Miracle-dz/UniFAR-FTUs huggingface dataset:
Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective

ABSTRACT The destruction of mitochondria through macroautophagy (autophagy) has been recognised as a major route of mitochondrial protein degradation since its discovery more than 50 years ago, but fundamental questions remain unanswered. First, how much mitochondrial protein turnover occurs through auto-phagy? Mitochondrial proteins are also degraded by nonautophagic mechanisms, and the proportion of mitochondrial protein turnover that occurs through autophagy is still unknown. Second, does auto-phagy degrade mitochondrial proteins uniformly or selectively? Autophagy was originally thought to degrade all mitochondrial proteins at the same rate, but recent work suggests that mitochondrial autophagy may be protein selective. To investigate these questions, we used a proteomics-based approach in the fruit fly Drosophila melanogaster, comparing mitochondrial protein turnover rates in autophagy-deficient Atg7 mutants and controls. We found that ~35% of mitochondrial protein turnover occurred via autophagy. Similar analyses using parkin mutants revealed that parkin-dependent mitophagy accounted for ~25% of mitochondrial protein turnover, suggesting that most mitochondrial autophagy specifically eliminates dysfunctional mitochondria. We also found that our results were incompatible with uniform autophagic turnover of mitochondrial proteins and consistent with protein-selective autophagy. In particular, the autophagic turnover rates of individual mitochondrial proteins varied widely, and only a small amount of the variation could be attributed to tissue differences in mitochondrial composition and autophagy rate. Furthermore, analyses comparing autophagy-deficient and control human fibroblasts revealed diverse autophagy-dependent turnover rates even in homogeneous cells. In summary, our work indicates that autophagy acts selectively on mitochondrial proteins, and that most mitochondrial protein turnover occurs through non-autophagic processes. Abbreviations: Atg5: Autophagy-related 5 (Drosophila); ATG5: autophagy related 5 (human); Atg7: Autophagy-related 7 (Drosophila); ATG7: autophagy related 7 (human); DNA: deoxyribonucleic acid; ER: endoplasmic reticulum; GFP: green fluorescent protein; MS: mass spectrometry; park: parkin (Drosophila); Pink1: PTEN-induced putative kinase 1 (Drosophila); PINK1: PTEN-induced kinase 1 (human); PRKN: parkin RBR E3 ubiquitin protein ligase (human); RNA: ribonucleic acid; SD: standard deviation; Ub: ubiquitin/ubiquitinated; WT: wild-type; YME1L: YME1 like ATPase (Drosophila); YME1L1: YME1 like 1 ATPase (human)
Trafficking of Women and Children in East Java, Indonesia

This study investigated the patterns and modes of the occurrence of cases of women and child trafficking in East Java Province, Indonesia. This includes the factors that cause women to become familiar with the trade of women and children. This qualitative descriptive study was conducted in four areas of the East Java Province, known as regions, prone to have victims of trafficking. To collect the data, the researcher conducted in-depth interviews with 115 respondents: 40 commercial sex workers (PSK), 4 transnational/contract marriage victims, 45 beggars, 25 housemaids, 1 victim of child trade trafficking, and 10 concerned experts (researchers and activists from nongovernmental organisations). The study found that economic factors, sociocultural factors and a brokers’ proactive recruitment of new victims were the factors that led to the trafficking of women and children. The patterns and forms of the trafficking of women and children in East Java are (1) for prostitution, (2), for forced marriage across different countries, (3) to be employed as beggars, (4) to be employed as domestic servants and (5) to trade trafficked child victims to others. The modes developed by the syndicate to traffic women and children are increasingly diverse and this includes through persuasion, deceit, violence and the mode that uses ‘gendam’ or hypnosis.
The Role of Genetic Polymorphism in the Formation of Arterial Hypertension, Type 2 Diabetes and their Comorbidity.

