Miracle-dz/UniFAR-FTUs huggingface dataset:
CRIS: complete reconstruction of immunoglobulin V-D-J sequences from RNA-seq data

Abstract Motivation B cells display remarkable diversity in producing B-cell receptors through recombination of immunoglobulin (Ig) V-D-J genes. Somatic hypermutation (SHM) of immunoglobulin heavy chain variable (IGHV) genes are used as a prognostic marker in B-cell malignancies. Clinically, IGHV mutation status is determined by targeted Sanger sequencing which is a resource-intensive and low-throughput procedure. Here, we describe a bioinformatic pipeline, CRIS (Complete Reconstruction of Immunoglobulin IGHV-D-J Sequences) that uses RNA sequencing (RNA-seq) datasets to reconstruct IGHV-D-J sequences and determine IGHV SHM status. Results CRIS extracts RNA-seq reads aligned to Ig gene loci, performs assembly of Ig transcripts and aligns the resulting contigs to reference Ig sequences to enumerate and classify SHMs in the IGHV gene sequence. CRIS improves on existing tools that infer the B-cell receptor repertoire from RNA-seq data using a portion IGHV gene segment by de novo assembly. We show that the SHM status identified by CRIS using the entire IGHV gene segment is highly concordant with clinical classification in three independent chronic lymphocytic leukemia patient cohorts. Availability and implementation The CRIS pipeline is available under the MIT License from https://github.com/Rashedul/CRIS. Supplementary information Supplementary data are available at Bioinformatics Advances online.
Exploring the implementation gap: organizational autonomy and line managers’ participation in human resource decision–making

ABSTRACT This article explores the assumption that the level of human resource (HR) autonomy of an organisation influences line managers’ participation in HR decision-making, and it seeks to understand to what extent such a participation affects the effective implementation of HR practices. The results of an empirical study of HR policies and practices in three public hospitals in Pakistan reveal that greater level of HR autonomy of an organisation, with less pressure to comply with public personnel policies, leads to increased participation of middle managers in HR decision-making. This, in turn, helps to reduce the gap between the intended and implemented HR practices, which is important for human resource management (HRM) – organisational performance linkage. These findings contribute to ongoing discussions related to HRM in the public sector context and line management enactment of HR practices by highlighting the profound implications of the institutional context on the HR management of public hospitals. Additionally, this research proposes a bottom-up approach to HR practices, through its focus on the participation of managers in HR decision-making as a possible solution to better implementation of HR practices.
Arid Australia as a source of plant diversity: the origin and climatic evolution of Ptilotus (Amaranthaceae)

In the present study, we tested the chronological and geographic origins of the mostly arid Australian Ptilotus (Amaranthaceae) and its close relatives (i.e. the ‘aervoids’) by reconstructing a dated phylogeny with near-comprehensive sampling for Ptilotus and estimating ancestral geographic ranges. We investigated climatic niche evolution within Ptilotus and identified likely climatic origins and subsequent niche shifts by reconstructing ancestral states of climatic variables on the phylogeny, which was visualised using a phyloecospace approach. Geospatial analyses were employed to identify probable diversification hotspots within Australia. We inferred that the aervoids originated in Oligocene Africa–Asia and that Ptilotus arrived in northern Australia by dispersal in the Early Miocene. Subsequent diversification of Ptilotus was rapid, giving rise to all major clades in the western Eremaean by the time of an aridification pulse in the Middle Miocene. Climatic niche shifts from the arid Eremaean into monsoonal northern and temperate southern Australia are apparent for multiple independent species groups. Our analyses support the hypothesis that a pre-adaptation to aridity and early arrival in an aridifying Australia were integral to the success of Ptilotus, and that the Eremaean has been a source of biodiversity in the genus and for independent radiations into neighbouring climatic zones.
A Climatological Study of the Mechanisms Controlling the Seasonal Meridional Migration of the Atlantic Warm Pool in an OGCM

