. 4D echocardiographic LA quantification was used to measure maximal and minimal LA volume (LAVmax and LAVmin, respectively), LA emptying fractions (LAEFtotal), and strain. Logistic regression was used to relate LA measures to high LA LGE (≥17 cm2). Of the 44 participants (mean age 76 years, 64% men, median LA LGE 13.1 cm2), 14 exhibited high LA LGE. These participants exhibited abnormalities in several LA functional measures but not LAVmax. In linear regressions, only increasing LAVmin, and decreasing LAEFtotal, and reservoir strain were associated with increasing LA LGE. Furthermore, increasing LAVmin was associated with a higher likelihood of high LA LGE [odds ratio (OR) = 1.19 (1.04–1.37)]. Decreasing LAEFtotal and reservoir strain were also associated with higher likelihood of LA LGE [OR = 1.18 (1.05–1.33)] and OR = 1.15 (1.02–1.30), per 1% decrease in LAEFtotal and reservoir strain, respectively]. These findings were consistent after multivariable adjustments. LAEFtotal provided the highest performance for detecting high LA LGE (area under the curve of 0.78).

Conclusion

LAVmin, LAEFtotal, and reservoir strain measured by 4D echocardiography are significantly associated with LA LGE. LAEFtotal provides the best performance for detecting high LA LGE.
Role of impaired iron transport on exercise performance in heart failure patients
Authors: Campodonico Jeness , Junod Daniele , Carulli Ermes , Lo Russo Gerardo , Gaudenzi Asinelli Margherita , Doni Francesco , Bonomi Alice , Agostoni Piergiuseppe
Published: December 2021

Aims

Impaired iron transport (IIT) occurs frequently in heart failure (HF) patients, even in the absence of anaemia and it is associated with a poor quality of life and prognosis. The impact of IIT on exercise capacity, as assessed by the cardiopulmonary exercise test (CPET), in HF is at present unknown. The aim of this article is to evaluate in HF patients the impact on exercise performance of IIT, defined as transferrin saturation (TSAT) <20%.

Methods and results

We collected data of 676 patients hospitalized for HF. All underwent laboratory analysis, cardiac ultrasound, and CPET. Patients were grouped by the presence/absence of IIT and anaemia (haemoglobin <13 and <12 g/dL in male and female, respectively): Group 1 (G1) no anaemia, no IIT; Group 2 (G2) anaemia, no IIT; Group 3 (G3) no anaemia, IIT; Group 4 (G4) anaemia and IIT. Peak oxygen uptake (peakVO2) reduced from G1 to G3 and from G2 to G4 (G1: 1266 ± 497 mL/min, G2: 1011 ± 385 mL/min, G3: 1041 ± 395 mL/min, G4: 833 ± 241 mL/min), whereas the ventilation to carbon dioxide relationship slope (VE/VCO2 slope) increased (G1: 31.8 ± 7.5, G2: 34.5 ± 7.4, G3: 36.1 ± 10.2, G4: 37.5 ± 8.4). At multivariate regression analysis, peakVO2 independent predictors were anaemia, brain natriuretic peptide (BNP), and left ventricular ejection fraction, whereas VE/VCO2 slope independent predictors were IIT and BNP.

Conclusion

In HF IIT is associated with exercise performance impairment independently from anaemia, and it is a predictor of elevated VE/VCO2 slope, a pivotal index of HF prognosis.
Terrestrial heat flow and its geodynamic implications in the northern Songliao Basin, Northeast China
Authors: Shi Yizuo , Jiang Guangzheng , Shi Shangming , Wang Zecheng , Wang Shejiao , Wang Zhuting , Hu Shengbiao
Published: December 2021

