bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ruminal microbiome and blood parameters in beef cattle fed with high-grain diets buffered with Lithothamnium calcareum
Authors: Lima Laís Gabrielly Freitas , Targueta Cíntia Pelegrineti , Nunes Rhewter , de Paula Raiany Soares , Apolinário Amanda Martins , Arnhold Emmanuel , Gomes Renata Rodrigues , Caixeta Luis Fernando de Sousa , Miyagi Eliane Sayuri , Corrêa Daniel Staciarini , Xavier Carlos Henrique , Telles Mariana Pires de Campos , Ferreira Reginaldo Nassar 
Published: December 2023

Context and aims DNA metabarcoding strategy was used to sequence the 16S rRNA region of ruminal fluid samples from Nellore cattle fed with concentrate-rich diets in response to modulatory effect of buffering additives calcarea seaweed (Lithothamnium calcareum) and sodium bicarbonate. Methods Besides characterising the richness and diversity indices of rumen bacterial community, the impact of potentially acidogenic diets on rumen pH, blood parameters, and short-chain fatty acid profile (SCFA) was investigated for which four male Nellore cattle were used, distributed in a 4 × 4 Latin square (treatments × periods). Treatments comprised the same highly concentrated basal diet, and were as follows: T1, without additive (CON); T2, inclusion of 90 g of sodium bicarbonate (BIC); T3, inclusion of 90 g of L. calcareum (L90); and T4, inclusion of 45 g of L. calcareum (L45). Data were analysed in R, in which diversity and abundance at gender level were analysed using Friedman’s test, with means being adjusted by False Discovery Rate (FDR) correction. The analyses of pH, biochemical parameters and SCFA were analysed using Scott–Knott test and means were evaluated with a significance level of 10% (P < 0.10). Key results We identified 1474 operational taxonomic units (OTUs) belonging to 52 genera and 16 phyla of bacteria domain. The results showed that bacterial microbiota were dominated by Firmicutes (44.12%), Bacteroidetes (28.29%), and Proteobacteria (5.88%). Animals fed with L90 demonstrated greater abundance and ruminal diversity for the Prevotella genus (P < 0.07% and P < 0.09% respectively), whereas cattle supplemented with L45 demonstrated greater diversity of the Fibrobacter genus (P < 0.05). There were differences in molar proportion for acetic (P < 0.07%) and valeric (P < 0.03%) acids in the period before feeding. Higher blood lactate concentrations were observed in animals supplemented with L45 (P < 0.06%), while animals that received treatments L90 and BIC presented lower levels of blood lactate. This metabolite was lower in animals fed with 90 g of sodium bicarbonate and L. calcareum daily. These treatments also reduced the concentration of acetic acid and increased that of valeric acid, and improved ruminal diversity. Conclusions and implications Our results supported this choice to improve ruminal function, with a great prospective of better weight-gain performance in Nellore cattle.
The interactive effect of insoluble-fibre inclusion and feed form on the performance, tibia bone quality, and gastrointestinal histomorphology of Hy-Line W-36 laying pullets
Authors: Efranji Sana , Sedghi Mohammad , Mahdavi Amir Hossein , Abdollahi Mohammad Reza 
Published: December 2023

