bluuebunny/crossref_metadata_2025_split huggingface dataset:
SAFMem: Accelerating Transformer Self-Attention Functionality via Memristor-Based Hardware
Authors: Bettayeb Meriem , Halawani Yasmin , Khan Muhammad Umair , Saleh Hani , Mohammad Baker 
Published: November 2023

Abstract

The adoption of transformer networks has experienced a notable surge in various AI applications. However, the increasedcomputational complexity, stemming primarily from the self-attention mechanism, parallels the manner in which convolutionoperations constrain the capabilities and speed of Convolutional Neural Networks (CNNs). The self-attention algorithm,specifically the Matrix-matrix Multiplication (MatMul) operations, demands a substantial amount of memory and computationalcomplexity, thereby restricting the overall performance of the transformer. This paper introduces an efficient hardwareaccelerator for the transformer network, leveraging memristor-based in-memory computing. The design targets the memorybottleneck associated with MatMul operations in the self-attention process, utilizing approximate analog computation andthe highly parallel computations facilitated by the memristor crossbar architecture. Remarkably, this approach resulted in areduction of approximately 10 times in the number of Multiply-Accumulate (MAC) operations in transformer networks, whilemaintaining 93.37% accuracy for the MNIST dataset, as validated by a comprehensive circuit simulator employing NeuroSim3.0. Simulation outcomes indicate an area utilization of 6895.7 μm2, a latency of 15.52 seconds, an energy consumption of3 mJ, and a leakage power of 59.55 μW . The methodology outlined in this paper represents a substantial stride towards ahardware-friendly transformer architecture for edge device, poised to achieve real-time performance.
Spatial variability in herbaceous plant phenology is mostly explained by variability in temperature but also by photoperiod and functional traits
Authors: Rauschkolb Robert , Bucher Solveig Franziska , Hensen Isabell , Ahrends Antje , Fernández-Pascual Eduardo , Heubach Katja , Jakubka Desiree , Jiménez-Alfaro Borja , König Andreas , Koubek Tomáš , Kehl Alexandra , Khuroo Anzar , Lindstädter Anja , Shafee Faizan , Mašková Tereza , Platonova Elena , Panico Patrizia , Plos Carolin , Primack Richard , Rosche Christoph , Shah Manzoor A , Sporbert Maria , Stevens Albert-Dieter , Tarquini Flavio , Tielbörger Katja , Träger Sabrina , Vange Vibekke , Weigelt Patrick , Bonn Aletta , Freiberg Martin , Knickmann Barbara , Nordt Birgit , Wirth Christian , Römermann Christine 
Published: November 2023

Abstract
Whereas temporal variability of plant phenology in response to climate change has already been well studied, the spatial variability of phenology is not well understood. Given that phenological shifts may affect the magnitude of biotic interactions, there is a need to investigate how the variability in environmental factors relates to the spatial variability in herbaceous species’ phenology by at the same time considering their functional traits to predict their general and species-specific responses to future climate change. In this project, we analysed phenology records of 148 herbaceous species, which were observed for a single year by the PhenObs network in 15 botanical gardens. For each species, we characterised the spatial variability in six different phenological stages across gardens. We used boosted regression trees to link these variabilities in phenology to the variability in environmental parameters (temperature, latitude, and local habitat conditions) as well as species traits (seed mass, vegetative height, specific leaf area, and temporal niche) hypothesised to be related to phenology variability.
We found that spatial variability in the phenology of herbaceous species was mainly driven by the variability in temperature but also photoperiod was an important driving factor for some phenological stages. In addition, we found that early-flowering and less competitive species indicated by small specific leaf area and vegetative height were more variable in their phenology. Our findings contribute to the field of phenology by showing that besides temperature, photoperiod and functional traits are important to be included when spatial variability of herbaceous species is investigated.
Genome Sequence of Microbulbifer thermotolerans HB226069 Reveals Its Versatility to Degrade Multiple Polysaccharides and Determination of the Alginate Lyases
Authors: Li Xue , Yang Miao , Mo Kunlian , Hu Yonghua , Gu Hanjie , Sun Dongmei , Bao Shixiang , Huang Huiqin 
Published: November 2023