BACKGROUND Hereditary component plays a significant role in the formation of insulin resistance (IR) - one of the pathogenetic links of arterial hypertension (AH) and type 2 diabetes mellitus (DM2). However, the genetic predisposition to IR can not be realized and does not manifest itself clinically in the absence of appropriate factors of the environment (excessive nutrition, low physical activity, etc.). OBJECTIVE The review summarizes the results of studies which describe the contribution of genetic polymorphism to the formation and progression of AH, DM2 and their comorbidity in various populations. RESULTS In many studies, it has been established that genetic polymorphism of candidate genes is influenced by the formation, course and complication of AH and DM2. According to research data, the modulating effect of polymorphism of some genetic markers of AH and DM2 on metabolism and hemodynamics has been established. The results of numerous studies have shown a higher frequency of occurrence of AH and DM2, as well as their more severe course with adverse genetic polymorphisms. At the same time, the role of genetic polymorphism in the formation of AH and DM2 differs in different populations. CONCLUSION Contradictory data on the influence of gene polymorphisms on the formation of AH and DM2 in different populations, as well as a small number of studies on the combined effects of several polymorphisms on the formation of comorbidity, determine the continuation of research in this direction.
SMS: A New Way of Communication and Promotion

Short Message Service (SMS) seems to be a more attractive way for communication between young people. Some companies think that SMS could also be important way for advertising their products and services. The purpose of this study is to investigate the attitudes of undergraduate university students regarding the use of SMS for advertising and marketing purposes in Greece. Data was collected through open and semi-structured interviews of 40 university students. The results showed to the researcher that students use SMS for their everyday communication but they are sceptical about the use of SMS as an advertising tool even though they believe that is a promising way of advertising.
Individual differences in the effects of priors on perception: A multi-paradigm approach

The present study investigated individual differences in how much subjects rely on prior information, such as expectations or knowledge, when faced with perceptual ambiguity. The behavioural performance of forty-four participants was measured on four different visual paradigms (Mooney face recognition, illusory contours, blur detection and representational momentum) in which priors have been shown to affect perception. In addition, questionnaires were used to measure autistic and schizotypal traits in the non-clinical population. We hypothesized that someone who in the face of ambiguous or noisy perceptual input relies heavily on priors, would exhibit this tendency across a variety of tasks. This general pattern would then be reflected in high pairwise correlations between the behavioural measures and an emerging common factor. On the contrary, our results imply that there is no single factor that explains the individual differences present in the aforementioned tasks, as further evidenced by the overall lack of robust correlations between the separate paradigms. Instead, a two-factor structure reflecting differences in the hierarchy of perceptual processing was the best fit for explaining the individual variance in these tasks. This lends support to the notion that mechanisms underlying the effects of priors likely originate from several independent sources and that it is important to consider the role of specific tasks and stimuli more carefully when reporting effects of priors on perception.
On the measurement of turbulence energy dissipation

The mean flow and turbulence fields and the turbulence energy dissipation rate in a vessel stirred by a hydrofoil impeller were analysed using the two-dimensional Particle Image Velocimetry (PIV) technique. The vessel diameter was T = 100 mm and was stirred by an impeller of diameter D = T/3, rotated at a speed of 2,165 r.p.m. to achieve a Reynolds number of 40,000 and ensure fully-turbulent flow in the vessel. The measurements were made with a 2-D PIV system comprising a PCO Sensicam SVGA camera and Nikon 55 mm lenses. The light from a 3W Argon laser was used to generate a light sheet with a fibre optic and a cylindrical lens fibre module. Measurements were performed for different spatial resolution configurations. In order to assess the accuracy of these measurements and of the PIV technique itself, the results were compared to the data obtained in the same vessel configuration with the LDA technique by Fentiman et al. (1998). The entire flow field in the vessel as well as smaller areas in the discharge stream region below the impeller were analysed. Particular attention is given to the effect, potential and limitation of spatial resolution on the estimation of energy dissipation. The energy dissipation was estimated using the direct definition, i.e. evaluating the instantaneous spatial gradients of the Reynolds stresses. Other methods available in literature were considered as well and the results compared. The effects of number of samples employed in the ensemble-averaging over the energy dissipation estimation was considered as well. The experiments show good agreement with many findings from other works on the analysis of turbulence properties and energy dissipation in stirred vessels. Moreover the performance of PIV in the turbulence energy dissipation estimation was found to be very similar to other earlier studies.
FABRICATION OF A SRF DEFLECTING CAVITY FOR THE ARIEL -LINAC

