Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrite Oxidizer Activity and Community Are More Responsive Than Their Abundance to Ammonium-Based Fertilizer in an Agricultural Soil

Autotrophic nitrification is mediated by ammonia oxidizing bacteria (AOB) or ammonia oxidizing archaea (AOA) and nitrite oxidizing bacteria (NOB). Mounting studies have examined the impact of nitrogen (N) fertilization on the dynamic and diversity of AOA and AOB, while we have limited information on the response of the activity, abundance, and diversity of NOB to N fertilization. We investigated the influence of organic and inorganic N fertilizers on soil NOB in silage corn field plots that received contrasting nitrogen (N) treatments: control (no additional N), ammonium sulfate (AS 100 and 200 kg N ha−1), and compost (200 kg N ha−1). Nitrifying community was examined using a universal marker (16S rRNA gene), functional gene markers (AOB amoA and Nitrospira nxrB), and metagenomics. The overall nitrifying community was not altered after the first fertilization but was significantly shifted by 4-year repeated application of ammonium fertilizers. Nitrospira were the dominant NOB (>99.7%) in our agricultural soil. Both community compositions of AOB and Nitrospira were significantly changed by ammonium fertilizers but not by compost after 4 years of repeated applications. All nitrifiers, including comammox, were recovered in soil metagenomes based on a gene-targeted assembly, but their sequence counts were very low. Although N treatment did not affect the abundance of Nitrospira nxrB determined by real-time quantitative PCR, ammonium fertilizers significantly promoted rates of potential nitrite oxidation determined at 0.15 mM nitrite in soil slurries. Understanding the response of both ammonia oxidizers and nitrite oxidizers to N fertilization may initiate or improve strategies for mitigating potential environmental impacts of nitrate production in agricultural ecosystems.
Improving the Efficiency of Solar Photovoltaic Power Generation Using Improved MPPT Method

The use of solar energy is a sensible and effective way to deal with the worldwide energy crisis. Studies of improving the efficiency of the solar portion are very necessary in order to reduce the cost of solar power. We have proposed several methods to improve the efficiency of solar energy on the basis of a transverse contrast method and have conducted surveys and research. The analysis showed that in order to enhance the performance of the solar power we should review the techniques for conversion of panels; the integration of automatic panels with solar energy; the use of maximum power monitoring technologies in solar power controls and the use of battery charging and discharge technology in battery storage; the use of total panorama technology The experience has shown that the use of these technologies will boost solar power generation output effectively.
Harnessing Natural Killer Cell Innate and Adaptive Traits in HIV Infection

Despite efficient virological suppression on antiretroviral therapy (ART), people living with HIV (PLWH), experience an increased burden of premature co-morbidities, such as cancer and end-organ disease. With remaining challenges in terms of access to therapy, adherence and potential long-term drug toxicity, improving their long-term healthcare outcome, including new strategies for HIV clearance, remains a global priority. There is, therefore, an ongoing need to better characterize and harness the immune response in order to develop new strategies and supplement current therapeutic approaches for a “functional” cure. Current efforts toward HIV eradication to enhance immune recognition and elimination of persistently infected cells have highlighted the need for an optimized “kill” approach. Natural killer (NK) cells play an important role in antiviral defense and by virtue of their innate and adaptive features hold great promise as a focus of “kill” efforts. Galvanized by advances in the cancer field, NK cell exploitation, represents a transformative approach to augment HIV therapeutic modalities, circumventing many of the limitations inherent to T cell approaches. In this review we will discuss recent advances in our understanding of the development of NK cell adaptive/memory responses in HIV infection and highlight new and exciting opportunities to exploit the beneficial attributes of NK cells for HIV immunotherapy.
A Tiny Complementary Oscillator With 1/f3 Noise Reduction Using a Triple-8-Shaped Transformer

