Miracle-dz/UniFAR-FTUs huggingface dataset:
The Oncolytic Virus in Cancer Diagnosis and Treatment

Cancer has always been an enormous threat to human health and survival. Surgery, radiotherapy, and chemotherapy could improve the survival of cancer patients, but most patients with advanced cancer usually have a poor survival or could not afford the high cost of chemotherapy. The emergence of oncolytic viruses provided a new strategy for us to alleviate or even cure malignant tumors. An oncolytic virus can be described as a genetically engineered or naturally existing virus that can selectively replicate in cancer cells and then kill them without damaging the healthy cells. There have been many kinds of oncolytic viruses, such as herpes simplex virus, adenovirus, and Coxsackievirus. Moreover, they have different clinical applications in cancer treatment. This review focused on the clinical application of oncolytic virus and predicted the prospect by analyzing the advantages and disadvantages of oncolytic virotherapy.
The Tumor Milieu Promotes Functional Human Tumor-Resident Plasmacytoid Dendritic Cells in Humanized Mouse Models

Particular interest to harness the innate immune system for cancer immunotherapy is fueled by limitations of immune checkpoint blockade. Plasmacytoid dendritic cells (pDC) are detected in a variety of solid tumors and correlate with poor clinical outcome. Release of type I interferons in response to toll-like-receptor (TLR)7 and TLR9 activation is the pDC hallmark. Mouse and human pDC differ substantially in their biology concerning surface marker expression and cytokine production. Here, we employed humanized mouse models (HIS) to study pDC function. We performed a comprehensive characterization of transgenic, myeloid-enhanced mouse strains (NOG-EXL and NSG-SGM3) expressing human interleukin-3 (hIL-3) and granulocyte-macrophage colony stimulating factor (GM-CSF) using identical humanization protocols. Only in HIS-NOG-EXL mice sufficient pDC infiltration was detectable. Therefore, we selected this strain for subsequent tumor studies. We analyzed pDC frequency in peripheral blood and tumors by comparing HIS-NOG-EXL with HIS-NOG mice bearing three different ovarian and breast tumors. Despite the substantially increased pDC numbers in peripheral blood of HIS-NOG-EXL mice, we detected TLR7/8 agonist responsive and thus functional pDCs only in certain tumor models independent of the mouse strain employed. However, HIS-NOG-EXL mice showed in general a superior humanization phenotype characterized by reconstitution of different myeloid subsets, NK cells and B cells producing physiologic IgG levels. Hence, we provide first evidence that the tumor milieu but not genetically introduced cytokines defines intratumoral (i.t.) frequencies of the rare pDC subset. This study provides model systems to investigate in vivo pro- and anti-tumoral human pDC functions.
Synthesis and Manipulation of Single-Crystalline Lithium Nickel Manganese Cobalt Oxide Cathodes: A Review of Growth Mechanism

Lithium nickel manganese cobalt oxide (NMC) cathodes are of great importance for the development of lithium ion batteries with high energy density. Currently, most commercially available NMC products are polycrystalline secondary particles, which are aggregated by anisotropic primary particles. Although the polycrystalline NMC particles have demonstrated large gravimetric capacity and good rate capabilities, the volumetric energy density, cycling stability as well as production adaptability are not satisfactory. Well-dispersed single-crystalline NMC is therefore proposed to be an alternative solution for further development of high-energy-density batteries. Various techniques have been explored to synthesize the single-crystalline NMC product, but the fundamental mechanisms behind these techniques are still fragmented and incoherent. In this manuscript, we start a journey from the fundamental crystal growth theory, compare the crystal growth of NMC among different techniques, and disclose the key factors governing the growth of single-crystalline NMC. We expect that the more generalized growth mechanism drawn from invaluable previous works could enhance the rational design and the synthesis of cathode materials with superior energy density.
Perinatal Exposure to Methoxychlor Affects Reproductive Function and Sexual Behavior in Mice