Context Adding fibre to the diet is one of the factors that help the growth and development of the digestive system of pullets during the rearing period. Insoluble-fibre inclusion enhances the grinding competence and functionality of gizzards and increases the retention time of digesta in the gastrointestinal tract. Aims The aim of this study was to investigate the interaction effects of insoluble fibre and the physical form of feed. Methods The interactive effect of two levels of sunflower hull (SH, 0 and 40 g/kg) and two feed forms (mash and pellet) on the growth of Hy-Line-W36 laying pullets from hatching until 8 weeks of age was investigated. For this purpose, 640 1-day-old chicks were randomly assigned to 64 cages. Key results Insoluble fibre had no effect on performance. Birds offered pelleted feed had a higher overall daily weight gain and daily feed intake than did those fed mash feed. A significant interaction between SH inclusion and feed form was observed for daily feed intake from 0 to 2 weeks. The pullets fed with mash feed without SH had a heavier weight of the gizzard than did the others. Feeding pelleted diets reduced caecum weight and the length of jejunum and ileum. Fibre inclusion resulted in a lower crypt depth in the jejunum. The jejunal villus height and muscle-layer thickness were higher in pellet-fed pullets. Feeding pelleted diets increased the tibia length and tibiotarsal index. The lowest propionate content of caecum was recorded in pellet-fed pullets without SH. Conclusions Overall, the inclusion of SH in diets had no significant effect on performance but improved the morphology of the intestine. Feeding pelleted diets improved the growth performance and intestinal morphology of pullets. Implications Compared to mash diets, feeding pelleted diets improved the performance. Adding fiber to the diet improves intestinal structure, which helps improve digestion and absorption of nutrients. Also, feed pelleting technology improves the effective parameters of the gastrointestinal tract in laying pullets. Also, the use of pelleted feed compared to mesh is associated with improved economic efficiency.
Environmental DNA as a detection tool for small-bodied, cryptic, threatened fish in a highly turbid freshwater lake system
Authors: Stoessel D. J. , Raadik T. A. , Adams M. , Shelley J. J. , Hately T. J. , Iervasi D. , Rose P. , Russell A. , Murphy N. 
Published: December 2023

Context Where conservation efforts are undertaken to decrease downward trends in fish populations, comparatively few resources are directed to small-bodied cryptic species. The true extent of the decline of many of these species is therefore often unknown. Where surveys have occurred, they are frequently limited by budget and hence effort. Consequently, there is a risk that rare species may not be physically captured despite their presence at a site. Such an outcome has dire consequences for the conservation of remnant populations of threatened fish. To counter possible false negative detections, environmental DNA is increasingly being used in conjunction with, or as a precursor to, physical surveys. The Southern Purple-spotted Gudgeon (Mogurnda adspersa) is a small, threatened freshwater fish native to Australia. Recent surveys captured M. adspersa in two highly turbid waterbodies in north-central Victoria. This capture represented the first detection of the species in the state in more than 20 years. Because these waterbodies are part of a network of hydrologically connected systems, it was suspected that the species likely had a broader distribution in the region. Aims To develop a probe-based eDNA assay for M. adspersa and compare its sensitivity against a physical sampling program. Methods Detection (presence/absence) between eDNA and traditional surveys was compared across multiple sites. Key results eDNA presents an effective tool for determining the presence of M. adspersa. The eDNA survey demonstrated significant clustering of eDNA detections towards the outlets of lakes sampled, suggesting concentrated eDNA at this point, or that, due to the channels being shallower, the eDNA of resident individuals may be less diluted. Conclusions Based on these results, future survey of rare, cryptic species in highly turbid lake systems should in the first instance include a broad scale eDNA survey, with sampling concentrated at outlet channels. Implications The likely most cost-effective approach to determining the presence/absence of rare species in lake systems is the collection of eDNA samples at outlet channels.
Skyrmion transport and annihilation in funnel geometries
Authors: Rocha F S , Bellizotti Souza J C , Vizarim N P , Reichhardt C J O , Reichhardt C , Venegas P A 
Published: December 2023

Abstract
Using atomistic simulations, we have investigated the transport and annihilation of skyrmions interacting with a funnel array under a current applied perpendicular to the funnel axis. We find that transport without annihilation is possible at low currents, when the motion is dominated by skyrmion–skyrmion interactions and skyrmions push each other through the funnel opening. Skyrmion annihilation occurs for higher currents when skyrmions in the upper half of the sample exert pressure on skyrmions in the bottom half of the sample due to the external current. Upon interacting with the funnel wall, the skyrmions undergo a size reduction that makes it easier for them to pass through the funnel opening. We find five phases as a function of the applied current and the size of the funnel opening: (i) pinned, (ii) transport without annihilation, (iii) transport with annihilation, (iv) complete annihilation, and (v) a reentrant pinning phase that only occurs for very narrow openings. Our findings provide insight into how to control skyrmion transport using funnel arrays by delineating regimes in which transport of skyrmions is possible as well as the conditions under which annihilation occurs.
Stainless steel cylindrical pot outer surface defect detection method based on cascade neural network
Authors: Qiao Jian , Sun Cihan , Cheng Xiaoqi , Yang Jingwei , Chen Nengda 
Published: December 2023