This letter presents a triple-8-shaped transformer-based complementary oscillator. It features tiny area, wide tuning range (TR), electromagnetic compatibility (EMC), and low flicker phase noise (PN), combining the merits of both <inline-formula> <tex-math notation="LaTeX">$LC$ </tex-math></inline-formula>-tank and ring oscillators. We identify that after suppressing the second-harmonic voltage by the complementary operation itself, the third-harmonic current entering the capacitive path is now the main cause of asymmetry in the rising and falling edges, leading to the <inline-formula> <tex-math notation="LaTeX">$1/f$ </tex-math></inline-formula> noise upconversion. By tuning the capacitance ratio between gate and drain nodes of the switching transistors, it mitigates the third-harmonic voltage and introduces a specific gate–drain phase shift, reducing the <inline-formula> <tex-math notation="LaTeX">$1/f^{3}$ </tex-math></inline-formula> PN. Fabricated in 22-nm FDSOI CMOS, the prototype occupies an area of 0.01 mm<sup>2</sup> and achieves <inline-formula> <tex-math notation="LaTeX">$1/f^{3}$ </tex-math></inline-formula> PN corner of 70 kHz, PN of −110 dBc/Hz @1MHz and Figure-of-Merit (FoM) of −182 dB at 9 GHz, 39% TR, resulting in the best FoM with normalized TR and area (FoM<sub>TA</sub>) of −214 dB@1 MHz.
CATI: Context-Assisted Type Inference from Stripped Binaries

Code analysis is a powerful way to eliminate vulnerabilities. Closed-source programs lack crucial information vital for code analysis because that information is stripped on compilation to achieve smaller executable size. Restoration has always been a challenge for experts. Variable type information is fundamental in this process because it helps to provide a perspective on program semantic. In this paper, we present an efficient approach for inferring types, and we overcome the challenge of scattered information provided by static analysis on stripped binaries. We discover that neighboring instructions are likely to operate the same type of variables, which are leveraged to enrich the features that we rely on. Therefore, we implement a system called CATI, which locates variables from stripped binaries and infers 19 types from variables. Experiments show that it infers variable type with 71.2% accuracy on unseen binaries. Meanwhile, it takes approximately 6 seconds to process a typical binary.
Pentagon Connected Five-Phase Induction Machine Working under One-Phase Fault

The presented paper deals with the five-phase induction motor (IM) having pentagon connected stator winding, which is working under one phase supply failure. Computation of the motor electromagnetic quantities are made using the space vector theory in the complex plane. Analysis is done assuming, the motor is supplied by a pulse width modulation (PWM) controlled inverter with sufficiently high modulation frequency. Only the first stator voltage harmonics is taken into consideration. On the base of measured IM parameters, trajectories of stator and rotor current space vectors were investigated. On their basis, the motor electromagnetic torque ripple waveform for failure supply mode is derived. Finally a possibility to reduce torque ripple in failure state is shown.
Evaluating a Visual Simultaneous Localization and Mapping Solution on Embedded Platforms

Simultaneous Localization and Mapping (SLAM) is an area of enormous growth in the robotics field. With the current evolution of microprocessors technology and the development of high-speed and precise SLAM solutions, running real-time SLAM algorithms on embedded platforms starts to become a feasible task. For this challenge to be achieved, evaluations on state-of-the-art SLAM methods running on the most up-to-date microcomputers at the moment must be done. This work presents results of ORB-SLAM2 running on both a Raspberry Pi 3B+ board and a NVIDIA Jetson Nano and suggests optimizations to be performed on future works.
The Lower Peripheral Blood Lymphocyte to Monocyte Ratio Following Completion of First Line Chemotherapy Is a Risk Factor for Predicting Relapse in Patients with Diffuse Large B-Cell Lymphoma