Numerous chemicals derived from human activity are now disseminated in the environment where their exert estrogenic endocrine disrupting effects, and therefore represent major health concerns. The present study explored whether Methoxychlor (MXC), an insecticide with xenoestrogens activities, given during the perinatal period (from gestational day 11 to postnatal day 8) and at an environmentally dose [20 μg/kg (body weight)/day], would affect reproductive physiology and sexual behavior of the offspring in mice. While MXC exposure did not induce any differences in the weight gain of animals from birth to 4 months of age, a clear difference (although in opposite direction according to the sexes) was observed on the anogenital distance between intact and exposed animals. A similar effect was also observed on preputial separation and vaginal opening, which reflects, respectively, in males and females, puberty occurrence. The advanced puberty observed in females was associated with an enhanced expression of kisspeptin cells in the anteroventral periventricular region of the medial preoptic area. Exposure to MXC did not induce in adult females changes in the estrous cycle or in the weight of the female reproductive tract. By contrast, males showed reduced weight of the epididymis and seminiferous vesicles associated with reduced testosterone levels and seminiferous tubule diameter. We also showed that both males and females showed deficits in mate preference tests. As a whole, our results show that MXC impacts reproductive outcomes.
Metabolite and Transcriptome Profiling on Xanthine Alkaloids-Fed Tea Plant (Camellia sinensis) Shoot Tips and Roots Reveal the Complex Metabolic Network for Caffeine Biosynthesis and Degradation

While caffeine is one of the most important bioactive metabolites for tea as the most consumed non-alcohol beverage, its biosynthesis and catabolism in tea plants are still not fully understood. Here, we integrated purine alkaloid profiling and transcriptome analysis on shoot tips and roots fed with caffeine, theophylline, or theobromine to gain further understanding of caffeine biosynthesis and degradation. Shoot tips and roots easily took up and accumulated high concentrations of alkaloids, but roots showed much faster caffeine and theophylline degradation rates than shoot tips, which only degraded theophylline significantly but almost did not degrade caffeine. Clearly feedback inhibition on caffeine synthesis or inter-conversion between caffeine, theophylline, and theobromine, and 3-methylxanthine had been observed in alkaloids-fed shoot tips and roots, and these were also evidenced by significant repression of TCS and MXMT genes critical for caffeine biosynthesis. Among these responsively repressed genes, two highly expressed genes TCS-4 and TCS-8 were characterized for their enzyme activity. While we failed to detect TCS-4 activity, TCS-8 displayed N-methyltransferase activities towards multiple substrates, supporting the complex metabolic network in caffeine biosynthesis in tea plants since at least 13 TCS-like N-methyltransferase genes may function redundantly. This study provides new insight into complex metabolic networks of purine alkaloids in tea plants.
α-Defensins Promote Bacteroides Colonization on Mucosal Reservoir to Prevent Antibiotic-Induced Dysbiosis

In addition to their established functions in host defense, accumulating evidence has suggested an emerging role for antimicrobial proteins (AMPs) in shaping commensal microbiota. However, the role of α-defensins, the most abundant AMPs of intestine, in regulating microbial ecology remains inconclusive. Here, we report that α-defensins promote commensal Bacteroides colonization by enhancing bacterial adhesion to the mucosal reservoir. Experiments utilizing mice deficient in matrix metalloproteinase 7 (MMP7), the α-defensin–activating enzyme, with rigorous littermate controls showed that α-defensin deficiency did not significantly influence steady-state intestinal microbiota. In contrast, α-defensins are essential for replenishment of commensal Bacteroides from the mucosal reservoir following antibiotics-induced dysbiosis, shown by markedly compromised recovery of Bacteroides in Mmp7−/− animals. Mechanistically, α-defensins promote Bacteroides colonization on epithelial surfaces in vivo and adhesion to epithelial cells in vitro. Moreover, α-defensins unexpectedly does not show any microbicidal activities against Bacteroides. Together, we propose that α-defensins promote commensal bacterial colonization and recovery to maintain microbial diversity upon environmental challenges.
In Silico, Molecular Docking and In Vitro Antimicrobial Activity of the Major Rapeseed Seed Storage Proteins