The tropical Atlantic Warm Pool is one of the main drivers of the marine intertropical convergence zone and the associated coastal Northeast Brazilian and West-African monsoons. Its meridional displacement is driven by the solar cycle, modulated by the atmosphere and ocean interactions, whose nature and respective proportions are still poorly understood. This paper presents a climatological study of the upper ocean and lower atmosphere contributions to the warm pool seasonal migration, using an Ocean General Circulation Model (OGCM). First, we provide quantitative, albeit simple, pieces of evidence on how the large amplitude of migration in the west, compared to the east, is mainly due to the strong east–west contrast of the background meridional SST gradient intensities, which is maintained by equatorial and eastern tropical upwellings. Our main results consist first in identifying a diagnostic equation for the migration speed of the two meridional boundary isotherms of the Warm Pool, expressed in terms of the various mixed-layer heat fluxes. We then evidence and quantify how, in general, the migration is forced by air–sea fluxes, and damped by ocean circulation. However, remarkable controls by the ocean are identified in some specific regions. In particular, in the northwestern part of the Warm Pool, characterized by a large temperature inversion area, the boreal spring northward movement speed depends on the restitution of the solar heating by the thermocline. Additionally, over the southern part of the Warm Pool, our study quantifies the key role of the equatorial upwelling, which, depending on the longitude, significantly accelerates or slows down the summer poleward migration.
Lithium Borocarbide LiBC as an Anode Material for Rechargeable Li-Ion Batteries

Graphite is the dominant anode material for commercial Li-ion batteries, whereas developing other graphite-like anode material has never been practically achieved to date. Here, we perform computational and experimental studies to demonstrate the feasibility of graphite-like LiBC as a high-capacity anode material for Li-ion batteries. Electrochemical measurements suggest that LiBC can deliver a reversible specific capacity of 450 mAh g–1 with an average voltage of 1.4 V vs Li+/Li. Analogous to graphite, both the discharged and charged LiBC preserve the layered structure. As far as we know, this is the first realization of a graphite-like anode material for Li-ion battery, which will shed light on the development of other graphite derivatives for energy storage.
Combining individual travel behaviour and collective preferences for next location prediction

Many mobility prediction models have emerged over the past decade to predict a user’s next location through the utilisation of user trajectories. However, the performance is constrained by the quantity of user trajectory data. This research introduces a new approach by combining knowledge of individual travel behaviour and collective preferences of users sharing similar daily activity patterns. First, users are clustered into different groups by their daily activity profiles. Second, each group’s collective preferences (i.e. activity and travel distance preferences) are extracted. Then, individual travel behaviour and collective preferences are integrated for the next location prediction. A mobile phone dataset from Shanghai, China, is used for model validation. The results show that the proposed model achieves a prediction accuracy of over 80% during most of the day. Moreover, there is a maximum increase of 16% in prediction accuracy compared with baseline models when users are highly mobile.
EFL Saudi Student's attitudes toward peer feedback activities in a writing class

PurposeThis study aims to examine Saudi female students' attitude toward peer feedback activity in writing classes with a list of questions for the students to follow during the activity, and to investigate the challenges that may prevent the use of such activity in Saudi EFL classes.Design/methodology/approachThis study used a mixed-methods to ensure the credibility of the data and obtain clear descriptions about the topic. The study instruments are (1) Writing Essays, (2) Writing Checklist, (3) Questionnaire and (4) Semi-structured interview. The data were analysis with SPSS and o 10 software.FindingsThe study results indicated that students had a positive attitude toward peer feedback with a checklist in EFL writing class. For instance, their second written essay (post) has improved and has fewer mistakes than the first one. Also, most of the participants stated that peer feedback has improved their writing quality and has enhanced their writing awareness of their weaknesses and mistakes. Moreover, the interview had highlighted the main challenges that could affect using peer feedback in writing class. Finally, the results indicate the efficiency of peer feedback with a checklist in similar teaching contexts.Research limitations/implicationsThe study focused on a small number of participants (30 students). Besides, the study dealt with students at university level only and the study focused on female students.Practical implicationsBased on the study finding, it is recommended that peer feedback should be integrated in all EFL writing classes at all levels. Based on the study finding, it is recommended that peer feedback should be incorporated in all EFL writing classes at all levels. Using checklist can help the students to become more independent learners and in time they will be able to correct their own mistakes.Originality/valueThis paper fulfills an identified need to identify how integrating peer feedback activity in writing class can improve the students' writing performance and help them to be independent learners.
Mobilizing Interference as Methodology and Metaphor in Disability Arts Inquiry

