Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of compost and inorganic fertilizer on organic carbon and activities of carbon cycle enzymes in aggregates of an intensively cultivated Vertisol

Background and aims This paper was primarily devoted to understand the interactions of soil aggregates, organic carbon (C) and carbon cycle enzymes in aggregates under different fertilization managements, aiming to identify the effects of organic and inorganic fertilizer amendments on soil organic C accumulation and the activities of carbon cycle enzymes within aggregates in Vertisol. Methods A Vertisol soil following 4-year compost and inorganic fertilizer amendments, i.e. no fertilizer (CK), mineral fertilizer (FR) and 60% compost N plus 40% fertilizer N (FRM), was collected to identify the dynamics of organic C, enzymes activities and their associations with macroaggregation using aggregate fractionation techniques. Results The organic C content in all FR and FRM treatments was 8.24–41.15% higher than that in CK. An increased amounts of carbon cycle enzymes in aggregates or 0–20 cm bulk soil were also observed in FRM plots. Compared to FR, FRM significantly strengthened the structural stability of macroaggregates and the intimate connection between enzyme activities and macroaggregates. Conclusions As a recommended measure, supplementation with organic manure such as compost strengthened the process of mutual promotion between carbon cycle enzymes and macroaggregates, and the synergistic effect would be highly beneficial to soil organic C sequestration.
Effect of Sofosbuvir Administration and Its Withdrawal on the Submandibular Salivary Gland of Adult Male Albino Rats: A Histological and Ultra-Structural Study

BACKGROUND: Sofosbuvir (SOF) was approved in 2013 as a part of first-line treatment for hepatitis C virus (HCV); it has activity against all genotypes with extrahepatic adverse effects have recently arisen. AIM: Investigating sofosbuvir-induced alterations in the rat submandibular salivary gland (SMSG). METHODS: A group of 80 adult albino rats weighing about ± 150 gm were used in the experiment. The rats were divided into 3 groups: Group I (control group) received distilled water, Group II (experimental group) divided into 2 subgroups and received SOF 40 mg/kg/day dissolved in distilled water for 1 and 3 months and Group III (recovery group) allowed for 1 month of recovery after SOF withdrawal. All animals were sacrificed; the SMSG was dissected, and specimens were examined histologically and ultra-structurally. RESULTS: Compared to Group I, Group II subgroup (1) showed acinar and ductal vacuolisation, discontinuity of the epithelial lining associated with retained secretion and congested blood vessels. These changes were found to be exaggerated in the subgroup (2) accompanied by acinar and ductal shrinkage, interstitial oedema, haemorrhage, chronic inflammatory cells infiltration and loss of gland compactness. Amelioration of the histological changes was detected in Group III after SOF withdrawal. The ultrastructural examination confirmed these histological results. CONCLUSION: SOF had induced apparent alterations in the structure and ultrastructure of SMSG. The SOF-induced alterations were time-dependent, attributed mainly to mitochondrial toxicity and partially ameliorated by its withdrawal.
Pharmacological Activity of Honeybush (Cyclopia intermedia) in Boar Spermatozoa during Semen Storage and under Oxidative Stress