A superconducting RF deflecting cavity has been designed and is being fabricated at TRIUMF to allow simultaneous beam delivery to both rare isotope production and an energy recovery linac. The 650 MHz cavity will operate in a TE-like mode in CW. The design has been optimised for high shunt impedance and minimal longitudinal footprint, reaching roughly 50% higher shunt impedance with 50% less length than comparable non-TM mode cavity geometries. Due to low power dissipation at 4K at the maximum required deflecting voltage of 0.6 MV, low cost manufacturing techniques have been employed in the construction of the cavity. These include the use of reactor grade Niobium and TIG welding in an inert atmosphere. Development of the manufacturing processes will be presented along with the status of fabrication.
Dry Beriberi Due to Thiamine Deficiency Associated with Peripheral Neuropathy and Wernicke’s Encephalopathy Mimicking Guillain-Barré syndrome: A Case Report and Review of the Literature

Patient: Female, 56 Final Diagnosis: Dry Beri Beri Symptoms: Anasarca • ascending paralysis • hypotension • unresponsiveness Medication: — Clinical Procedure: — Specialty: Neurology Objective: Challenging differential diagnosis Background: Beriberi due to thiamine (vitamin B1) deficiency has two clinical presentations. Patients with dry beriberi present with neuropathy, and patients with wet beriberi present with heart failure, with or without neuropathy. Dry beriberi can mimic the most common form of Guillain-Barré syndrome (GBS), an acute inflammatory demyelinating polyradiculoneuropathy (AIDP). Severe thiamine deficiency results in Wernicke’s encephalopathy. This report of a case of dry beriberi and Wernicke’s encephalopathy due to thiamine deficiency includes a review of the literature. Case Report: A 56-year old woman with a history of gallstone pancreatitis and protein-calorie malnutrition was treated six months previously with total parenteral nutrition (TPN). She initially presented at another hospital with paresthesia of the lower limbs, arms, and neck, and symptoms of encephalopathy. Initial diagnosis of GBS was made, based on magnetic resonance imaging (MRI) and cerebrospinal fluid (CSF) findings. Despite five days of intravenous immunoglobulin (IVIG) treatment, her encephalopathy worsened, requiring transfer to our hospital, where she required intubation and treatment with vasopressors. A repeat MRI of her brain showed changes consistent with Wernicke’s encephalopathy. Following treatment with high-dose intravenous thiamine, her mental status improved within 48 hours, and by the third hospital day, she no longer required intubation. Conclusions: Symptoms and signs of dry beriberi due to thiamine deficiency can mimic those of acute or chronic GBS. However, thiamine repletion leads to rapid clinical improvement and can prevent irreversible neurologic sequelae, including Korsakoff syndrome. Clinicians should consider thiamine deficiency in malnourished patients presenting with symptoms and signs of GBS.
Preparation of chitosan nanoparticle containing recombinant StxB antigen of EHEC and evaluation its immunogenicity in BALB/c mice

Background and Objectives: Escherichia coli O157:H7 is one of the most important food pathogens that produces colitis and bloody urine in humans. The Stx2B subunit is considered as one of the candidates for vaccine due to its immunogenic and adjuvant properties. Designing a mucosal vaccine using nanoparticles for protecting the antigen against degradation and controlling the release of antigen are important. The objective of the current study was to prepare nanoparticles containing the Stx2B subunit of E. coli O157:H7 and evaluation of its immunogenicity in the mouse model. Materials and Methods: E. coli BL21 DE3 and pET28a-stxB were used for expression of the stx2b gene. After inducing gene expression, purification of the Stx2b protein was performed. Then, chitosan nanoparticle containing recombinant Stx2B was prepared and administered to BALB/c mice. IgA and IgG titers in serum and IgA titers in feces of immunized and control mice were evaluated by the ELISA method. Results: After expression and purification of the Stx2B recombinant protein, an expected band of 13 kDa was observed on the SDS-PAGE gel and confirmed by Western Blot analysis. The size of the nanoparticle containing Stx2B was 290 nm. In the immunized mice, IgG and IgA titers were significantly increased. The immunized mice were challenged against E. coli O157:H7 Stx+ and the shedding analysis showed that colonization of bacteria in the intestinal tract decreased. Conclusion: Oral administration of nanoparticles containing Stx2B as a candidate for the vaccine can induce a systemic and mucosal immune response against Stx2 toxin and can provide acceptable protection.
Heterogeneous iota carrageenan-based palladium catalysts for organic synthesis

