Miracle-dz/UniFAR-FTUs huggingface dataset:
Host Blood Gene Signatures Can Detect the Progression to Severe and Cerebral Malaria

Malaria is a major international public health problem that affects millions of patients worldwide especially in sub-Saharan Africa. Although many tests have been developed to diagnose malaria infections, we still lack reliable diagnostic biomarkers for the identification of disease severity, especially in endemic areas where the diagnosis of cerebral malaria is very difficult and requires the exclusion of all other possible causes. Previous host and pathogen transcriptomic studies have not yielded homogenous results that can be harnessed into a reliable diagnostic tool. Here we utilized a multi-cohort analysis approach using machine-learning algorithms to identify blood gene signatures that can distinguish severe and cerebral malaria from moderate and non-cerebral cases. Using a Regularized Random Forest model, we identified 28-gene and 32-gene signatures that can reliably distinguish severe and cerebral malaria, respectively. We tested the specificity of both signatures against other common infectious diseases to ensure the signatures reliability and suitability as diagnostic markers. The severe and cerebral malaria gene-signatures were further integrated through k-top scoring pairs classifiers into ten and nine gene pairs that could distinguish severe and cerebral malaria, respectively. These signatures have various implications that can be utilized as blood diagnostic tools for malaria severity in endemic countries.
The Molecular Basis and Therapeutic Aspects of Cisplatin Resistance in Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is a kind of malignant tumors with low survival rate and prone to have early metastasis and recurrence. Cisplatin is an alkylating agent which induces DNA damage through the formation of cisplatin-DNA adducts, leading to cell cycle arrest and apoptosis. In the management of advanced OSCC, cisplatin-based chemotherapy or chemoradiotherapy has been considered as the first-line treatment. Unfortunately, only a portion of OSCC patients can benefit from cisplatin treatment, both inherent resistance and acquired resistance greatly limit the efficacy of cisplatin and even cause treatment failure. Herein, this review outline the underlying mechanisms of cisplatin resistance in OSCC from the aspects of DNA damage and repair, epigenetic regulation, transport processes, programmed cell death and tumor microenvironment. In addition, this review summarizes the strategies applicable to overcome cisplatin resistance, which can provide new ideas to improve the clinical therapeutic outcome of OSCC.
Growth Hormone Deficiency and Treatment in Childhood Cancer Survivors

Growth hormone (GH) deficiency is a common pituitary hormone deficiency in childhood cancer survivors (CCS). The identification, diagnosis, and treatment of those individuals at risk are important in order to minimize associated morbidities that can be ameliorated by treatment with recombinant human GH therapy. However, GH and insulin-like growth factor-I have been implicated in tumorigenesis, so there has been concern over the use of GH therapy in patients with a history of malignancy. Reassuringly, GH therapy has not been shown to increase risk of tumor recurrence. These patients have an increased risk for development of meningiomas, but this may be related to their history of cranial irradiation rather than to GH therapy. In this review, we detail the CCS who are at risk for GHD and the existing evidence on the safety profile of GH therapy in this patient population.
Direct but Not Indirect Methods Correlate the Percentages of Sperm With Altered Chromatin to the Intensity of Chromatin Damage