Simple Summary Nowadays, pig breeding is mostly conducted by artificial insemination using diluted semen stored for 1 to 5 days. During semen handling and storage, sperm quality usually declines, mainly because of oxidative stress and bacterial contamination. As cheap and natural sources of antioxidants, medicinal plants have become an alternative to the most common additives used in semen extenders. In this regard, several indigenous plants from Southern Africa have shown pharmacological activity in different animal cell types, although their effects on sperm cells have not been explored extensively. In the present study, we tested the effects of honeybush (Cyclopia intermedia) aqueous extract as a preservative of boar semen during 5 days of storage and under induced oxidative stress. Overall, this plant extract enhanced several sperm quality parameters and did not show any toxic effects. Supplementation with honeybush extract was able to improve the preservative properties of a long-term semen extender, thus confirming the beneficial use of plant extracts as natural additives for boar sperm. Abstract In recent decades, an increasing number of ethnopharmacological studies have been dedicated to medicinal plants from South African fynbos. Among these plants, honeybush (Cyclopia spp.) has become a popular tea, mainly due to its healthy properties and caffeine-free status. The antioxidant, antimutagenic, and antimicrobial properties of this plant have been reported in several cell types, but its effects on reproductive function are still unknown. Here, we assessed the effects of honeybush (Cyclopia intermedia) on boar sperm parameters under induced oxidative stress (Fe2+/ascorbate) and during five days of semen storage at 17 °C without oxidative stress. In both experiments, four concentrations (200, 50, 12.5, and 3.125 µg/mL) of fermented honeybush were tested. Our results show that honeybush enhances sperm parameters, and no toxic effects were observed at any of the tested extract concentrations. Interestingly, honeybush (12.5 µg/mL) improved the sperm motility and kinetic parameters, preserved the plasma membrane integrity, and reduced the lipid peroxidation in the samples exposed to Fe2+/ascorbate (p < 0.05). In the stored samples, positive effects of honeybush on sperm parameters (motility, kinetics, acrosome, and mitochondria) were observed from 48 h until 120 h of semen storage (p < 0.05). Our results clearly show the protective effects of honeybush on sperm samples, thus promoting its use as a natural source of antioxidants for boar semen.
A comparative study of partogram in normal labour with and without a constant caring companion

Background: In today's world with the concept of changing childbirth, where there is a 'women centered approach', the idea of a constant caring companion has reemerged. In a busy labour ward patients may deliver safely but it may contribute to patient's dissatisfaction, as they do not feel cared for. The constant caring companion would prove an important asset to the doctor and nurses involved in the management of the women in labour. Methods: Prospective study carried out in 120 patients meeting inclusion criteria. Results: Patients with constant caring companion had significant lower percentage (13.3%) of pain level as compared to those without companion. The mean satisfaction score of the patients with ccc was 90.66 whereas the score of the group without ccc was 30.33 which statistically highly significant. 42 of the patients with ccc and 39 patients without ccc opted for known female relative as constant caring companion. All woman in the study group and 97% in the control group would recommend a constant caring companion to the pregnant woman. Conclusions: Women with a constant caring companion have a more fulfilling and satisfactory experience of the labour process which cannot be said about the women without ccc. Since no negative impact was observed due to the presence of a constant caring companion, this practice may be recommended. The constant caring companion would prove an important asset to the doctor involved in the management of labouring women.
Lessons learned after 20 years' experience with penile fracture

ABSTRACT Objective: To report our experience over the past 20 years in the diagnosis and surgical treatment of penile fracture (PF). Materials and methods: Between January 1997 and January 2017, patients with clinical diagnosis of PF were admitted to our facility and retrospectively assessed. Medical records were reviewed for clinical presentation, etiology and operative findings. Postoperative complications, sexual and urinary function were evaluated. Results: Sexual trauma was the main etiological factor, responsible for 255 cases (88.5%): 110 (43.1%) occurred with the “doggy style” position, 103 (40.3%) with “man on top” position, 31 (12.1%) with the “woman on top” position and 11 (4.3%) in other sexual positions. The most common findings in the clinical presentation were hematoma, in all cases and detumescence in 238 (82.6%). Unilateral corpus cavernosum injuries were found in 199 (69%) patients and bilateral in 89 (31%) patients. Urethral injuries were observed in 54 (18.7%) cases. Nine (14.7%) patients developed erectile dysfunction and eight (13.1%) had penile curvature. Only two (3.7%) patients had complications after urethral reconstruction. Conclusions: PF has typical clinical presentation and no need for additional tests in most cases. Hematoma and immediate penile detumescence are the most common clinical findings. Sexual activity was the most common cause. The ‘doggy style’ and ‘man-on-top’ was the most common positions and generally associated with more severe lesions. Concomitant urethral injury should be considered in cases of highenergy trauma. Surgical reconstruction produces satisfactory results, however, it can lead to complications, such as erectile dysfunction and penile curvature.
Anharmonicity Explains Temperature Renormalization Effects of the Band Gap in SrTiO3.