Heat flow data are essential for understanding lithospheric dynamics. As a petroliferous basin, a large number of boreholes have been drilled during hydrocarbon exploration and production in the northern part of Songliao Basin, Northeast China. Meanwhile, the data on crustal structures, core samples and formation temperatures have been accumulated, which provide an opportunity for understanding the thermal state of the basin. Based on the temperature data from both Drilling Stem Test and continuous steady-state logging profiles, together with the systematic analysis of the thermal properties of rock samples, we present a new heat flow map of the northern Songliao Basin with significantly increased number of heat flow sites. The northern Songliao Basin is characterized by relatively high geothermal gradients and high heat flow for sedimentary basins. The heat flow values range from 44.4 to 95.0 mW m–2 with an average of 67.2 ± 12.8 mW m–2, and the geothermal gradients range from 21 to 59 °C km–1 with an overall average of 41.7 °C km–1. Heat production from sedimentary covers accounts for about 4.5 mW m–2 at the site of Well SK-2. Furthermore, based on the crustal structures revealed by previous seismic studies, lithospheric thermal structures are analysed and compared among different structural units of the basin. A thinned thermal lithosphere with a thickness of ∼65 km is found beneath the Central downwarp and the Southeast uplift in which a large part of the heat flow is mantle derived. The Western Slope exhibits a moderate heat flow value and a thicker thermal lithosphere with thickness greater than 110 km. From the perspective of the geothermal state of the lithosphere, the regional geodynamics related to the Mesozoic lithosphere stretching and the subduction of the Pacific Plate are discussed.
Quantile-based Random Kaczmarz for corrupted linear systems of equations
Authors: Steinerberger Stefan
Published: December 2021

We consider linear systems $Ax = b$ where $A \in \mathbb{R}^{m \times n}$ consists of normalized rows, $\|a_i\|_{\ell ^2} = 1$, and where up to $\beta m$ entries of $b$ have been corrupted (possibly by arbitrarily large numbers). Haddock, Needell, Rebrova & Swartworth propose a quantile-based Random Kaczmarz method and show that for certain random matrices $A$ it converges with high likelihood to the true solution. We prove a deterministic version by constructing, for any matrix $A$, a number $\beta _A$ such that there is convergence for all perturbations with $\beta < \beta _A$. Assuming a random matrix heuristic, this proves convergence for tall Gaussian matrices with up to $\sim 0.5\%$ corruption (a number that can likely be improved).
Optical flux and colour variability of blazars in the ZTF survey
Authors: Negi Vibhore , Joshi Ravi , Chand Krishan , Chand Hum , Wiita Paul , Ho Luis C , Singh Ravi S
Published: December 2021

We investigate the temporal and colour variability of 897 blazars, comprising 455 BL Lacertae objects (BL Lacs) and 442 Flat Spectrum Radio Quasars (FSRQs), selected from the Roma-BZCAT catalogue, using the multiband light curves from the Zwicky Transient Facility (ZTF DR6) survey. Assessing the colour variability characteristics over ∼2 yr time-scales, we found that 18.5 per cent (84 out of 455) BL Lacs showed a stronger bluer-when-brighter (BWB) trend, whereas 9.0 per cent (41 out of 455) showed a redder-when-brighter (RWB) trend. The majority (70 per cent) of the BL Lacs showing RWB are host galaxy dominated. For the FSRQ subclass, 10.2 per cent (45 out of 442) objects showed a strong BWB trend and 17.6 per cent (78 out of 442) showed a strong RWB trend. Hence, we find that BL Lacs more commonly follow a BWB trend than do FSRQs. This can be attributed to the more dominant jet emission in the case of BL Lacs and the contribution of thermal emission from the accretion disc for FSRQs. In analysing the colour behaviour on shorter time windows, we find many blazars evince shorter partial trends of BWB or RWB nature (or occasionally both). Some of such complex colour behaviours observed in the colour–magnitude diagrams of the blazars may result from transitions between the jet-dominated state and the disc-dominated state and vice versa.
Investigation of Rocket Effect in BRC 18 using Gaia EDR3
Authors: Saha Piyali , Gopinathan M , Ojha D K , Neha Sharma
Published: December 2021