This article interrogates the limits and possibilities of interference as methodology and metaphor in video-based research aiming to disrupt ableist understandings of disability that create barriers to health care. We explore the overlapping terrain of diffractive and interference methodologies, teasing apart the metaphorical-material uses and implications of interference for video-makers in our project. Using the digital/multimedia stories created and an interview as research artifacts, we illuminate how interference manifested in disabled makers’ lives, how interference operated through the research apparatus, and how the videos continue to hold agency through their durability in the virtual realm. Drawing on feminist post-philosophies of matter (Barad) and use (Ahmed), we argue that the videos disrupt the gaze that fetishizes disabled bodies, thereby interfering with cultural-clinical processes that abnormalize disability. The research apparatus interfered with makers’ subjectivities yet also brought people together to generate something new—a community that creates culture and contests its positioning as marginal.
Optimal retrofit for a school under seismic hazard including risk assessment

ABSTRACT The paper proposes a formulation to select the optimal retrofit strategy for a damaged school under seismic hazard, by applying risk and reliability assessment techniques. The formulation considers the cost-effectiveness of alternative retrofit strategies, including failure consequences, to get adequate balance (CE: Balance is an uncountable noun) between the costs and the gains on reliability. The proposed alternatives should produce a failure probability below the target value, which is obtained by minimising the present value of the expected life-cycle cost. The failure consequences include the potential life loss, injuries, expenditures due to off-campus resumption of classes and loss/damage of contents. Exceedance of the shear force and bending moment capacities and the allowable inter-story drift are the considered limit states. A relationship between the cost and the increment on reliability is proposed and calibrated for the case study; MCS is applied to calculate the failure probabilities. An example of a two-story building is a school located in the Tlaxcala State; for this case, the target failure probability is 1.6 × 10−4. The optimal retrofit strategy is the one that corresponds to the minimum expected life-cycle cost. The proposal may serve to generate risk, reliability and resilience-based retrofit recommendations for schools under seismic hazard.
Activity of detoxification enzymes in Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae) after exposure to Beauveria bassiana (Balsamo)

Rhynchophorus ferrugineus is a devastating pest of palms worldwide. An integrated management strategy largely depends on chemical insecticides but due to concerns about human health risks and environmental pollution, it’s essential to emphasize on the integrated pest management (IPM). In the current research the activities of detoxification enzymes esterases (EST), alkaline phosphatases (ALP), acid phosphatases (ACP), glutathione S-transferases (GST), and acetylcholinesterase (AChE) in R. ferrugineus collected from Punjab, Baluchistan, Sindh and Khyber Pakhtunkhwa (KPK) provinces of Pakistan were estimated after infection of Beauveria bassiana on 3rd-, 5th- and 7th-day post-treatment. The insects were exposed by immersion method with different concentrations of B. bassiana. The significant increase in activities of ALP (6.09), ACP (2.51), AChE (21.28) and EST (8.61) μmol/min/mg protein was observed in KPK population, while a significant increase in the activity of GST (5.23 μmol/min/mg protein) was recorded in Baluchistan population on 7th- day. The detection of elevated activities of detoxification enzymes showed the possibility of the resistance development against B. bassiana in R. ferrugineus.
A WT-LUBE-PSO-CWC Wind Power Probabilistic Forecasting Model for Prediction Interval Construction and Seasonality Analysis