Background In addition to their use as an edible oil and condiment crop, mustard and rapeseed (Brassica napus L., B. juncea (L.) Czern. , B. nigra (L.) W.D. J.Koch, B. rapa L. and Sinapis alba L. ) have been commonly used in traditional medicine for relieving pain, coughs and treating infections. The seeds contain high amounts of oil, while the remaining by-product meal after oil extraction, about 40% of seed dry weight, has a low value despite its high protein-content (~85%). The seed storage proteins (SSP) 2S albumin-type napin and 12S globulin-type cruciferin are the two predominant proteins in the seeds and show potential for value adding to the waste stream; however, information on their biological activities is scarce. In this study, purified napin and cruciferin were tested using in silico, molecular docking, and in vitro approaches for their bioactivity as antimicrobial peptides. Materials and Methods The 3D-structure of 2S albumin and 12S globulin storage proteins from B. napus were investigated to predict antimicrobial activity employing an antimicrobial peptide database survey. To gain deeper insights into the potential antimicrobial activity of these SSP, in silico molecular docking was performed. The purified B. napus cruciferin and napin were then tested against both Gram-positive and Gram-negative bacteria for in vitro antimicrobial activity by disc diffusion and microdilution antimicrobial susceptibility testing. Results In silico analysis demonstrated both SSP share similar 3D-structure with other well studied antimicrobial proteins. Molecular docking revealed that the proteins exhibited high binding energy to bacterial enzymes. Cruciferin and napin proteins appeared as a double triplet and a single doublet, respectively, following SDS-PAGE. SDS-PAGE and Western blotting also confirmed the purity of the protein samples used for assessment of antimicrobial activity. Antimicrobial susceptibility testing provided strong evidence for antimicrobial activity for the purified napin protein; however, cruciferin showed no antimicrobial activity, even at the highest dose applied. Discussion In silico and molecular docking results presented evidence for the potential antimicrobial activity of rapeseed cruciferin and napin SSP. However, only the in vitro antimicrobial activity of napin was confirmed. These findings warrant further investigation of this SSP protein as a potential new agent against infectious disease.
Observation on Anatomical Structure and Ultra-structure of Mesocoat during Development of Ginkgo biloba L.

The results of observation on anatomical structure and ultra-structure of mesocoat during develop-ment of Ginkgo biloba L.cv. 'Fo-zhi' indicated that,the increment course of grain weight and diameter could be expressed as a single-sigmoid curve,the diameter increase of the seed was earlier than grain weight.The main growth period of grain weight was similar to the process of lignifications of mesocoat.Nuclei condensation,chromatin margination and nucleus degeneration occurred,it showed a character of programmed cell death(PCD).
Citizen Science for the Prediction of Climate Extremes in South Africa and Namibia

Seasonal-to-interannual variations of rainfall over southern Africa, key to predicting extreme climatic events, are predictable over certain regions and during specific periods of the year. This predictability had been established by testing seasonal forecasts from models of varying complexity against official station rainfall records typically managed by weather services, as well as against gridded data sets compiled through a range of efforts. Members of the general public, including farmers, additionally have extended records of rainfall data, often as daily values spanning several decades, which are recorded and updated regularly at their farms and properties. In this paper, we show how seasonal forecast modelers may use site recorded farm rainfall records for the development of skillful forecast systems specific to the farm. Although the uptake of seasonal forecasts in areas with modest predictability such as southern Africa may be challenging, we will show that there is potential for financial gain and improved disaster risk farm management by co-developing with farmers forecast systems based on a combination of state-of-the-art climate models and farm rainfall data. This study investigates the predictability of seasonal rainfall extremes at five commercial farms in southern Africa, four of which are in the austral summer rainfall areas, while one is located in the winter rainfall area of the southwestern Cape. We furthermore calculate a measure of cumulative profits at each farm, assuming a “fair odds” return on investments made according to forecast probabilities. The farmers are presented with hindcasts (re-forecasts) at their farms, and potential financial implications if the hindcasts were used in decision-making. They subsequently described how they would use forecasts for their farm, based on their own data.
Just What I See? Implications of Congruence Between Supervisors’ and Employees’ Perceptions of Pay Justice for Employees’ Work-Related Attitudes and Behaviors