Abstract
Polysaccharide-degrading bacteria are key participants in the global carbon cycle and algal biomass recycling. Herein, a polysaccharide lyase-producing strain HB226069 was isolated from Sargassum sp. from QingGe Port, Hainan, China. Results of the phylogenetic of 16S rRNA gene and genotypic analysis clearly indicate that the isolate should be classified as Microbulbifer thermotolerans. The whole genome is a 4,021,337 bp circular chromosome with the G + C content of 56.5%. Analysis of the predicted genes indicates that strain HB226069 encodes 161 CAZymes, and abundant putative enzymes involved in polysaccharide degradation were predicted, including alginate lyase, fucosidase, agarase, xylanase, cellulase, pectate lyase, amylase, and chitinase. Three of the putative polysaccharide lyases from PL7 and PL17 families were involved in alginate degradation. The alginate lyases of strain HB226069 showed the maximum activity 117.4 U/mL at 50°C, pH 7.0 and 0.05 M FeCl3, while exhibited the best stability at 30°C and pH 7.0. The thin layer chromatography (TLC) and Electrospray Ionization Mass Spectrometry (ESI-MS) analysis indicated that the alginate oligosaccharide degraded by the partially purified alginate lyases contained oligosaccharides of DP2-DP5 and monosaccharide while reacting for 36 h. The complete genome of M. thermotolerans HB226069 enriches our understanding of the mechanism of polysaccharide lyase production and provides support for its potential application in polysaccharide degradation.
CVRmap - A Complete Cerebrovascular Reactivity Mapping Post-Processing BIDS Toolbox
Authors: Rovai Antonin , Lolli Valentina , Trotta Nicola , Goldman Serge , De Tiège Xavier 
Published: November 2023

Abstract
Cerebrovascular Reactivity (CVR) refers to the ability of cerebral blood vessels to dilate or constrict under the effect of vasoactive substances and can be estimated using functional Magnetic Resonance Imaging (fMRI). Computation of CVR maps is relevant in various brain diseases and requires specialized data processing. We introduce CVRmap, an opensource software that automates the computation of CVR map. The toolbox complies with the Brain Imaging Data Structure (BIDS) standards.
Do corticosteroids affect immunotherapy efficacy in malignancy? – A systematic review
Authors: Byron Yoni , Yegorova-Lee Sonya , Tio Martin 
Published: November 2023

Abstract
Background: Early studies indicated that corticosteroids may limit the survival benefit from immunotherapy. We conducted this systematic review to evaluate the effect corticosteroids have on immunotherapy in patients with malignancy, when adjusted for potentially confounding effects of corticosteroids given for palliative indications.
Methods: 3 electronic databases (PubMed, Embase, and Medline) were searched on 1st of February 2023. Studies that measured response or survival to immunotherapy in people receiving corticosteroids for non-cancer indications compared to either no corticosteroids or corticosteroids for cancer-related indications were included. Studies exclusively evaluating the effect of corticosteroids administered for immune-related adverse events (irAE) were excluded to avoid immortal time bias. Pooled odds and hazard ratios with 95% confidence intervals (CI) were calculated using a random effects model. Study heterogeneity was assessed using the I2 statistic, and publication bias was evaluated by funnel plot and Egger's regression model.
Results: 8426 titles were identified on our search. 8 studies met our inclusion criteria for meta-analysis. Administration of corticosteroids does not have a statistically significant effect on survival and response to immunotherapy when administered for non-cancer related indications, with a pooled odds ratio for overall response rate 0.92 (95% CI 0.58-1.44); pooled hazard ratio (HR) for progression free survival 0.87 (95% CI 0.68-1.12); and pooled HR for overall survival 0.79 (95% CI 0.59-1.05).
Conclusion: This systematic review indicates that administration of corticosteroids does not affect response to immunotherapy nor survival outcomes, when removing confounding palliative corticosteroid indications. These results are limited by the retrospective nature of the studies included, small sample sizes, lack of information about corticosteroid dosing the inclusion of irAE in 2 of the studies which could bias the results.
Targeting MTAP creates a therapeutic vulnerability to PARP inhibition in brain metastatic TNBC by disrupting MAT2A mediated methionine metabolism
Authors: Lou Zhenkun , Zeng Xiangyu , Zhao Fei , Zhang Lingxin , Weinshilboum Richard M , Tao Kaixiong 
Published: November 2023