Although sperm chromatin damage, understood as damage to DNA or affectations in sperm protamination, has been proposed as a biomarker for sperm quality in both humans and livestock, the low incidence found in some animals raises concerns about its potential value. In this context, as separate methods measure different facets of chromatin damage, their comparison is of vital importance. This work aims at analyzing eight techniques assessing chromatin damage in pig sperm. With this purpose, cryopreserved sperm samples from 16 boars were evaluated through the following assays: TUNEL, TUNEL with decondensation, SCSA, alkaline and neutral sperm chromatin dispersion (SCD) tests, alkaline and neutral Comet assays, and chromomycin A3 test (CMA3). In all cases, the extent of chromatin damage and the percentage of sperm with fragmented DNA were determined. The degree of chromatin damage and the percentage of sperm with fragmented DNA were significantly correlated (p < 0.05) in direct methods (TUNEL, TUNEL with decondensation, and alkaline and neutral Comet) and CMA3, but not in the indirect ones (SCD and SCSA). Percentages of sperm with fragmented DNA determined by alkaline Comet were significantly (p < 0.05) correlated with TUNEL following decondensation and CMA3; those determined by neutral Comet were correlated with the percentage of High DNA Stainability (SCSA); those determined by SCSA were correlated with neutral and alkaline SCD; and those determined by neutral SCD were correlated with alkaline SCD. While, in pigs, percentages of sperm with fragmented DNA are directly related to the extent of chromatin damage when direct methods are used, this is not the case for indirect techniques. Thus, the results obtained herein differ from those reported for humans in which TUNEL, SCSA, alkaline SCD, and alkaline Comet were found to be correlated. These findings may shed some light on the interpretation of these tests and provide some clues for the standardization of chromatin damage methods.
Akt Phosphorylation of Hepatitis C Virus NS5B Regulates Polymerase Activity and Hepatitis C Virus Infection

Hepatitis C virus (HCV) is a single-stranded RNA virus of positive polarity [ssRNA(+)] that replicates its genome through the activity of one of its proteins, called NS5B. This viral protein is responsible for copying the positive-polarity RNA genome into a negative-polarity RNA strand, which will be the template for new positive-polarity RNA genomes. The NS5B protein is phosphorylated by cellular kinases, including Akt. In this work, we have identified several amino acids of NS5B that are phosphorylated by Akt, with positions S27, T53, T267, and S282 giving the most robust results. Site-directed mutagenesis of these residues to mimic (Glu mutants) or prevent (Ala mutants) their phosphorylation resulted in a reduced NS5B in vitro RNA polymerase activity, except for the T267E mutant, the only non-conserved position of all those that are phosphorylated. In addition, in vitro transcribed RNAs derived from HCV complete infectious clones carrying mutations T53E/A and S282E/A were transfected in Huh-7.5 permissive cells, and supernatant viral titers were measured at 6 and 15 days post-transfection. No virus was rescued from the mutants except for T53A at 15 days post-transfection whose viral titer was statistically lower as compared to the wild type. Therefore, phosphorylation of NS5B by cellular kinases is a mechanism of viral polymerase inactivation. Whether this inactivation is a consequence of interaction with cellular kinases or a way to generate inactive NS5B that may have other functions are questions that need further experimental work.
Host-Related Laboratory Parameters for Leprosy Reactions

Leprosy reactions are acute inflammatory episodes that complicate the course of a Mycobacterium leprae infection and are the major cause of leprosy-associated pathology. Two types of leprosy reactions with relatively distinct pathogenesis and clinical features can occur: type 1 reaction, also known as reversal reaction, and type 2 reaction, also known as erythema nodosum leprosum. These acute nerve-destructive immune exacerbations often cause irreversible disabilities and deformities, especially when diagnosis is delayed. However, there is no diagnostic test to detect or predict leprosy reactions before the onset of clinical symptoms. Identification of biomarkers for leprosy reactions, which impede the development of symptoms or correlate with early-onset, will allow precise diagnosis and timely interventions to greatly improve the patients' quality of life. Here, we review the progress of research aimed at identifying biomarkers for leprosy reactions, including its correlation with not only immunity but also genetics, transcripts, and metabolites, providing an understanding of the immune dysfunction and inflammation that underly the pathogenesis of leprosy reactions. Nevertheless, no biomarkers that can reliably predict the subsequent occurrence of leprosy reactions from non-reactional patients and distinguish type I reaction from type II have yet been found.
A Novel Real-Time Reverse Transcription Loop-Mediated Isothermal Amplification Detection Platform: Application to Diagnosis of COVID-19

