Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation, cloning and expression of the Brucella melitensis Omp31 gene.

Summary Brucellosis is a zoonotic disease transmitted to humans either from animals or from their products. Although brucellosis can be found worldwide, the Mediterranean Basin, South and Central America, Eastern Europe, Asia, Africa, the Caribbean, and the Middle East have currently been listed as high-risk regions. The genus Brucella is classified in at least nine species. Brucella melitensis is the global pathogenic species of Brucella. The outer membrane protein 31, (Omp31) from B. melitensis is considered as a protective immunogen and an important candidate vaccine. Contamination of purified Omp31 protein by biochemical methods has made some restrictions in practical experiments. In this study, the Omp31coding gene of B. melitensis Rev 1 strain was inserted in pET32b(+) plasmid with extra His-tag sequence. The integrity of the constructed plasmid was confirmed using restriction enzyme mapping and sequencing. Omp31 was expressed after induction with IPTG in Escherichia coli BL21. Recombinant Omp31 (rOmp31) was purified by chromatography through Ni-agarose. The electrophoresis showed successful purification and immunoblotting confirmed immunereactivity of rOmp31. Obtained rOmp31 could be used as a research experimental tool in protection assays to find its potential as a vaccine candidate.
Quantitative Analysis of the Proteome and the Succinylome in the Thyroid Tissue of High-Fat Diet-Induced Hypothyroxinemia in Rats

Hypothyroidism is a common disease, and its molecular mechanism still needs further investigation. Lysine succinylation is found to be involved in various metabolic processes associated with hypothyroidism. We performed quantitative analysis on lysine succinylome in thyroids of rats with hypothyroxinemia, which was induced through the administration of a high-fat diet. Overall, 129 differentially expressed proteins were quantified. Downregulated proteins were enriched in the thyroid hormone synthesis and thyroid hormone signaling pathways and were mainly localized in the mitochondria. In addition, 172 lysine succinylation sites on 104 proteins were obviously changed. Decreased succinylated proteins were involved in diverse metabolic pathways and were primarily localized in mitochondria. Finally, the mitochondrial oxygen consumption rates of human normal thyroid epithelial cells were measured to further verify the role of lysine succinylation. The mitochondrial oxygen consumption rates were markedly blunted in the cells treated with palmitic acid (all p < 0.05), and the changes were reversed when the cells were treated with palmitic acid and desuccinylase inhibitor together (all p < 0.05). Thus, we theorize that the thyroid differentially expressed proteins and changed succinylation levels played potential roles in the mitochondria-mediated energy metabolism in the high-fat diet-induced hypothyroxinemia rat model.
Association between Gout, Urate-Lowering Therapy, and Risk of Developing Type 2 Diabetes Mellitus: A Nationwide Population-Based Retrospective Cohort Study

Gout is the most prevalent inflammatory arthritis in adults. Although the link between gout and type 2 diabetes mellitus (T2DM) has been documented, our understanding of the association between urate-lowering therapy (ULT) among gout patients and T2DM development remains poor. We included 69,326 patients with new-onset gout in 2000-2011. Each case was matched randomly with 1 patient without gout during the study period, and 69,326 patients were recognized as the comparison cohort. A Cox proportional hazard regression model was used to analyze differences in the risk of T2DM development between patients with and without gout after considering related comorbidities. After adjusting for potential confounders, the case group had a higher risk of T2DM than the control cohort (adjusted hazard ratio (aHR) = 1.30, 95%confidence interval (CI) = 1.24-1.38; P < 0.001). Gout patients without appropriate ULT had significantly higher risk of T2DM development than the control cohort (aHR = 1.39; 95%CI = 1.30-1.48; P < 0.001). Among gout patients, those receiving ULT excluding probenecid (aHR = 0.80; 95%CI = 0.64-1.00), all had significantly lower risk of T2DM than gout patients without ULT (all aHR < 0.90; all P < 0.001). In this study, we found that gout increased the risk of T2DM; however, patients with any ULT exhibited a lower risk of T2DM than gout patients without any ULT (all aHR < 0.90, P < 0.001; excluding probenecid).
ROS-Mediated Therapeutic Strategy in Chemo-/Radiotherapy of Head and Neck Cancer