Abstract
Addressing issues such as surface geometric distortion, high reflection, and the challenge of detecting minor defects on the external surfaces of stainless steel pots, this paper presents a novel approach for detecting defects on the external surfaces of cylindrical stainless steel pots based on high-resolution line-scan imaging. The method begins by creating a real-time inspection system that includes a line-scan camera and a strip light source. This system achieves distortion-free, high-resolution image acquisition of the outer surfaces of stainless steel cylindrical pots by establishing linear constraints on pot size, rotary table rotation speed, and line-scan frame rate. Subsequently, a You Only Look Once and fully convolutional network cascade neural network surface defect detection strategy is introduced, utilizing dual-channel images of the original and enhanced images as inputs. This approach enables the characterization of subtle defects in high-resolution image data. Finally, we conducted experiments using the proposed method on the provided dataset, and the results demonstrate the effectiveness of this approach in detecting various types of product defects. The mean pixel accuracy achieved a remarkable 91.69%, while the mean intersection over union score reached an impressive 83.59%. These findings provide an effective technical means for the qualitative detection of the types of defects on the surface of stainless steel pots and the quantitative measurement of the size of the defects.
Downdraft influences on the differences of PM2.5 concentration: insights from a mega haze evolution in the winter of northern China
Authors: Chen Zhenyi , Ji Chengli , Mao Jiajia , Wang Zhicheng , Jiao Zhiming , Gao Lina , Xiang Yan , Zhang Tianshu 
Published: December 2023

Abstract
A significant haze event occurred in northern China from 16 to 21 November 2022. This study analyzed the haze spatial evolution, and meteorological influences by integrating ground and satellite measurements. Most data were obtained using aerosol lidar and wind lidar observations in suburban (Nanjiao Observation Station, NJOS) and urban Beijing (Haidian Observation Station, HDOS). The observations at NJOS and HDOS indicate the presence of a distinct layer of haze restricted to a height of up to 1500 m above the surface. However, the aerosol intensity at HDOS was comparatively lower (aerosol extinction coefficient: 1.39 ± 0.27 km−1) than at NJOS (1.77 ± 0.38 km−1), with approximately one day of time lag in response to the southerly winds. Though NJOS and HDOS presented a similar wind stratification structure, the downdraft under 1000 m influenced the surface air quality were significantly different. The intense downdraft at the lower height at HDOS prevented the vertical upward diffusion of accumulated ground pollutants, whose effect was similar to that of the inversion layer. That led to a more stable increasing trend of PM2.5 at HDOS, with the shallowest planet boundary layer height of 242 m on 20 November. By contrast, NJOS in the transportation path was more regularly influenced by the southerly flow and presented cyclical PM2.5 concentration. This study shows downdraft in urban environments acting as an accelerator for urban episodic PM2.5 pollution, suggesting the complicated contribution from meteorological factors.
Optimization of cold spray process parameters to maximize adhesion and deposition efficiency of Ni+Al2O3 coatings
Authors: Shorinov Oleksandr , Dolmatov Anatolii , Polyviany Sergii , Balushok Kostyantyn 
Published: December 2023