The ongoing Corona virus disease (COVID-19) outbreak has become a huge global health concern. Here, we reported a novel detection platform based on the loop-mediated isothermal amplification (LAMP), termed real-time reverse transcription LAMP (rRT-LAMP) and applied it for the diagnosis of COVID-19 (COVID-19 rRT-LAMP). rRT-LAMP integrates reverse transcription, LAMP amplification, restriction endonuclease cleavage and real-time fluorescence detection into one-pot reaction, and facilitates the diagnosis of COVID-19 at 64°C for only 35 min. The ORF1ab (opening reading frame 1a/b) and NP (nucleoprotein) genes of SARS-CoV-2 were detected for diagnosing COVID-19. The limit of detection (LoD) of COVID-19 rRT-LAMP assay was 14 copies (for each marker) per vessel, and no positive results were obtained from non-SARS-CoV-2 templates. To demonstrate its feasibility, a total of 33 oropharynx swab samples collected from COVID-19 patients also were diagnosed as SARS-CoV-2 infection using COVID-19 rRT-LAMP protocol. No cross-reactivity was yielded from 41 oropharynx swab samples collected from non-COVID-19 patients. These data suggesting that the COVID-19 rRT-LAMP assay is a potential detection tool for the diagnosis of SARS-CoV-2 infection in clinical, field and disease control laboratories, and will be valuable for controlling the COVID-19 epidemic.
Treatment of Oil-Contaminated Water by Modified Polysilicate Aluminum Ferric Sulfate

In this experiment, a variety of inorganic materials were simply compounded with Polysilicate Aluminum Ferric Sulfate (PSAFS) to treat emulsified oil-contaminated water. Manganese sulfate (MnSO4), magnesium sulfate (MgSO4), and zinc sulfate (ZnSO4) were selected as the materials to modify PSAFS in order to obtain a coagulant with good flocculation performance. During the preparation of modified PSAFS, metal manganese, magnesium, and zinc were introduced for modification, and four factors were used to optimize the best proportion of modifiers and PSAFS. The results showed that the order of demulsification and oil-removal ability is as follows: Mn-PSAFS (Mn-modified PSAFS) > Zn-PSAFS (Zn-modified PSAFS) > Mg-PSAFS (Mg-modified PSAFS) > PSAFS. Modified PSAFS was characterized by infrared spectroscopy (IR) and a Scanning Electron Microscope (SEM). In the range of 604 cm−1 to 1200 cm−1, due to the complexation reaction between metal ions and polysilicic acid, the absorption peaks of the modified PSAFS and PSAFS were significantly different. SEM results revealed that the particles of the spatial network structure were fibrous and arranged more closely (0.5 mm × 50.0 mm) than others. This study provided that the modified PSAFS had good potential application in treating emulsified oily wastewater in the future.
Wavelength dependent nonlinear optical response of tetraphenylethene aggregation-induced emission luminogens

Since the discovery of the striking aggregation-induced emission (AIE) phenomenon, tremendous efforts have been devoted to the exploration of brilliant organic solid-state light emitting materials and their underlying mechanistic theories. While AIE is well established in linear optics, the nonlinear optical (NLO) properties of the AIE luminogens (AIEgens) remain relatively unexplored. Here, we present a detailed study of the NLO properties of crystalline prototypical AIEgens based on tetraphenylethene (TPE). The results disclose a highly efficient NLO response of TPE crystals which is strongly dependent on the wavelength of the incident near infrared (NIR) light. TPE exhibits mainly two-photon excited fluorescence (TPF) upon excitation at 700 nm < λ < 800 nm, while it exhibits three-photon excited fluorescence (3PF) if pumped at 800 nm < λ < 840 nm. For pump wavelengths longer than 840 nm, mainly second harmonic generation (SHG) is observed. The introduction of halogen atoms into the TPE backbone results in comparable NLO hyperpolarizabilities, but allows for future derivations and functionalizations. The exploration of the nonlinear optical properties of AIEgens might open a new avenue to a next generation of multifunctional organic and composite photonic materials and devices.
Internal combustion engine waste heat recovery by a thermoelectric generator inserted at combustion chamber walls