Soft phonon modes in strongly anhamonic crystals are often neglected in calculations of phonon-related properties. Herein we experimentally measure the temperature effects on the band gap of cubic SrTiO3, and compare with first-principles calculations by accounting for electron-phonon coupling using harmonic and anharmonic phonon modes. The harmonic phonon modes show an increase in the band gap with temperature using either Allen-Heine-Cardona theory or finite-displacement approach, and with semi-local or hybrid exchange-correlation functionals. This finding is in contrast with experimental results that show a decrease in the band gap with temperature. We show that the disagreement can be rectified by using anharmonic phonon modes that modify the contributions not only from the significantly corrected soft modes, but also from the modes that show little correction in frequencies. Our results confirm the importance of soft-phonon modes that are often neglected in the computation of phonon-related properties and particularly in electron-phonon coupling.
Clinical performance of non‐invasive prenatal testing for trisomies 21, 18 and 13 in twin pregnancies: A cohort study and a systematic meta‐analysis

The objective of this study was to report on the clinical performance of non‐invasive prenatal testing (NIPT) for trisomies 21, 18 and 13 in twin pregnancies and to define the performance of NIPT by combining our cohort study results with published studies in a systematic meta‐analysis.
Deciphering the Role of Multiple Thioredoxin Fold Proteins of Leptospirillum sp. in Oxidative Stress Tolerance

Thioredoxin fold proteins (TFPs) form a family of diverse proteins involved in thiol/disulfide exchange in cells from all domains of life. Leptospirillum spp. are bioleaching bacteria naturally exposed to extreme conditions like acidic pH and high concentrations of metals that can contribute to the generation of reactive oxygen species (ROS) and consequently the induction of thiol oxidative damage. Bioinformatic studies have predicted 13 genes that encode for TFP proteins in Leptospirillum spp. We analyzed the participation of individual tfp genes from Leptospirillum sp. CF-1 in the response to oxidative conditions. Genomic context analysis predicted the involvement of these genes in the general thiol-reducing system, cofactor biosynthesis, carbon fixation, cytochrome c biogenesis, signal transduction, and pilus and fimbria assembly. All tfp genes identified were transcriptionally active, although they responded differentially to ferric sulfate and diamide stress. Some of these genes confer oxidative protection to a thioredoxin-deficient Escherichia coli strain by restoring the wild-type phenotype under oxidative stress conditions. These findings contribute to our understanding of the diversity and complexity of thiol/disulfide systems, and of adaptations that emerge in acidophilic microorganisms that allow them to thrive in highly oxidative environments. These findings also give new insights into the physiology of these microorganisms during industrial bioleaching operations.
The Meaning of Bonds: The Relationships Among Grief Rituals, Support From Relatives and Friends, and the Mental Health of Shiduers

Previous studies have sporadically explored the effect of various bonds on the mental health of shiduers (i.e., parents who lost their only child). However, research has rarely classified different bonds to systematically describe their effects. This study administered a self-compiled questionnaire, the Center for Epidemiologic Studies Depression Scale, the Zung Self-Rating Anxiety Scale, the posttraumatic stress disorder Checklist, the Prolonged Grief Questionnaire, the Posttraumatic Growth Inventory, and the Adult Dispositional Hope Scale to 466 shiduers. The commemoration rituals that occur soon after the loss predict a lower level of posttraumatic stress disorder. Similarly, the commemoration rituals that occur on special days predict lower levels of depression and anxiety. In contrast, the continuation of commemoration rituals on ordinary days predicts higher levels of depression and prolonged grief. Support from family members and relatives, other shiduers, and nonshiduer friends are all beneficial to shiduers’ mental health.
Identification and Functional Study of Chitin Metabolism and Detoxification-Related Genes in Glyphodes pyloalis Walker (Lepidoptera: Pyralidae) Based on Transcriptome Analysis