Background and objective: During routine follow up, there is no specific predictor to ascertain relapse after standard first line chemotherapy in diffuse large cell lymphoma. Therefore, this study was designed to assess the prognostic significance of the ratio between absolute lymphocyte and monocyte counts (LMR) in the peripheral blood to verify relapse in diffuse large B cell lymphoma. Patients and methods: A total of 139 patients with newly diagnosed diffuse large B cell lymphoma (DLBCL) were evaluated and treated with CHOP or R-CHOP between the years 2009 and 2016. Three months following completion of first line therapy, Lymphocyte/monocyte ratio (LMR) was calculated from the routine automated complete blood cell count (CBC) attained a plateau after the bone marrow recovery after first line chemotherapy. The absolute lymphocyte count/absolute monocyte count ratio (LMR) was calculated by dividing the ALC by the AMC. Results: ROC curve analysis of 139 patients established 2.8 as cutoff point of LMR for relapse with AUC of 0.97 (95% CI 0.93 - 0.99, P ≤ 0.001). Cox regression analysis was performed to identify factors predicting relapse. In univariate regression analysis, ALC (95% CI 0.003 - 0.03, p ≤ 0.001), AMC (95% CI 15.4 - 128.8, p ≤ 0.001), LMR (95% CI 0.001 - 0.01, p ≤ 0.001), and LDH (95% CI 0.1 - 0.5, p ≤ 0.001) following completion of therapy are significant factors for relapse. Other significant factors for relapse are Ann Arbor stage (95% CI 1.1 - 6.9, P = 0.03), extranodal sites (95% CI 1.2 - 6.1, P = 0.01), age (95% CI 1.3 - 6.5, P = 0.01) and treatment of CHOP protocol (95% CI 0.05 - 0.6, P = 0.007). In a multivariate analysis LMR following completion of therapy was predictive for relapse (95% CI 0.001 - 0.2, P = 0.005). ALC was also significant in multivariate analysis (95% CI 0.01 - 0.8, P = 0.03). LDH following completion of therapy (95% CI 0.2 - 14.9, P = 0.5), AMC following completion of therapy (95% CI 0.3 - 43.1, P = 0.3), age (95% CI 0.9 - 205.4, P = 0.06), extra-nodal sites (95% CI 0.04 - 9.8, P = 0.8), Ann Arbor stage (95% CI 0.3 - 28.7, P = 0.3), and Treatment of CHOP protocol (95% CI 0.01 - 2.4, P = 0.2) were not statistically significant. Conclusion: This study observed that LMR assessed after first line chemotherapy during routine follow up is an independent predictor of relapse and clinical outcome in DLBCL patients. LMR at follow up can be used a simple inexpensive biomarker to alert clinicians for relapse during follow up after standard first line chemotherapy in DLBCL patients.
Sentiment Analysis of Arabic Jordanian Dialect Tweets

Sentiment Analysis (SA) of social media contents has become one of the growing areas of research in data mining. SA provides the ability of text mining the public opinions of a subjective manner in real time. This paper proposes a SA model of Arabic Jordanian dialect tweets. Tweets are annotated on three different classes; positive, negative, and neutral. Support Vector Machines (SVM) and Naive Bayes (NB) are used as supervised machine learning classification tools. Preprocessing of such tweets for SA is done via; cleaning noisy tweets, normalization, tokenization, namely, Entity Recognition, removing stop words, and stemming. The results of the experiments conducted on this model showed encouraging outcomes when Arabic light stemmer/segment is applied on Arabic Jordanian dialect tweets. Also, the results showed that SVM has better performance than NB on such tweets’ classifications.
Are codon usage patterns in unicellular organisms determined by selection‐mutation balance?

Strongly biased codon usage is common in unicellular organisms, particularly in highly expressed genes. The bias is most simply explained as a balance between selection and mutation, with selection favouring those codons which are more efficiently translated. In a review Ikemura (1985) has proposed four rules for predicting which codons will be preferred, based on the properties of the transfer RNAs responsible for translating messenger RNA into protein. In this paper codon usage in E. coli and yeast is re‐examined using the recent compilation of Maruyama et al. (1986). The codon adaptation index of Sharp and Li (1986a) is used as a measure of gene expression to investigate the importance of this factor. It is found that Ikemura's rules successfully predict preferred codons for yeast, but that two of them work less well for E. coli, and it is suggested that some of the apparent bias in weakly expressed genes of E. coli may be due to contextual effects on mutation rates.
Cost Function Design for Stable Performance of Modulated Model Predictive Control for Grid-Tied Inverters

This paper proposes a quadratic cost function for Modulated Model Predictive Control, $\mathrm{M}^{2}$ PC, designed in a way such as to guarantee that the states of the inverter under consideration will converge to the desired steady-state operating point. Simulation results are presented comparing the performance of the implemented $\mathrm{M}^{2}$ PC and a classical resonant current controller for a grid-tied two-level inverter with L filter. The simulation results have demonstrated the good performance of the proposed approach, showing the stability and performance despite the model of the implemented $\mathrm{M}^{2}$ PC.
What do Users Expect of Bidirectional Transformations?