In this study, a thermoelectric module has been inserted at the wall of the combustion chamber of an internal combustion engine (ICE) to improve its performance by taking the advantage of the high‐temperature difference between ICE combustion gases and coolant fluid. A mathematical analysis under steady‐state conditions has been introduced to investigate the effects of the proposed system. The generated electrical power has been studied versus many parameters such as revolution per minute (RPM), compression ratio of the engine, coolant fluid type, and coolant fluid temperature. The proposed position in this study has many features over the other positions, as the promising innovative position can achieve great results. A typical spark ignition (SI) engine has been used with a suitable thermoelectric generation (TEG) inserted at the wall of the engine's combustion chamber. As a result, 600 W of electrical energy was produced by the proposed system and the efficiency was increased by 2.75% at 4000 RPM which is interestingly better than other TEGs inserted on the exhaust pipe or the radiator of the automobile.
Women Entrepreneurship Development in Yemen: The Role of Decision-Making Empowerment

This research was conducted to examine the impact of decision-making empowerment on women entrepreneurship development in Yemen. Two dimensions of decision-making empowerment were used; economic decision making, and household decision-making empowerment. This study employed the quantitative approach and the method of collecting data was the online-questionnaire. The targeted sample size of this study was 200 business women in Yemen and the response rate was 96.5%. The results of the correlational analysis show that there is a clear strong positive correlation between decision-making empowerment and women entrepreneurship development. In addition, the two dimensions; economic decision making, and household decision-making have a significant relationship with women entrepreneurship development. The results of the regression analysis reveal that decision-making empowerment has a significant impact on women entrepreneurship development and the economic decision-making empowerment and household decision-making empowerment were explaining women entrepreneurship development. It can be concluded that empowering women by allowing them to participate in economic and household decision-making appears to be one of the important factors for developing women's entrepreneurship in particular, which in turn will help reduce poverty as well as achieve economic growth.
Seismicity of La Réunion island

The island of La Réunion is made up of two main shield volcanoes: Piton des Neiges and Piton de la Fournaise. A wide variety of seismic events is observed, including but not limited to: tectonic events, volcano-tectonic earthquakes, volcanic tremors, long-period and very-long-period earthquakes. The seismicity of La Réunion island illuminates di ﬀ erent levels of its volcanic plumbing system. In the shallowest part of Piton de la Fournaise, earthquakes are clustered below the volcano summit area and often occur as intense seismic swarms during magma intrusions. Seismic activity is also observed below the East ﬂank of Piton de la Fournaise, shaping an eastward dipping structure possibly accommodating seaward displacements of the volcano. At larger depths, episodes of upward seismicity migrations indicate magmatic recharges of the shallow reservoir from deeper parts of the volcano plumbing system. Earthquakes are also observed below the oceanic crust in a zone of underplating between Piton des Neiges and Piton de la Fournaise. A major event at Piton de la Fournaise was the collapse of its summit caldera in April 2007. This activity resulting in a summital depression of 330 m was accompanied by very-long-period earthquakes with magnitudes ranging from M W = 4.4 to M W = 5.4. Another noticeable activity in La Réunion island is an active seismic swarm located within the oceanic crust under the North ﬂank of Piton des Neiges. The origin of this sustained seismic activity is still unclear and is currently investigated, thanks to the deployments of additional stations in the region.
Effects of Extrusion Conditions on Physical Properties of Sorghum Based Extruded Products

Extrusion cooking is a high temperature short time multivariable unit operation. In this study, response surface methodology (RSM) was used to evaluate the effect of feed parameters i.e., feed moisture (8-16%), blend ratio of sorghum:barley:bengal gram, (70:15:15 to 50:35:15) and machine parameters of twin screw extruder i.e., barrel temperature (120-200oC) and screw speed (120-200 rpm) on physical properties of extrudates i.e., mass flow rate, bulk density and moisture content. The results showed that maximum mass flow rate (0.974 g/s) was observed with the blend ratio 60:25:15, having 8 percent moisture (w.b) extruded at 160oC barrel temperature and a screw speed of 160 rpm. The bulk density of extrudates was found minimum (0.08 g/cc) at 10% moisture content, 65:20:15 blend ratio, 180oC barrel temperature and 180 rpm screw speed and the moisture content of extrudates was found minimum (4.74%) at 10% moisture content, 55:30:15 blend ratio, 180oC barrel temperature and 140 rpm screw speed.
Successful Application of Site-directed Mutagenesis Polymerase Chain Reaction to Mutate TMS 11 of the Staphylococcal Multidrug Efflux Protein QacA