Abstract
The paper considers the conducted study of the complex effect of low-pressure cold spraying parameters, namely the nozzle inlet temperature, stand-off distance, and powder feed rate on the adhesion and deposition efficiency of coatings from a Ni+Al2O3 powder on VT3-1 titanium alloy substrate. Based on predetermined information, the main levels and intervals of factor variation were selected. The dependence of the adhesion and deposition efficiency on the selected variables was approximated by a second-order polynomial. In accordance with the developed matrix of the experiment (central compositional design), a coating of the studied powder was deposited. The average value of these parameters was determined using standard methods for studying the adhesion strength (ASTM C603) and the deposition efficiency for thermal spray coatings. Based on the results of experimental data, regression equations were obtained for adhesion and deposition efficiency. For the purpose of checking the adequacy of the model, an analysis of variance was performed. It was confirmed that the obtained empirical dependences can be used to predict the adhesion and deposition efficiency of cold spraying of coatings from a Ni+Al2O3 powder on VT3-1 titanium alloy in the specified ranges of values of spraying parameters. Multi-factor optimization of the spraying parameters in order to obtain maximum values of adhesion strength and deposition efficiency was performed using the response surface methodology in the Stat-Ease 360 software. Three-dimensional and contour graphs of the dependence of the adhesion and deposition efficiency on the studied parameters were developed from the obtained empirical models. The optimal combination of parameters of low-pressure cold spraying, which ensures the maximum adhesion (34.78 MPa) and deposition efficiency (29.46%) of the Ni+Al2O3 coating mixture, is the nozzle inlet temperature—537 °C, stand-off distance—11 mm, and powder feed rate—0.6 g s−1.
Parsley: a web app for parsing data from plate readers
Authors: Csibra Eszter , Stan Guy-Bart 
Published: December 2023

Abstract

Summary
As demand for the automation of biological assays has increased over recent years, the range of measurement types implemented by multiwell plate readers has broadened and the list of published software packages that caters to their analysis has grown. However, most plate readers export data in esoteric formats with little or no metadata, while most analytical software packages are built to work with tidy data accompanied by associated metadata. ‘Parser’ functions are therefore required to prepare raw data for analysis. Such functions are instrument- and data type-specific, and to date, no generic tool exists that can parse data from multiple data types or multiple plate readers, despite the potential for such a tool to speed up access to analysed data and remove an important barrier for less confident coders. We have developed the interactive web application, Parsley, to bridge this gap. Unlike conventional programmatic parser functions, Parsley makes few assumptions about exported data, instead employing user inputs to identify and extract data from data files. In doing so, it is designed to enable any user to parse plate reader data and can handle a wide variety of instruments (10+) and data types (53+). Parsley is freely available via a web interface, enabling access to its unique plate reader data parsing functionality, without the need to install software or write code.

Availability and implementation
The Parsley web application can be accessed at: https://gbstan.shinyapps.io/parsleyapp/. The source code is available at: https://github.com/ec363/parsleyapp and is archived on Zenodo: https://zenodo.org/records/10011752.
Genetic basis of anatomical asymmetry and aberrant dynamic functional networks in Alzheimer’s disease
Authors: Rubido Nicolás , Riedel Gernot , Vuksanović Vesna 
Published: December 2023

Abstract
Genetic associations with macroscopic brain networks can provide insights into healthy and aberrant cortical connectivity in disease. However, associations specific to dynamic functional connectivity in Alzheimer’s disease are still largely unexplored. Understanding the association between gene expression in the brain and functional networks may provide useful information about the molecular processes underlying variations in impaired brain function. Given the potential of dynamic functional connectivity to uncover brain states associated with Alzheimer’s disease, it is interesting to ask: How does gene expression associated with Alzheimer’s disease map onto the dynamic functional brain connectivity? If genetic variants associated with neurodegenerative processes involved in Alzheimer’s disease are to be correlated with brain function, it is essential to generate such a map. Here, we investigate how the relation between gene expression in the brain and dynamic functional connectivity arises from nodal interactions, quantified by their role in network centrality (i.e. the drivers of the metastability), and the principal component of genetic co-expression across the brain. Our analyses include genetic variations associated with Alzheimer’s disease and also genetic variants expressed within the cholinergic brain pathways. Our findings show that contrasts in metastability of functional networks between Alzheimer’s and healthy individuals can in part be explained by the two combinations of genetic co-variations in the brain with the confidence interval between 72% and 92%. The highly central nodes, driving the brain aberrant metastable dynamics in Alzheimer’s disease, highly correlate with the magnitude of variations from two combinations of genes expressed in the brain. These nodes include mainly the white matter, parietal and occipital brain regions, each of which (or their combinations) are involved in impaired cognitive function in Alzheimer’s disease. In addition, our results provide evidence of the role of genetic associations across brain regions in asymmetric changes in ageing. We validated our findings on the same cohort using alternative brain parcellation methods. This work demonstrates how genetic variations underpin aberrant dynamic functional connectivity in Alzheimer’s disease.
Neural consequences of binaural beat stimulation on auditory sentence comprehension: an EEG study
Authors: Kim Jeahong , Kim Hyun-Woong , Kovar Jessica , Lee Yune Sang 
Published: December 2023