Perceiving a pay system as just has been suggested to be a precondition for individualized pay to have a motivating effect for employees. Supervisors’ enacted justice is central for understanding the effects that pay setting can have on employee attitudes and behavior. Yet, enacted justice has received little research attention, in regard to both organizational justice and pay-related topics. This study examines the effects of employees’ perceived pay justice and supervisors’ enacted justice, as well as the degree of congruence, on employees’ work-related attitudes and behaviors. Questionnaire data from employees (N = 566) matched with data from their pay-setting supervisors (N = 208), employed in a Swedish manufacturing company, were analyzed. Results of polynomial regression with response surface analysis show that employees’ perceptions of pay justice were important for their work-related attitudes and behaviors and that supervisor–employee congruence regarding pay justice was positively related to employees’ attitudes and behavior, particularly when the ratings concerned high levels of justice. The results not only highlight the importance of developing a pay system that is perceived as just by employees but also emphasize the importance of reaching a congruence between supervisors’ and employees’ perceptions of high fairness, as this has positive implications for employees’ attitudes and behaviors.
Immunisation with recombinant polymorphic membrane protein D elicits robust protection against sexually transmitted Chlamydia trachomatis infection

Chlamydia trachomatis (Ct) is the most common sexually transmitted bacterial pathogen worldwide, responsible for ~90 million new cases of disease each year, with asymptomatic infections giving rise to sequelae such as pelvic inflammatory disease, ectopic pregnancy and infertility in women. Aggressive ‘seek and treat’ public health measures have not stemmed the rise of Ct infections, leading to proposal of the ‘arrested immunity’ hypothesis, where herd immunity within a population is blunted following earlier treatment with antibiotics. This suggests vaccination as the next key step in potentially eliminating Ct infections. Due to the paucity of robust clinical data, protective immune parameters have largely been derived from studies in mice, where pathogen-specific Th1-type immunity involving CD4+ T cells has been the focus of preclinical vaccine development. Our study represents the first preclinical characterization of a novel, rationally designed second-generation lipid adjuvant (SLA) in combination with the highly conserved recombinant Ct polymorphic membrane protein D (rPmpD) antigen. We demonstrate robust protection against urogenital Ct infection in the C57BL/6 murine model, characterized by significantly enhanced resistance to infection and reduction in mean bacterial load. However, enhanced Th1-type immunity was not found to correlate with relative protection, which rather coincided with the presence of robust rPmpD-specific serum and cervico-vaginal IgG titres. Prior to our study, the only convincing evidence of neutralizing antibodies effecting protection against chlamydial infection in vivo has emerged from studies employing the antigenically variable Ct MOMP as a vaccine immunogen. We propose that anti-rPmpD antibodies may play a significant role in vaccine-induced protection against urogenital Ct challenge, and that the role of antibodies warrants further investigation in future Ct vaccine development.
Feature screening of quadratic inference functions for ultrahigh dimensional longitudinal data

This paper is concerned with feature screening for the ultrahigh dimensional additive models with longitudinal data. The proposed method utilizes the quadratic inference functions to construct the marginal screening measurement, which takes the within-subject correlation into consideration and is more efficient and robust than some parametric model assumptions for the working covariance matrix in each subject or experimental unit. We also show that the proposed method enjoys the sure screening property under some regularity conditions. Monte Carlo simulation studies and a real data application are conducted to examine the performance of the proposed method.
Response of Food Barley (Hordeum Vugarae L.) To Boron Blend Fertilizer Rates on Alisols in Southern Highlands of Ethiopia