A bidirectional transformation (bx) is a means of maintaining the consistency of two or more related sources of information. Existing bx frameworks attempt to capture what it means for a bx to be well-behaved by proposing various laws. In many cases, however, it is still unclear if such laws really capture "desirable" behaviour from a user's perspective. We argue that knowing most users' expectations is not only useful as input for designing, extending, and improving existing bx frameworks and tools, but also when attempting to choose the most suitable bx tool for a specific application scenario and group of users. In addition, being aware of intuitive expectations that cannot be fulfilled by a chosen bx tool (perhaps for good reasons! ) is equally important; when designing and implementing consistency maintainers, such mismatches between users' expectations and tool characteristics should be made explicit and discussed with all stakeholders. In this paper, we designed and performed an experiment asking 65 computer science students to answer questions regarding the expected behaviour of a synchroniser. Our contribution is twofold: (i) we propose an experiment design that can be adapted and repeated for a specific group of users, and (ii) we present and discuss empirical data obtained from two runs of the experiment.
Role of Non-coding RNAs in the Pathogenesis of Endometriosis

Endometriosis is a disorder characterized by the presence of endometrial glands and stroma like lesions outside of the uterus. Although several hypothesis have tried to explain the underlying cause of endometriosis, yet the main cause remained obscure. Recent studies have shown contribution of non-coding RNAs in the pathogenesis of endometriosis. Two classes of these transcripts namely long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have mostly attracted attention of researchers. Several studies have reported aberrant expression of these transcripts in affected tissues from patients as well as animal models. Modulation of important signaling pathways such as PI3K/AKT, P38-MAPK, ERK1/2-MAPK and Wnt-β catenin by miRNAs and lncRNAs have potentiated these molecules as biomarkers or therapeutic agents in endometriosis. Single nucleotide polymorphisms with miR-126, miR-143 and miR-146b have been associated with risk of endometriosis. Moreover, miRNAs and lncRNAs control inflammatory responses, cell proliferation, angiogenesis and tissue remodeling, thus understanding the role of these transcripts in endometriosis is a possible way to develop novel diagnostic tests and therapeutic targets for this disorder.
Identifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN

In the last decade, a large number of genome-wide association studies have uncovered many single-nucleotide polymorphisms (SNPs) that are associated with complex traits and confer susceptibility to diseases, such as cancer. However, so far only a few heritable traits with medium-to-high penetrance have been identified. The vast majority of the discovered variants only leads to disease in combination with other still unknown factors. Furthermore, while many studies aimed to link the effect of SNPs to changes in molecular phenotypes, the analysis has been often focused on testing associations between a single SNP and a transcript, hence disregarding the dysregulation of gene regulatory networks that has been shown to play an essential role in disease onset, notably in cancer. Here we take a systems biology approach and develop GVITamIN (Genetic VarIaTIoN functional analysis tool), a new statistical and computational approach to characterize the effect of a SNP on both genes and transcriptional regulatory programs. GVITamIN exploits a novel statistical approach to combine the usually small effect of disease-susceptibility SNPs, and reveals important potential oncogenic mechanisms, hence taking one step further in the direction of understanding the SNP mechanism of action. We apply GVITamIN on a breast cancer cohort and identify well-known cancer-related transcription factors, such as CTCF, LEF1, and FOXA1, as TFs dysregulated by breast cancer-associated SNPs. Furthermore, our results reveal that SNPs located on the RAD51B gene are significantly associated with an abnormal regulatory activity, suggesting a pivotal role for homologous recombination repair mechanisms in breast cancer.
Digital Range-Gated Surveillance Device without an Image Intensifier