Deterministic forecasting models have been used through the years to provide accurate predictive outputs in order to efficiently integrate wind power into power systems. However, such models do not provide information on the uncertainty of the prediction. Probabilistic models have been developed in order to present a wider image of a predictive outcome. This paper proposes the lower upper bound estimation (LUBE) method to directly construct the lower and upper bound of prediction intervals (PIs) via training an artificial neural network (ANN) with two outputs. To evaluate the PIs, the minimization of a coverage width criterion (CWC) cost function is proposed. A particle swarm optimization (PSO) algorithm along with a mutation operator is further implemented, in order to optimize the weights and biases of the neurons of the ANN. Furthermore, wavelet transform (WT) is adopted to decompose the input wind power data, in order to simplify the pre-processing of the data and improve the accuracy of the predictive results. The accuracy of the proposed model is researched from a seasonal perspective of the data. The application of the model on the publicly available data of the 2014 Global Energy Forecasting Competition shows that the proposed WT-LUBE-PSO-CWC forecasting technique outperforms the state-of-the-art methodology in important evaluation metrics.
The Hadamard product and recursively defined sequences

In this paper the approach to obtaining nonrecurrent formulas for some recursively defined sequences is illustrated. The most interesting result in the paper is the formula for the solution of quadratic map-like recurrence. Also, some formulas for the solutions of linear difference equations with variable coefficients are obtained. At the end of the paper, some integer sequences associated with a quadratic map are considered.
Sentence-Level BERT and Multi-Task Learning of Age and Gender in Social Media

Social media currently provide a window on our lives, making it possible to learn how people from different places, with different backgrounds, ages, and genders use language. In this work we exploit a newly-created Arabic dataset with ground truth age and gender labels to learn these attributes both individually and in a multi-task setting at the sentence level. Our models are based on variations of deep bidirectional neural networks. More specifically, we build models with gated recurrent units and bidirectional encoder representations from transformers (BERT). We show the utility of multi-task learning (MTL) on the two tasks and identify task-specific attention as a superior choice in this context. We also find that a single-task BERT model outperform our best MTL models on the two tasks. We report tweet-level accuracy of 51.43% for the age task (three-way) and 65.30% on the gender task (binary), both of which outperforms our baselines with a large margin. Our models are language-agnostic, and so can be applied to other languages.
OMLA: An Oracle-Less Machine Learning-Based Attack on Logic Locking

Hardware-based attacks on the semiconductor supply chain are emerging due to the globalization of the design flow. Logic locking is a design-for-trust scheme that promises protection throughout the supply chain. While attacks have heavily relied on an oracle to break logic locking, machine learning (ML)-based attacks demonstrate the daunting possibility of breaking locking even without an oracle. Although very potent, current ML-based attacks recover only a subset of the transformations introduced by locking. We aim to address this shortcoming by developing an oracle-less graph neural network-based attack called OMLA, questioning once again the security of logic locking. Our experiments on ISCAS-85 and ITC-99 benchmarks demonstrate that OMLA achieves a key-prediction accuracy up to 97.22% and outperforms state-of-the-art SnapShot and SAIL attacks for all evaluated benchmarks.
Vitamin C-Assisted Fabrication of Aerogels from Industrial Graphene Oxide for Gaseous Hexamethyldisiloxane Adsorption

Volatile methyl siloxanes (VMSs) as a trace impurity in biogas decreases its energy utilization, and thus need to be removed. In this paper, a one-step hydrothermal reduction was performed to produce three-dimensional reduced graphene oxide aerogels (rGOAs) using industrial-grade graphene oxide (IGGO) as raw material and vitamin C (VC) as a reductant to facilitate the fabrication of rGOAs. The synthesis of rGOAs was a simple, green, and energy-efficient process. The developed rGOAs were characterized using the Brunauer–Emmett–Teller method, Raman spectrometry, scanning electron microscopy, Fourier-transform infrared spectroscopy, X-ray diffraction measurements and contact angle. The results obtained showed that rGOA-1 with a VC/IGGO ratio of 1/1 (m/m) exhibited a hierarchical porous structure and super-hydrophobicity, yielding a high specific surface area (137.9 m2 g−1) and superior water contact angle (143.8°). The breakthrough adsorption capacity of rGOA-1 for hexamethyldisiloxane (L2, a VMS model) was 11 times higher than that of IGGO. Low inlet concentration and bed temperature were considered beneficial for the L2 adsorption. Interestingly, rGOA-1 was less sensitive to water, and it was readily regenerated for reuse by annealing at 80 °C. The rGOAs have been demonstrated to have great potential for the removal of siloxanes from biogas.
Providing Input-Discriminative Protection for Local Differential Privacy