Staphylococcus aureus is a major problem in both the clinical setting and within the community. S. aureus can quickly develop resistance to a wide range of antibiotics through a number of different mechanisms, of which, using transporters located in the cell membrane to pump antibiotics out of the cell is the most serious concern. In staphylococcal species, QacA, one such important transporter, is encoded by qacA. QacA is 55kD in size and has 14 transmembrane segments (TMS) (TMS 1-TMS 14). This research describes the mutation process of the amino acid residues in TMS 11 of QacA using site-direct PCR. In this research, 15 primers were successfully designed for site-directed mutagenesis PCR. The site-mutagenesis PCR was successfully conducted to create 15 qacA mutants. These mutants will be used in further functional research of QacA.
Signs of Central Hypersensitivity, Stress, and Anxiety following Treatment for Breast Cancer: A Case Control Study

Background With treatment for breast cancer, women treated may present significant sensory abnormalities in the upper extremity. However, there are no conclusive studies that have evaluated pressure pain thresholds (PPT) in the shoulder of postoperated women for breast cancer. The aim of this study was to compare PPT in the shoulder, stress, anxiety, depression symptoms, and quality of sleep among postoperated women for breast cancer (PO group) and asymptomatic women of shoulder pain (control group). Methods 40 women participated (n = 20, PO group, age: average ± standard deviation, 49.2 ± 8.3 years; body mass index (BMI): 27.5 ± 3.0 kg/cm2; surgery time: 22.2 ± 34.4 months; n = 20, control group, 46.9 ± 8.1 years; BMI: 26.8 ± 3.5 kg/cm2). The PPT was evaluated with a digital algometer at 32 points in the shoulder region and one control point in the tibialis anterior. Stress, anxiety, and depression were evaluated with the Depression, Anxiety and Stress Scale 21 (DASS-21) and the quality of sleep by the Pittsburgh Sleep Quality Index. Results Significant differences were observed over 1.5 kgf/cm2 in 33 points evaluated (p < 0.01) with a small to high effect size (Cliff's delta range = 0.16; 0.92) and higher levels of anxiety and stress in the PO group (anxiety: median [first; third quartile], 5[3; 12.5]; stress: 9.7 ± 4.7 (7.8; 11.8)) in comparison with the control group (anxiety: 2.5[1; 4.8]; stress: 6.7 ± 3.31 (5.2; 8.3), (p < 0.05)). No significant differences were found between the groups in depression and sleep quality (p > 0.05). Conclusion Postoperated women for breast cancer present hyperalgesia in the shoulder anterior and posterior region, low PPT in the tibialis anterior, and higher levels of stress and anxiety compared to the control group.
Potential application of chitosan-based nanoparticles containing essential oils against mosquitoes, moths and beetles

The association between the use of synthetic insecticides and the appearance of resistant insects, human poisoning and the environment contamination generated the need to develop new forms to pest control, and essential oils stand out as an alternative. However, due to their volatility and instability, their use in native form is unfeasible. It is possible to circumvent these problems by their encapsulation, and the use of polymeric nanoparticles for this purpose has many advantages, since these systems prevent the oil degradation, and control its release. The first in vivo trials of chitosan nanoparticles containing essential oils with insecticidal activity were published in the late 2010s. Considering the growing interest in this subject, as can be seen from the increase in the number of publications, this review aimed to gather all the papers that presented biological assays using essential oils encapsulated in chitosan nanoparticles against insects. Further, the techniques used to prepare these nanoparticles are also discussed. It was possible to note that the technique called complex coacervation led to smaller particles and most articles describing in vivo tests of chitosan nanoparticles containing essential oils assess their larvicidal activity. Among the tested nanoparticles, the one that had the best larvicidal activity in acute toxicity tests were those obtained by complexing of chitosan with cashew gum and those with the best residual activity were the cross-linked with glutaraldehyde. Chitosan nanoparticles containing essential oils also increased their insecticidal activity in toxicity tests against adult beetles.