Head and neck cancer is a highly genetic and metabolic heterogeneous collection of malignancies of the lip, oral cavity, salivary glands, pharynx, esophagus, paranasal sinuses, and larynx with five-year survival rates ranging from 12% to 93%. Patients with head and neck cancer typically present with advanced stage III, IVa, or IVb disease and are treated with comprehensive modality including chemotherapy, radiotherapy, and surgery. Despite advancements in treatment modality and technique, noisome recurrence, invasiveness, and resistance as well as posttreatment complications severely influence survival rate and quality of life. Thus, new therapeutic strategies are urgently needed that offer enhanced efficacy with less toxicity. ROS in cancer cells plays a vital role in regulating cell death, DNA repair, stemness maintenance, metabolic reprogramming, and tumor microenvironment, all of which have been implicated in resistance to chemo-/radiotherapy of head and neck cancer. Adjusting ROS generation and elimination to reverse the resistance of cancer cells without impairing normal cells show great hope in improving the therapeutic efficacy of chemo-/radiotherapy of head and neck cancer. In the current review, we discuss the pivotal and targetable redox-regulating system including superoxide dismutases (SODs), tripeptide glutathione (GSH), thioredoxin (Trxs), peroxiredoxins (PRXs), nuclear factor erythroid 2-related factor 2/Kelch-like ECH-associated protein 1 (Nrf2/keap1), and mitochondria electron transporter chain (ETC) complexes and their roles in regulating ROS levels and their clinical significance implicated in chemo-/radiotherapy of head and neck cancer. We also summarize several old drugs (referred to as the non-anti-cancer drugs used in other diseases for a long time) and small molecular compounds as well as natural herbs which effectively modulate cellular ROS of head and neck cancer to synergize the efficacy of conventional chemo-/radiotherapy. Emerging interdisciplinary techniques including photodynamic, nanoparticle system, and Bio-Electro-Magnetic-Energy-Regulation (BEMER) therapy are promising measures to broaden the potency of ROS modulation for the benefit of chemo-/radiotherapy in head and neck cancer.
Offloading Computations to Mobile Devices and Cloudlets via an Upgraded NFC Communication Protocol

The increasing complexity of smartphone applications and services necessitate high battery consumption, but the growth of smartphones’ battery capacity is not keeping pace with these increasing power demands. To overcome this problem, researchers gave birth to the Mobile Cloud Computing (MCC) research area. In this paper, we advance on previous ideas, proposing and implementing a Near Field Communication (NFC)-based computation offloading framework. This research is motivated by the advantages of NFC's short distance communication, its better security, and its low battery consumption characteristics. We design a new NFC communication protocol that overcomes the limitations of the default NFC protocol; removing the need for constant user interaction, the one–way communication restraint, and the limit on low data size transfer. Via the implemented framework, parts of mobile applications can be offloaded to other mobile devices or cloudlets equipped with an NFC reader. We present experimental results of the energy consumption and the time duration of computationally and data intensive representative applications: (i) RSA key generation and encryption, (ii) gaming/puzzles, (iii) face detection, (iv) media download from the Internet, and (v) data transferring between the mobile and the cloudlet. We show that when the helper device is more powerful than the device offloading the computations, the execution time of the tasks is reduced. Finally, we show that devices that offload application parts considerably reduce their energy consumption due to the low–power NFC interface and the benefits of offloading.
Positive dielectrophoresis–based Raman-activated droplet sorting for culture-free and label-free screening of enzyme function in vivo