Glyphodes pyloalis Walker (Lepidoptera: Pyralididae) is a serious pest in the sericulture industry, which has caused damage and losses in recent years. With the widespread use of insecticides, the insecticide resistance of G. pyloalis has becomes increasingly apparent. In order to find other effective methods to control G. pyloalis, this study performed a transcriptome analysis of the midgut, integument, and whole larvae. Transcriptome data were annotated with KEGG and GO, and they have been shown to be of high quality by RT-qPCR. The different significant categories of differentially expressed genes between the midgut and the integument suggested that the transcriptome data could be used for next analysis. With the exception of Dda9 (GpCDA5), 19 genes were involved in chitin metabolism, most of which had close protein–protein interactions. Among them, the expression levels of 11 genes, including GpCHSA, GpCDA1, GpCDA2, GpCDA4, GPCHT1, GPCHT2a, GPCHT3a, GPCHT7, GpTre1, GpTre2, and GpRtv were higher in the integument than in the midgut, while the expression levels of the last eight genes, including GpCHSB, GpCDA5, GpCHT2b, GpCHT3b, GpCHT-h, GpPAGM, GpNAGK, and GpUAP, were higher in the midgut than in the integument. Moreover, 282 detoxification-related genes were identified and can be divided into 10 categories, including cytochrome P450, glutathione S-transferase, carboxylesterase, nicotinic acetylcholine receptor, aquaporin, chloride channel, methoprene-tolerant, serine protease inhibitor, sodium channel, and calcium channel. In order to further study the function of chitin metabolism-related genes, dsRNA injection knocked down the expression of GpCDA1 and GpCHT3a, resulting in the significant downregulation of its downstream genes. These results provide an overview of chitin metabolism and detoxification of G. pyloalis and lay the foundation for the effective control of this pest in the sericulture industry.
Recurrent Germline BRCA2 Gene Mutation in Lithuanian Family

Approximately 10% of all breast cancer (BC) cases are familial and caused by inheritance of mutant BRCA1, BRCA2, or some other genes from the same DNA reparation pathway. Genetic counseling in families with cancer history is a powerful means for early cancer detection and active risk reduction through preventive interventions. This is the first report of the rare inherited BRCA2 frameshift-deletion mutation c. 3847_3848delGT in one Lithuanian pedigree with the intense familial history of BC. Three BRCA2-positive blood relatives with BC of different biological types were identified in this pedigree with the same type mutation. All three cases were diagnosed with advanced stage ductal carcinoma. Markedly, polymorphic cells and numerous mitoses were identified in BC from the cases. Two patients from the family were diagnosed with the triple negative tumors, while one case had early onset of the hormone positive BC. Despite the variation in clinical and biological presentation of BC, all cases showed a good response to conventional treatment. In conclusion, the strong influence of BRCA2 mutation on the onset of BC of various biological types reveals the complexity of genetic counselling in families with BC history.
Therapeutic Treatment with Abdominal Adipose Mesenchymal Cells Does Not Prevent Elastase-Induced Emphysema in Rats.

OBJECTIVES Emphysema and chronic bronchitis have different pathophysiologies but both are significant components of chronic obstructive lung disease (COPD). The levels of Matrix metalloproteinase (MMP)-9 in the bronchoalveloar lavage fluid (BALF) and in serum indicate the presence of emphysema. Intratracheal administration of elastase has been used to create a rat model of emphysema. Adipose tissue-derived mesenchymal stem cells (MSC) have been postulated to prevent or reverse emphysema, however, this has not been examined in the rat model of elastase-induced emphysema. MATERIALS AND METHODS In this study, 31 Wistar albino rats aged 6-8 weeks and weighing 250-300 g were assessed. On day 1, the animals were treated intratracheally with 0.5 mL saline (control group, n=10), i.e., 0.5 mL saline solution containing 0.1 IU porcine pancreatic elastase (PPE) (Elastase group, n=12) or PPE plus MSC (Elastase-MSC group, n=9) was adminstered per animal. MSCs suspended in serum were injected via the caudal vein on day 21. At least 106 cells were injected. All animals were sacrificed on day 42 and the emphysema index (EI) was calculated, along with measuring the BALF and serum MMP-9 concentrations. RESULTS Porcine pancreatic elastase induced a significant degree of emphysema in the PPE groups as compared to the control group, which was determined by the EI index (p=0.008). This was not reversed by MSC treatment. The EI remained significantly low in comprison with the controls (p=0.001) and measured no different from the Elastase-treated animals. There was no statistically significant difference between the BALF and serum MMP-9 levels between the control and treatment groups. CONCLUSION Our findings suggest that therapeutic treatment with adipose tissue-derived MSC in rats has no effect on emphysema or on MMP9 expression, which is a known marker of emphysema.
Household water storage management, hygiene practices and associated drinking water quality in rural India.