ABSTRACT Continuous use of only N and P containing fertilizers are claimed to be the causes of other secondary and micronutrients depletion, resulting in low crop productivity in Ethiopia. In this study, on-farm trials were conducted to compare the effect of multinutrient blended fertilizer – also called boron blend (NPSB: 18. 1 N – 36.1 P2O5 – 6.7S – 0.71B) on the yield and yield components of food barley grown in Alisols in southern Ethiopia during 2017 and 2018 cropping seasons. Seven treatments involving five levels of born-blend fertilizer (50, 100, 150, 200, and 300 kg NPSB kg ha−1) were compared against a compound fertilizer (100 kgha−1 NPS) and the conventionally used 150 kg ha−1 di-ammonium phosphate (DAP). The seven treatments were replicated five times using farm fields as replicates and arranged in randomized complete block design (RCBD). Results revealed significant yield advantages of applying micronutrient containing fertilizers compared to fertilizers without micronutrients. The marginal rate of return analysis showed that the application of 100 NPSB kg ha−1 was the most profitable and agronomically efficient. Season and the soil fertility variation among farmers had a significant (p < .001) effect on food barley yield. Application of Boron blend fertilizer had 500 kg ha−1 grain yield advantage compared to equivalent amount of DAP that was highly promoted by the extension system. B-blended fertilizer was advantageous when applied during good rainy seasons in Alisols of Ethiopian highlands. For good performances of B-blended fertilizers, taking into account the soil moisture availability is advised for both better productivity and agronomic efficiency.
Out-of-order execution of database queries

Intra-query parallelism is a key for database software to offer acceptable responsiveness for data-intensive queries. Many researchers have studied how to achieve greater execution parallelism for database queries. Partitioning is a representative approach, which divides a query into multiple sub-tasks and executes them in parallel. However, given a new query, optimal division is not necessarily obvious. Database software utilizes heuristic rules or statistical information to decide how to divide the query before execution. As yet another approach to achieve execution parallelism, this paper presents out-of-order database execution (OoODE), a massively-parallel query execution method to offer significant speedup for database queries consistently. OoODE dynamically decomposes query work by making the best use of the exact knowledge of the potential execution parallelism for each operation ready to be performed during query execution. With OoODE, the database software is allowed to automatically squeeze out the execution parallelism that the query inherently holds. Hence, for a wide spectrum of queries, OoODE performs significantly faster than the serial (non-parallelized) execution, while it performs better than or comparably with alternative parallelizing methods without the need for dividing the query before execution. This paper presents the experiments that we conducted using the prototyped database software and demonstrates that OoODE is two to three orders of magnitude faster than the serial execution, whereas it is substantially (up to 2.07 times) faster than the best achievable case of partitioning. Besides, OoODE performs two to four orders of magnitude faster than major DBMSs.
nKV in action

Massive data transfers in modern data-intensive systems resulting from low data-locality and data-to-code system design hurt their performance and scalability. Near-data processing (NDP) designs represent a feasible solution, which although not new, has yet to see widespread use. In this paper we demonstrate various NDP alternatives in nKV, which is a key/value store utilizing native computational storage and near-data processing. We showcase the execution of classical operations (GET, SCAN) and complex graph-processing algorithms (Betweenness Centrality) in-situ, with 1.4x-2.7x better performance due to NDP. nKV runs on real hardware - the COSMOS+ platform.
Redesigning Query Engines for White-box Compression

Modern columnar databases heavily use compression to reduce memory footprint and boost query execution. These techniques, however, are implemented as a ”black box”, since their decompression logic is hard-coded and part of the table scan infrastructure. We proposed a novel compression model called White-box compression that views compression actions as functions over the physical columns stored in a block. Because these functions become visible as expressions in the query plan, many more optimizations can be made by the database system, boosting query execution speed. These functions are learnt from the data and also allow the data to be stored much more compactly, by decomposing string values, storing data in appropriate data-types automatically, and exploiting correlations between columns. White-box compression opens up a whole new set of research questions. We started with (1) How to learn white-box compression expressions (functions) from the data automatically? This Ph.D. research will subsequently study (2) How to leverage white-box compression with (run-time) query optimizations? (3) How can we integrate white-box compression in a query engine, if the white-box functions may be diﬀerent for each block of data?