The paper describes range-gated surveillance device designed for search and rescue operations in limited visibility conditions. The device is based on interline CCD image sensor and range-gating method of the device is realized without use of an image intensifier. The paper provides the design features of the device. Also main specifications of it are given.
IκB Kinase Subunits α and γ Are Required for Activation of NF-κB and Induction of Apoptosis by Mammalian Reovirus

ABSTRACT Reoviruses induce apoptosis both in cultured cells and in vivo. Apoptosis plays a major role in the pathogenesis of reovirus encephalitis and myocarditis in infected mice. Reovirus-induced apoptosis is dependent on the activation of transcription factor NF-κB and downstream cellular genes. To better understand the mechanism of NF-κB activation by reovirus, NF-κB signaling intermediates under reovirus control were investigated at the level of Rel, IκB, and IκB kinase (IKK) proteins. We found that reovirus infection leads initially to nuclear translocation of p50 and RelA, followed by delayed mobilization of c-Rel and p52. This biphasic pattern of Rel protein activation is associated with the degradation of the NF-κB inhibitor IκBα but not the structurally related inhibitors IκBβ or IκBε. Using IKK subunit-specific small interfering RNAs and cells deficient in individual IKK subunits, we demonstrate that IKKα but not IKKβ is required for reovirus-induced NF-κB activation and apoptosis. Despite the preferential usage of IKKα, both NF-κB activation and apoptosis were attenuated in cells lacking IKKγ/Nemo, an essential regulatory subunit of IKKβ. Moreover, deletion of the gene encoding NF-κB-inducing kinase, which is known to modulate IKKα function, had no inhibitory effect on either response in reovirus-infected cells. Collectively, these findings indicate a novel pathway of NF-κB/Rel activation involving IKKα and IKKγ/Nemo, which together mediate the expression of downstream proapoptotic genes in reovirus-infected cells.
Squirrel-Seed Interactions: The Evolutionary Strategies and Impact of Squirrels as Both Seed Predators and Seed Dispersers

For many squirrel species, their intense – arguably coevolutionary – interactions with seed and nut producing trees have significantly shaped their biology and diversity. Here we provide an overview of this relationship in a range of forest types worldwide. We first review the evidence for how forest composition (conifer, hardwood, mixed hardwood and overall diversity of tree species) influences interactions between squirrels and seed trees and, ultimately, the role of squirrels as either seed predators or seed dispersers. We review, for example, the intense selective pressure squirrels exert on conifer trees as seed predators and the diversity of morphological traits and behavioral strategies that allow them to efficiently exploit this critical resource. In contrast, we show how the squirrel’s role shifts to one of seed disperser in hardwood forests and how the specifics of this interaction varies further with forest structure, forest composition and climatic conditions. We then review the growing evidence for the tight ecological and evolutionary dance between the squirrels and the oaks that has shaped the biology of both across the globe. We show how a suite of seed (acorn) characteristics (e.g., chemical gradients, germination schedules, seedling morphology and tolerance-resistance strategies) are all intimately tied to the scatter-hoarding decisions of several squirrel species. And, based on studies in oak forests in Central America, Mexico, North America, and Eurasia, we also highlight the behavioral strategy of embryo excision now reported for six species across at least four genera of squirrels. This behavior, glaringly absent in other scatter-hoarding rodents worldwide, is now known be an innate trait in at least two species, one in Asia and another in North America. We review extensive recent research on one species of squirrel, the Siberian chipmunk (Tamias sibiricus), which exhibits a suite of behavioral strategies unique to that of other squirrels that independently contributes to seed dispersal and establishment. Finally, we outline numerous remaining questions concerning plants and other taxa of squirrels still open to investigation.
Impact of Hydroxychloroquine on Antibody Responses to the SARS-CoV-2 Coronavirus

• Humoral immunity is a crucial aspect in mitigating the COVID-19 pandemic. • Hydroxychloroquine and chloroquine are lysosomotropic drugs that affect antigen-presenting pathways and B-cell activation. • Chloroquine inhibits antibody responses to vaccines, but reports about this effect apparently have not been called to the attention of investigators in the field of COVID-19. • Studies on immunity to Sars-CoV-2 must take into account treatment regimens for COVID-19.