We introduce a novel, high-speed Raman-activated cell sorter (pDEP-RADS) that screens enzymes in vivo. The potential of Raman-activated cell sorting (RACS) is inherently limited by conflicting demands for signal quality and sorting throughput. Here, we present positive dielectrophoresis–based Raman-activated droplet sorting (pDEP-RADS), where a periodical pDEP force was exerted to trap fast-moving cells, followed by simultaneous microdroplet encapsulation and sorting. Screening of yeasts for triacylglycerol (TAG) content demonstrated near-theoretical-limit accuracy, ~120 cells min−1 throughput and full-vitality preservation, while sorting fatty acid degree of unsaturation (FA-DU) featured ~82% accuracy at ~40 cells min−1. From a yeast library expressing algal diacylglycerol acyltransferases (DGATs), a pDEP-RADS run revealed all reported TAG-synthetic variants and distinguished FA-DUs of enzyme products. Furthermore, two previously unknown DGATs producing low levels of monounsaturated fatty acid–rich TAG were discovered. This first demonstration of RACS for enzyme discovery represents hundred-fold saving in time consumables and labor versus culture-based approaches. The ability to automatically flow-sort resonance Raman–independent phenotypes greatly expands RACS’ application.
Molecular recognition of human islet amyloid polypeptide assembly by selective oligomerization of thioflavin T

Single-molecule imaging reveals the oligomerization state specificity of drug on its protein receptor. Selective oligomerization is a common phenomenon existing widely in the formation of intricate biological structures in nature. The precise design of drug molecules with an oligomerization state that specifically recognizes its receptor, however, remains substantially challenging. Here, we used scanning tunneling microscopy (STM) to identify the oligomerization states of an amyloid probe thioflavin T (ThT) on hIAPP8–37 assembly to be exclusively even numbers. We demonstrate that both adhesive interactions between ThT and the protein substrate and cohesive interactions among ThT molecules govern the oligomerization state of the bounded ThT. Specifically, the work of the cohesive interaction between two head/tail ThTs is determined to be 6.4 kBT, around 50% larger than that of the cohesive interaction between two side-by-side ThTs (4.2 kBT). Overall, our STM imaging and theoretical understanding at the single-molecule level provide valuable insights into the design of drug compounds using the selective oligomerization of molecular probes to recognize protein self-assembly.
Approximate inference systems (AxIS): end-to-end approximations for energy-efficient inference at the edge

The rapid proliferation of the Internet-of-Things (IoT) and the dramatic resurgence of artificial intelligence (AI) based application workloads has led to immense interest in performing inference on energy-constrained edge devices. Approximate computing (a design paradigm that yields large energy savings at the cost of a small degradation in application quality) is a promising technique to enable energy-efficient inference at the edge. This paper introduces the concept of an approximate inference system (AxIS) and proposes a systematic methodology to perform joint approximations across different subsystems in a deep neural network-based inference system, leading to significant energy benefits compared to approximating individual subsystems in isolation. We use a smart camera system that executes various convolutional neural network (CNN) based image recognition applications to illustrate how the sensor, memory, compute, and communication subsystems can all be approximated synergistically. We demonstrate our proposed methodology using two variants of a smart camera system: (a) Camedge, where the CNN executes locally on the edge device, and (b) Camcloud, where the edge device sends the captured image to a remote cloud server that executes the CNN. We have prototyped such an approximate inference system using an Altera Stratix IV GX-based Terasic TR4-230 FPGA development board. Experimental results obtained using six CNNs demonstrate significant energy savings (around 1.7× for Camedge and 3.5× for Camcloud) for minimal (< 1%) loss in application quality. Compared to approximating a single subsystem in isolation, AxIS achieves additional energy benefits of 1.6×--1.7× (Camedge) and 1.4×--3.4× (Camcloud) on average for minimal application-level quality loss.
Solid-phase inclusion as a mechanism for regulating unfolded proteins in the mitochondrial matrix