Abstract
Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer with limited therapeutic strategy and unfavorable prognosis, especially for patients bearing brain metastasis. Here, we demonstrate that MTAP gene deletion or MTAP inhibition by MTAP inhibitor, MTDIA, sensitizes breast cancer cells to poly (ADP-ribose) polymerase (PARP) inhibitor (PARPi). Mechanistically, PARPi suppresses the expression of methionine adenosyltransferase 2A (MAT2A) by inducing METTL16 auto-inhibition mediated intron retention. Given that MAT2A and MTAP are key enzymes in methionine metabolism, the dual inhibition of MAT2A and MTAP disrupts methionine metabolism and leads to reduced s-adenosylmethionine. Dietary methionine restriction further boosts the combined anti-tumor efficacy of MTAP depletion/inhibition and PARPi. Most importantly, in brain metastatic TNBC, due to the natural low methionine environment in the brain, the combination of MTAP depletion/inhibition and PARPi confers significant therapeutic efficacy. Therefore, our findings provide a promising strategy for inhibiting primary or brain metastatic TNBC.
BAP regulates lateral bud outgrowth to promote tillering in Paphiopedilum callosum (Orchidaceae)
Authors: Yin Yuying , Zhong Ronghui , Li Yefei , Guo Beiyi , Li Lin , Ma Guohua , Wu Kunlin , Fang Lin , Zeng Songjun 
Published: November 2023

Abstract
Background:
Paphiopedilum orchids have a high ornamental value, and flower abundance is a key horticultural trait. Most Paphiopedilum plants exhibit weak tillering ability, with their tiller buds often entering a dormant state post-formation. Tiller production plays a crucial role in enhancing flower abundance and is potentially regulated by plant hormones. However, the effect of hormones on tillering in Paphiopedilumplants is still unclear.
Results:
In this study, we investigated the promotion of tillering in P. callosum through exogenous root irrigation of benzylaminopurine(BAP). We observed a dose-dependent promotion of tiller production by BAP, with the strongest effect observed at a concentration of 400mg/L. By comparing the expression of key genes in P. ‘SCBG Yingchun’ (with strong tiller ability) and P callosum (with weak tiller ability), we found that BAP promotes tillering by interacting with abscisic acid (ABA). This interaction involves down-regulation of the ABA degradation gene PcCYP707A, leading to a reduction in ABA content, and the subsequent down-regulation of dormancy-associated genes (PcDRMH1, PcSVP) to release bud dormancy. Additionally, BAP promotes sustained outgrowth of tiller buds by increasing the level of indole-3-acetic acid (IAA) through up-regulation of the IAA synthesis gene PcYUC2 and the transport gene PcPINIC. These findings provide insights into the regulatory mechanisms of BAP in tiller bud outgrowth in P. callosum.
Conclusions:
Our results indicated that the application of BAP promotes lateral bud outgrowth and increases tiller production in P. callosum. HPLC results showed exogenous BAP affects the levels of endogenous hormones, including IAA, CTKs, and ABA. Transcriptomic data combined with qPCR analyses suggest that the genes PcCYP707, PcYUC2, PcPINIC PcDRMH1, PcSVPmay play key roles in regulating tiller bud outgrowth. This study presents the first comprehensive report of BAP-promoted tillering in P. callosum, which should provide a foundational basis for further mechanistic studies on tiller development in Paphiopedilum species and other non-model plants.
Pseudo-static Solution of Active Earth Pressure Against Relief Shelf Retaining Wall Rotating Around Heel Under Seismic Load
Authors: Que Yun , Zhang Jisong , Chen Fuquan , Long Chengcheng 
Published: November 2023