Household drinking water storage is commonly practiced in rural India. Fecal contamination may be introduced at the water source, during collection, storage or access. Within a trial of a community-level water supply intervention, we conducted five quarterly household-level surveys to collect information about water, sanitation and hygiene practices in rural India. In a random sub-sample of households, we tested stored drinking water samples for Escherichia coli, concurrently observing storage and access practices. We conducted 9961 surveys and collected 3296 stored water samples. Stored water samples were frequently contaminated with E. coli (69%), and E. coli levels were highest during the wet season. Most households contributing two or more drinking water samples had detectable E.coli in some (47%) or all (44%) samples. Predictors of stored water contamination with E. coli included consumption of river water and open defecation; consumption of reverse osmosis-treated water and safe water access practices appeared to be protective. Until households can be reached with on-premises continuous safe water supplies, suboptimal household water storage practices are likely to continue. Improvements to source water quality alone are unlikely to prevent exposure to contaminated drinking water unless attention is also given to improving household water storage, access and sanitation practices.
Alvarado Score, Ultrasound, and CRP: How to Combine Them for the Most Accurate Acute Appendicitis Diagnosis

Background: The aim of the current study was to investigate whether the usage of three diagnostic methods of acute appendicitis which are Alvarado score, C- reactive protein (CRP) levels and ultrasound (US) in combination improves diagnostic accuracy significantly. Patients and Methods: Data were analyzed in 254 patients with suspected appendicitis who had a sonographic examination and a CRP value. The patients were classified into four groups according to both Alvarado score and US findings. US results, Alvarado score, and CRP levels were compared. Results: The most specific test among three diagnostic methods was sonography. Combination of an Alvarado score higher or equal to 5, a high CRP level (≥ 0.8) and a sonographic examination as appendicitis with visualization of an inflamed or perforated appendix was more specific than US alone. An Alvarado score higher or equal to 5 (86.2%) was found to be the most sensitive criteria. Conclusions: Using Alvarado score, US and CRP levels in combination provides us to confirm or rule out acute appendicitis safely.
A Community-sensor index as a tool for public health surveillance of malaria drug resistance

Infectious diseases like tuberculosis, malaria and the human immunodeficiency virus are both preventable and curable but cause about half of the deaths in the developing world. They affect people in the prime of their productive lives, inflicting a very heavy impact on development, opportunities and livelihood. Poverty is the end result with an enormous toll on the economy of developing nations. As such, the community goes for the cheapest medications that work and therefore can report on the effectiveness of drugs as an effect of many activities upstream that cause parasite unresponsiveness to therapy. The aim of this study was to investigate the relationship between community auto-medication and molecular markers of drug resistance in malaria to detect and provide evidence for when the community feels a drug is not or no longer effective. This would propose a better management policy towards decreasing drug resistance. This would be achieved by promoting proper therapy-seeking habits and thus ensure a higher quality of life and a higher productive capacity of workers. A survey was first carried out in 8 localities to observe various aspects of therapy-seeking behaviour. The knowledge and practice of malaria management and prevention were quite poor, favouring the prevalence of drug resistant parasites. To establish an index for community-sensing of drug resistance, the prevalence of the mutation of the dhfr gene at position 108 in parasites was used in which Y = -2.5X + 48, where Y = prevalence of mutations (Pm) and X = level of self-prescription. This was confirmed by the extrapolation of the self-prescription of Fansidar (12%) against a value of 18%. This study shows that the therapy-seeking habits of a community can be used to demonstrate the prevalence of mutations to Fansidar and hence possibly to other antimalarial drugs presenting resistance. Key words: Therapy-seeking behaviour, auto-medication, community-sensing, molecular markers, surveillance indicators, drug resistance.