Abstract
A growing literature has shown that binaural beat (BB)—generated by dichotic presentation of slightly mismatched pure tones—improves cognition. We recently found that BB stimulation of either beta (18 Hz) or gamma (40 Hz) frequencies enhanced auditory sentence comprehension. Here, we used electroencephalography (EEG) to characterize neural oscillations pertaining to the enhanced linguistic operations following BB stimulation. Sixty healthy young adults were randomly assigned to one of three listening groups: 18-Hz BB, 40-Hz BB, or pure-tone baseline, all embedded in music. After listening to the sound for 10 min (stimulation phase), participants underwent an auditory sentence comprehension task involving spoken sentences that contained either an object or subject relative clause (task phase). During the stimulation phase, 18-Hz BB yielded increased EEG power in a beta frequency range, while 40-Hz BB did not. During the task phase, only the 18-Hz BB resulted in significantly higher accuracy and faster response times compared with the baseline, especially on syntactically more complex object-relative sentences. The behavioral improvement by 18-Hz BB was accompanied by attenuated beta power difference between object- and subject-relative sentences. Altogether, our findings demonstrate beta oscillations as a neural correlate of improved syntactic operation following BB stimulation.
Monitoring of First-line Drug Resistance Mutations Outside the Scope of Xpert MTB/RIF Ultra is Needed for Successful Control of DR-TB in Southern Mozambique
Authors: Mariner-Llicer Carla , Saavedra Cervera Belén , Mambuque Edson , Gomes Neide , Munguambe Shilzia , Villamayor Luis , Cancino-Muñoz Irving , Torres-Puente Manuela , Nguenha Dinis , Respeito Durval , Tembe Gustavo , López Mariana G , Comas Iñaki , García-Basteiro Alberto L 
Published: December 2023

Abstract
Multidrug-resistant(MDR) tuberculosis in Southern Africa is of great concern, exacerbated by the spread of a clone harboring a mutation missed by Xpert Ultra. In Southern Mozambique, the presence of such mutation and rising cases of non-MDR isoniazid resistance highlights the need to ensure accurate detection of antimicrobial-resistance in the country.
Time Is of the Essence: Achieving Prompt and Effective Antimicrobial Therapy of Bloodstream Infection With Advanced Hospital Information Systems
Authors: Morquin David , Lejeune Jordan , Agostini Céline , Godreuil Sylvain , Reynes Jacques , Le Moing Vincent , Lamy Brigitte 
Published: December 2023

Abstract
The early administration of appropriate antibiotic therapy is crucial for the survival of patients with bacteremia. Current research focuses on improving analytical times through technology, whereas there have been very few efforts to improve postanalytical times even though they represent 40% of the time between blood taking and appropriate treatment administration. One of the clues is the efficiency and appropriateness of the result communication system.
Here, we review all delays in the entire process with the aim of improving time to appropriate treatment administration. We discuss causes for long times to adjust treatment once microbiological results are released. We argue that the pervasive health information system in this organization serves as both a bottleneck and a rigid framework. Finally, we explore how next-generation hospital information systems should be designed to effectively assist the doctors in treating patients with bacteremia.