Abstract

In practical engineering, the design process of most retaining walls must take into account earthquake resistance. It is crucial to prevent the overturning of retaining walls, particularly when the foundation's bearing capacity is weak. In this paper, the seismic active earth pressure (ES) of a relieving retaining wall in RB displacement mode is taken as the research object. By observing shear dissipation graphs across various operating conditions, the distribution law of each sliding surface is summarized, and three typical failure modes are obtained. The corresponding calculation model was established, and the earth pressure in each region was derived by the inclined strip method combined with the limit equilibrium method. Then the resultant force and its action point were obtained. By comparing the theoretical and numerical solutions with the previous studies, the correctness of the derived formula is proved, and it is found that the formula can be applied to static conditions. The variation of earth pressure distribution and resultant force under seismic acceleration are studied. The unloading plate’s position, the wall heel’s length, and seismic acceleration will weaken the unloading effect. On the contrary, the length of the unloading plate and the friction angle of filling will strengthen the unloading effect.
Stress-based topology optimization using BESO method with incremental structural nonlinear analysis
Authors: Zhang Hu-zhi , He Qing-chao , Chen Zhan-dong , Feng Fei-fan , Yin Bin 
Published: November 2023

Abstract

To enhance the applicability of optimization methods in civil engineering, particularly for structural members utilizing cement-based materials like concrete, this study introduces a stress-based topology optimization approach employing the Bi-directional Evolutionary Structural Optimization (BESO) method in conjunction with incremental structural nonlinear analysis. The primary objective of this method is to minimize the peak equivalent stress experienced by the structural components. It relies on the utilization of the p-norm condensation function to approximate the peak equivalent stress, alongside the establishment of sensitivity through the adjoint method. This method has demonstrated its aptness in optimizing structures containing highly nonlinear material constituents. By configuring the p-value within a specified range of 4–6 during the optimization process, consistent achievement of solutions aligned with the predefined objectives, based on element sensitivity, is feasible. This sensitivity is derived by applying a filter to the initial sensitivity calculated from the stress outcomes of the incremental structural nonlinear analysis. Subsequently, the data is meticulously filtered to procure a more robust and dependable solution that aligns more closely with the overarching optimization objective.
Dynamic Organelle Changes and Autophagic Processes in Lily Pollen Germination
Authors: Yen Chih-Chung , Hsu Chia-Mei , Jiang Pei-Luen , Jauh Guang-Yuh 
Published: November 2023

Abstract
Pollen germination is a crucial process in the life cycle of flowering plants, signifying the transition of quiescent pollen grains into active growth. This study delves into the dynamic changes within organelles and the pivotal role of autophagy during lily pollen germination—initially, mature pollen grains harbor undifferentiated organelles, including amyloplasts, mitochondria, and the Golgi apparatus. However, germination unveils remarkable transformations, such as the redifferentiation of amyloplasts accompanied by starch granule accumulation. We investigate the self-sustained nature of amylogenesis during germination, shedding light on its association with osmotic pressure. Employing BODIPY 493/503 staining, we tracked lipid body distribution throughout pollen germination, both with or without autophagy inhibitors (3-MA, NEM). Typically, lipid bodies undergo polarized movement from pollen grains into elongating pollen tubes, which is crucial for directional growth. Inhibiting autophagy disrupted this essential lipid body redistribution, underscoring the interaction between autophagy and lipid body dynamics. Notably, tubular endoplasmic reticulum (ER)-like structure their participation in autophagy. Starch granules, lipid bodies, and membrane remnants observed within vacuoles further reinforce the involvement of autophagic processes. The autophagy inhibitors, particularly BFA, significantly impede germination and growth, affecting Golgi morphology. Immunogold labeling substantiates the pivotal role of the ER in forming autophagosome-like compartments and protein localization. Our proposed speculative model of pollen germination encompasses proplastid differentiation and autophagosome formation. This study advances our understanding of organelle dynamics and autophagy during pollen germination, providing valuable insights into plant reproductive physiology.
Carbonation and modeling study for process liquor in batch mode using flue gas in the mining and mineral processing industry
Authors: SHARMA VIPIN KUMAR , Thamida Sunil Kumar , Reddy B. Naveen Kumar 
Published: November 2023