Bright-rimmed clouds (BRCs) are ideal candidates to study radiation-driven implosion mode of star formation as they are potential sites of triggered star formation, located at the edges of Hii regions, showing evidence of ongoing star formation processes. BRC 18 is located towards the eastern edge of relatively closer (∼400 pc) H ii region excited by λ Ori. We made R-band polarimetric observations of 17 candidate young stellar objects (YSOs) located towards BRC 18 to investigate any preferred orientation of the discs with respect to the ambient magnetic field and the direction of energetic photons from λ Ori. We found that the discs are oriented randomly with respect to the projected magnetic field. Using distances and proper motions from the Gaia EDR3 of the candidate YSOs, we investigated the possible acceleration of BRC 18, away from λ Ori due to the well-known ‘Rocket Effect’, by assuming that both the candidate YSOs and BRC 18 are kinematically coupled. The relative proper motions of the candidate YSOs are found to show a trend of moving away from λ Ori. We computed the offset between the angle of the direction of the ionization front and the relative proper motion of the candidate YSOs and found it to lie close to being parallel to each other. Additionally, we found 12 sources that are co-moving with the known candidate YSOs towards BRC 18. These co-moving sources are most likely to be young and are missed in previous surveys conducted to identify potential YSOs of the region.
Early Multicenter Experience With Imipenem-Cilastatin-Relebactam for Multidrug-Resistant Gram-Negative Infections
Authors: Rebold Nicholas , Morrisette Taylor , Lagnf Abdalhamid M , Alosaimy Sara , Holger Dana , Barber Katie , Justo Julie Ann , Antosz Kayla , Carlson Travis J , Frens Jeremy J , Biagi Mark , Kufel Wesley D , Moore William J , Mercuro Nicholas , Raux Brian R , Rybak Michael J
Published: December 2021

A multicenter case series of 21 patients were treated with imipenem-cilastatin-relebactam. There were mixed infection sources, with pulmonary infections (11/21,52%) composing the majority. The primary pathogen was Pseudomonas aeruginosa (16/21, 76%), and 15/16 (94%) isolates were multidrug-resistant. Thirty-day survival occurred in 14/21 (67%) patients. Two patients experienced adverse effects.
Measuring Voluntary Control Over Hallucinations: The Yale Control Over Perceptual Experiences (COPE) Scales
Authors: Mourgues Catalina , Hammer Allison , Fisher Victoria , Kafadar Eren , Quagan Brittany , Bien Claire , Jaeger Hale , Thomas Rigi , Sibarium Ely , Negreira Alyson M , Sarisik Elif , Polisetty Vasishta , Nur Eken Hatice , Imtiaz Ayyub , Niles Halsey , Sheldon Andrew D , Powers Albert R
Published: December 2021

Auditory verbal hallucinations (AVH) frequently cause significant distress and dysfunction, and may be unresponsive to conventional treatments. Some voice-hearers report an ability to fully control the onset and offset of their AVH, making them significantly less disruptive. Measuring and understanding these abilities may lead to novel interventions to enhance control over AVH. Fifty-two voice-hearers participated in the pilot study. 318 participants with frequent AVH participated in the validation study. A pool of 59 items was developed by a diverse team including voice-hearers and clinicians. After the pilot study, 35 items were retained. Factorial structure was assessed with exploratory (EFA, n = 148) and confirmatory (CFA, n = 170) factor analyses. Reliability and convergent validity were assessed using a comprehensive battery of validated phenomenological and clinical scales. CFA on the final 18 items supported two factors for a Methods of Control Scale (5 items each, average ω = .87), and one factor for a Degree of Control Scale (8 items, average ω = .95). Correlation with clinical measures supported convergent validity. Degree of control was associated with positive clinical outcomes in voice-hearers both with and without a psychosis-spectrum diagnosis. Degree of control also varied with quality of life independently of symptom severity and AVH content. The Yale control over perceptual experiences (COPE) Scales robustly measure voice-hearers’ control over AVH and exhibit sound psychometric properties. Results demonstrate that the capacity to voluntarily control AVH is independently associated with positive clinical outcomes. Reliable measurement of control over AVH will enable future development of interventions meant to bolster that control.