Formation of solid-phase protein aggregates in mitochondria is associated with mitochondrial lipid metabolism. Proteostasis declines with age, characterized by the accumulation of unfolded or damaged proteins. Recent studies suggest that proteins constituting pathological inclusions in neurodegenerative diseases also enter and accumulate in mitochondria. How unfolded proteins are managed within mitochondria remains unclear. Here, we found that excessive unfolded proteins in the mitochondrial matrix of yeast cells are consolidated into solid-phase inclusions, which we term deposits of unfolded mitochondrial proteins (DUMP). Formation of DUMP occurs in mitochondria near endoplasmic reticulum–mitochondria contact sites and is regulated by mitochondrial proteins controlling the production of cytidine 5′-diphosphate–diacylglycerol. DUMP formation is age dependent but accelerated by exogenous unfolded proteins. Many enzymes of the tricarboxylic acid cycle were enriched in DUMP. During yeast cell division, DUMP formation is necessary for asymmetric inheritance of damaged mitochondrial proteins between mother and daughter cells. We provide evidence that DUMP-like structures may be induced by excessive unfolded proteins in human cells.
Embedding error correction into crossbars for reliable matrix vector multiplication using emerging devices

Emerging memory devices are an attractive choice for implementing very energy-efficient in-situ matrix-vector multiplication (MVM) for use in intelligent edge platforms. Despite their great potential, device-level non-idealities have a large impact on the application-level accuracy of deep neural network (DNN) inference. We introduce a low-density parity-check code (LDPC) based approach to correct non-ideality induced errors encountered during in-situ MVM. We first encode the weights using error correcting codes (ECC), perform MVM on the encoded weights, and then decode the result after in-situ MVM. We show that partial encoding of weights can maintain DNN inference accuracy while minimizing the overhead of LDPC decoding. Within two iterations, our ECC method recovers 60% of the accuracy in MVM computations when 5% of underlying computations are error-prone. Compared to an alternative ECC method which uses arithmetic codes, using LDPC improves AlexNet classification accuracy by 0.8% at iso-energy. Similarly, at iso-energy, we demonstrate an improvement in CIFAR-10 classification accuracy of 54% with VGG-11 when compared to a strategy that uses 2× redundancy in weights. Further design space explorations demonstrate that we can leverage the resilience endowed by ECC to improve energy efficiency (by reducing operating voltage). A 3.3× energy efficiency improvement in DNN inference on CIFAR-10 dataset with VGG-11 is achieved at iso-accuracy.
Traveling and standing waves mediate pattern formation in cellular protrusions

Excitable waves evolve into standing patterns and lead to the various dynamic and static protrusions seen in migrating cells. The mechanisms regulating protrusions during amoeboid migration exhibit excitability. Theoretical studies have suggested the possible coexistence of traveling and standing waves in excitable systems. Here, we demonstrate the direct transformation of a traveling into a standing wave and establish conditions for the stability of this conversion. This theory combines excitable wave stopping and the emergence of a family of standing waves at zero velocity, without altering diffusion parameters. Experimentally, we show the existence of this phenomenon on the cell cortex of some Dictyostelium and mammalian mutant strains. We further predict a template that encompasses a spectrum of protrusive phenotypes, including pseudopodia and filopodia, through transitions between traveling and standing waves, allowing the cell to switch between excitability and bistability. Overall, this suggests that a previously-unidentified method of pattern formation, in which traveling waves spread, stop, and turn into standing waves that rearrange to form stable patterns, governs cell motility.
Theories and Models of Emotions, Attitudes, and Self-Efficacy in the Context of Programming Education

Research into the relationship between learning computing and students' attitudes, beliefs, and emotions often builds on theoretical frameworks from the social sciences in order to understand how these factors influence, for example, students' motivation, study practices, and learning results. In this paper we explore the computing education research literature to identify new theoretical constructs that have emerged from this research. We focus on empirical work in programming education that extends or adapts theories or instruments from the social sciences or that independently develops theories specific to programming. From an initial data set of more than 3800 papers published in the years 2010--2019, we identify 50 papers that present a range of domain-specific theoretical constructs addressing emotions, affect, beliefs, attitudes, and self-efficacy. They include 11 validated instruments and a number of statistical models, but also grounded theories and pedagogical models. We summarize the main results of many of these constructs and provide references for all of them. We also investigate how these constructs have informed further research by analysing over 850 papers that cite these 50 papers. We categorize the ways that theories can inform further research, and give examples of papers in each of these categories. Our findings indicate that among these categories, instruments have been most widely used in further research, thus affirming their value in the field.
Conservation in a Region of Political Instability: Bwindi Impenetrable Forest, Uganda