Abstract

​The mining and mineral processing industry generates significant amounts of process liquor containing sufficient concentrations of sodium hydroxide (NaOH). This abstract presents a technical overview of the carbonation process applied to process liquor using boiler flue gas as a source of carbon dioxide (CO2). The carbonation of process liquor using boiler flue gas offers several advantages. Firstly, it provides a sustainable solution for CO2 capture and storage, reducing the environmental impact of the mining and mineral processing industry. Secondly, the carbonation process results in the production of stable carbonate or bicarbonate compounds that can be used as valuable byproducts or raw materials in other industrial processes. Furthermore, the carbonation of process liquor can lead to improved process efficiency and reduced operational costs by facilitating the removal of impurities and the recovery of valuable metals or minerals. Factors such as temperature, pressure, pH, CO2 concentration, and reaction time must be carefully controlled to ensure efficient carbonation and maximize CO2 utilization. Trials were conducted for the effective carbonation of process liquor generated in the mineral processing industry, which contains caustic lye. This technical paper discusses successful experiments conducted for the carbonation of process liquor and further modelling and implementation of this study.
Comparative Effect of Ketogenic and Chitosan-Based Diets on Submandibular Salivary Gland Morphology in Rats: A Histological and Immuno-Histochemical Analysis
Authors: Aboulfotoh Mahmoud 
Published: November 2023

Abstract
Objective: This study was carried out in the submandibular salivary glands (SSGs) of rats to demonstrate the effect of a ketogenic diet (KD) in comparison with dietary chitosan supplementation.
Method: Eighteen albino rats were randomly divided into three equal groups. Rats in Group I were fed a balanced diet and considered controls. Meanwhile, those of Groups II and III were fed a KD, a balanced diet with high molecular weight chitosan, respectively. After 45 days, rats were euthanized, and the SSGs were dissected carefully for staining with hematoxylin and eosin (H&E), alpha-smooth muscle actin (α-SMA) immunohistochemical staining, and Congo red special stain. Quantitative data from α-SMA staining and Congo red staining were statistically analyzed using one-way ANOVA followed by Tukey's multiple comparisons post hoc test.
Results: Regarding Congo red and α-SMA staining, one-way ANOVA revealed a significant difference between the three groups. For α-SMA staining and Congo red staining, Group II had the highest mean values of 91.41 ± 3.30 and 68.10 ± 5.04, respectively, while Group I had the lowest values of 56.13 ± 3.96 and 16.87 ± 2.19, respectively. Group III had mean values of 60.70 ± 3.55 for α-SMA and 19.50 ± 1.78 for Congo red. Tukey's multiple comparisons post hoc test revealed significant differences between groups I & II and between groups II & III (P ˂ 0.05). Meanwhile, there was a nonsignificant difference between groups I and III (P ˃ 0.05).
Conclusion: A KD has a deleterious effect on rats' SSG, and dietary chitosan supplementation ameliorates these damaging effects.
Taxonomic implications of the leaf anatomy of twelve species of Senna ser. Bacillares (Leguminosae) from northeastern Brazil
Authors: Souto Flávio Sousa , Silva Anauara Lima e , Santos Edinalva Alves Vital dos , Agra Maria de Fátima 
Published: November 2023

Abstract

The leaf anatomy of twelve species of Senna ser. Bacillares (Leguminosae) from northeastern Brazil was examined to provide taxonomic support for the group. Forty-three specimens were analyzed using light microscopy, following the usual techniques in plant anatomy. Four different petiole profiles were observed: circular, semicircular, hexagonal, and pentagonal; most petioles showed adaxial projections, those being strongly prominent in S. chrysocarpa and S. quinquangulata. Six different leaf rachis profiles were observed: pentagonal, elliptic, obovate, circular, semicircular, and irregularly triangular. The vascular systems of the petioles and leaf rachisies showed similar patterns, forming 4-7 central bundles and two accessory bundles. The midrib was plane-convex in all species, with an arched vascular bundle surrounded by sclerenchyma. The dorsiventral mesophyll has a uniseriate palisade, with 4-7-seriate spongy parenchyma. Five different leaflet edge outlines were observed: rounded, recurved, acute, acuminate, and truncate; the truncate type was exclusive to S. angulate, while S. gardneriwas acuminate. Idioblasts of druses and prismatic crystals were observed in the petioles, leaf rachises, and midribs of all species; crystalline sand was observed in the petioles and leaf rachises of S. angulata and S. pluribracteata, in the petiole of S. gardneri, and in the rachis of S. splendida. The sets of different anatomical characters of the petioles, leaf rachises, and leaflet edges of all of the species studied provided additional support to the taxonomy of Sennaser. Bacillares and reinforced the importance of anatomical studies to the taxonomy and systematics of this group.