Local Differential Privacy (LDP) provides provable privacy protection for data collection without the assumption of the trusted data server. In the real-world scenario, different data have different privacy requirements due to the distinct sensitivity levels. However, LDP provides the same protection for all data. In this paper, we tackle the challenge of providing input-discriminative protection to reflect the distinct privacy requirements of different inputs. We first present the Input- Discriminative LDP (ID-LDP) privacy notion and focus on a specific version termed MinID-LDP, which is shown to be a finegrained version of LDP. Then, we focus on the application of frequency estimation and develop the IDUE mechanism based on Unary Encoding for single-item input and the extended mechanism IDUE-PS (with Padding-and-Sampling protocol) for item-set input. The results on both synthetic and real-world datasets validate the correctness of our theoretical analysis and show that the proposed mechanisms satisfying MinID-LDP have better utility than the state-of-the-art mechanisms satisfying LDP due to the input-discriminative protection.
Spatiotemporal Variation of Water Supply and Demand Balance under Drought Risk and Its Relationship with Maize Yield: A Case Study in Midwestern Jilin Province, China

Under the background of global warming, the frequent occurrence and long-term persistence of drought events have substantial negative effects on agricultural production. As the main maize production area in midwestern Jilin Province, frequent drought and a shortage of irrigation water pose substantial threats to the production of maize. We analyzed the balance of water supply and demand in each growth period and the degree of maize yield affected by drought. The results indicate that the FIO-ESM climate model can effectively simulate the changes in temperature and precipitation, and was highly applicable to the study area. From 1980 to 2020, the drought risk indices for the sowing to jointing, jointing to tasseling, tasseling to milk-ripe, and milk-ripe to maturity stages were 0.62, 0.52, 0.48, and 0.60, respectively. In the future, the chances of a RCP8.5 scenario drought risk and an enhanced RCP4.5 scenario have eased. Spatially, the high-risk areas shift in a “west−central−southwest” pattern. Effective precipitation will decrease in the future, while the increasing water requirement of maize increases the dependence on irrigation water. The irrigation requirement index is more than 70% for all periods, particularly in the milk-ripe to maturity stage. The relative meteorological yields were positively correlated with the CWDI of the whole growth period, with the rate of reduction in maize yield and the yield reduction coefficient of variation at a high level of risk between 1980 and 2020. In the future, the negative impact of drought risk on the yield of maize lessened with no obvious trend in production. In particular, the rate of reduction and reduction coefficient of variation for the RCP8.5 scenario were 1.24 and 1.09, respectively.
Recent Perspectives in Biochar Production, Characterization and Applications

This chapter presents the most promising features and applications of biochar along with their optimal pyrolysis conditions. Biochars have a range of physicochemical properties depending on the feedstock and pyrolysis conditions, which greatly affect their wide applications. The biochar production and its characteristics, including the effect of feedstocks and different process-parameters on the properties and yield of biochar are thoroughly examined. The higher pyrolysis-temperature can give higher carbon-contents, pH, and surface-areas of biochars while volatiles and molar-ratios of O/C, H/C and N/C decrease with pyrolysis-temperature. Higher carbon-content and neutral-pH biochars have high affinity for organic pollutants due to high surface areas, making them attractive for adsorption and catalysis purposes. Biochars with higher-pH are preferred for soil application to correct soil-acidity. Thus, the pyrolysis temperature should be selected as per the final application of the biochar. Characterization of biochars of different feedstocks and pyrolysis conditions is reviewed and presented along with their proximate and ultimate analysis.