Abstract: Bwindi Impenetrable is the most important forest in Uganda for conservation of biodiversity. It contains over half the world's mountain gorillas. It is surrounded by densely populated agricultural land and lies within a region of political instability. Gazetted as a forest reserve in 1932, little forest now remains outside its boundaries. Transformation of nearby communal swampland to farmland, much owned by a few individuals, shows the probable fate of Bwindi if it had not been declared a protected area. Widespread illegal logging and other activities were among reasons why the status of the forest was raised to national park in 1991. This resulted in local resentment, fed by inadequate consultation and concern about the local people's loss of access to resources. Fires were set in the forest and threats made against the gorillas. Three schemes to provide benefits from the existence of the forest to communities and involve them in park management were then instituted: agreements allowing controlled harvesting of resources in the park, receipt of some revenue from tourism, and establishment of a trust fund partly for community development. Tension between people and park has been reduced. This case demonstrates the importance of protected areas and community involvement in such circumstances. Community support is especially critical, as here, when resources available to park managers are limited and political instability endemic.
Widespread energy limitation to life in global subseafloor sediments

The global subseafloor biosphere subsists under extreme and widespread energy limitation. Microbial cells buried in subseafloor sediments comprise a substantial portion of Earth’s biosphere and control global biogeochemical cycles; however, the rate at which they use energy (i.e., power) is virtually unknown. Here, we quantify organic matter degradation and calculate the power utilization of microbial cells throughout Earth’s Quaternary-age subseafloor sediments. Aerobic respiration, sulfate reduction, and methanogenesis mediate 6.9, 64.5, and 28.6% of global subseafloor organic matter degradation, respectively. The total power utilization of the subseafloor sediment biosphere is 37.3 gigawatts, less than 0.1% of the power produced in the marine photic zone. Aerobic heterotrophs use the largest share of global power (54.5%) with a median power utilization of 2.23 × 10−18 watts per cell, while sulfate reducers and methanogens use 1.08 × 10−19 and 1.50 × 10−20 watts per cell, respectively. Most subseafloor cells subsist at energy fluxes lower than have previously been shown to support life, calling into question the power limit to life.
ICD-11 Prolonged Grief Disorder Criteria: Turning Challenges Into Opportunities With Multiverse Analyses

Recently, prolonged grief disorder (PGD), a diagnosis characterized by severe, persistent and disabling grief, was formally included in the 11th revision of the International Classification of Diseases [ICD-11; (1): Table 1]. To meet PGDICD-11 criteria one needs to experience persistent and pervasive longing for the deceased and/or persistent and pervasive cognitive preoccupation with the deceased, combined with any of 10 additional grief reactions assumed indicative of intense emotional pain for at least six months after bereavement. Contrary to the 5th revision of the Diagnostical and Statistical Manual of Mental Disorders [DSM-5; (11)] and the 10th revision of the International Classification of Diseases [ICD-10; (12)], the ICD-11 only uses a typological approach, implying that diagnosis descriptions are simple and there is no strict requirement for the number of symptoms one needs to experience to meet the diagnostic threshold. Some researchers have argued that PGDICD-11’s typological approach is helpful, as it will lead to greater sensitivity in case identification in clinical practice and increased cross-cultural applicability (13). Others have highlighted that the typological approach allows for flexible diagnostic algorithms in research, so that PGDICD-11 criteria can be adapted to resemble the characteristics of both stricter and more lenient precursor criteria (14). In the current contribution, we take a different, complementary position. We highlight a series of challenges in using the PGD criteria for research purposes and discuss the application of a method that employs flexibility of PGDICD-11 diagnostic approach to address these challenges, which may help in working toward the unbiased, structured, and transparent identification of optimal criteria for disturbed grief.