Novel heterogeneous iota-carrageenan-based palladium catalysts were prepared and used in Suzuki cross coupling, Heck coupling and the transfer hydrogenation of olefins while using various substrates and solvents. In all of these reactions, heterogeneous systems based on xerogels or hydrogels were found to be active, and in certain cases, they yielded higher conversions than those of the homogeneous parent systems. Moreover, all the catalysts could be easily separated from the reaction mixtures and recycled without loss of activity.
A Distributed Hierarchical SGD Algorithm with Sparse Global Reduction

Reducing communication in training large-scale machine learning applications on distributed platform is still a big challenge. To address this issue, we propose a distributed hierarchical averaging stochastic gradient descent (Hier-AVG) algorithm with infrequent global reduction by introducing local reduction. As a general type of parallel SGD, Hier-AVG can reproduce several popular synchronous parallel SGD variants by adjusting its parameters. We show that Hier-AVG with infrequent global reduction can still achieve standard convergence rate for non-convex optimization problems. In addition, we show that more frequent local averaging with more participants involved can lead to faster training convergence. By comparing Hier-AVG with another popular distributed training algorithm K-AVG, we show that through deploying local averaging with fewer number of global averaging, Hier-AVG can still achieve comparable training speed while frequently get better test accuracy. This indicates that local averaging can serve as an alternative remedy to effectively reduce communication overhead when the number of learners is large. Experimental results of Hier-AVG with several state-of-the-art deep neural nets on CIFAR-10 and IMAGENET-1K are presented to validate our analysis and show its superiority.
Proteomics profiling of plasma exosomes in epithelial ovarian cancer: A potential role in the coagulation cascade, diagnosis and prognosis

Ovarian cancer remains the most lethal type of cancer among all gynecological malignancies. The majority of patients are diagnosed with ovarian cancer at the late stages of the disease. Therefore, there exists an imperative need for the development of early ovarian cancer diagnostic techniques. Exosomes, secreted by various cell types, play pivotal roles in intercellular communication, which emerge as promising diagnostic and prognostic biomarkers for ovarian cancer. In this study, we present for the first time, at least to the best of our knowledge, the proteomics profiling of exosomes derived from the plasma of patients with ovarian cancer via liquid chromatography tandem mass spectrometry (LC-MS/MS) with tandem mass tagging (TMT). The exosomes enriched from patient plasma samples were characterized by nanoparticle tracking analysis (NTA), dynamic light scattering (DLS), transmission electron microscopy (TEM) and western blot analysis. The size of the plasma exosomes fell into the range of 30 to 100 nm in diameter. The exosomal marker proteins, CD81 and TSG101, were clearly stained in the exosome samples; however, there was no staining for the endoplasmic reticulum protein, calnexin. A total of 294 proteins were identified with all exosome samples. Among these, 225 proteins were detected in both the cancerous and non-cancerous samples. Apart from universal exosomal proteins, exosomes derived from ovarian cancer patient plasma also contained tumor-specific proteins relevant to tumorigenesis and metastasis, particularly in epithelial ovarian carcinoma (EOC). Patients with EOC often suffer from coagulation dysfunction. The function of exosomes in coagulation was also examined. Several genes relevant to the coagulation cascade were screened out as promising diagnostic and prognostic factors that may play important roles in ovarian cancer progression and metastasis. On the whole, in this study, we successfully isolated and purified exosomes from plasma of patients with EOC, and identified a potential role of these exosomes in the coagulation cascade, as well as in the diagnosis and prognosis of patients. differentially expressed genes, functional enrichment analysis, protein-protein interaction, diagnostic and prognostic biomarkers
How near are urban inhabitants to high- amenity nature? Exploring and testing a new indicator for Dutch, Danish, and German cities

Nature is widely acknowledged to contribute to people’s well-being. This study introduces a city-level indicator of well-being that assesses the proximity of the inhabitants of 148 cities in the Netherlands, Denmark, and Germany to nature that is of high-amenity. High-amenity nature is operationalized by combining unique systematic data on people’s perceptions of what are the locations of attractive natural areas with data on natural land cover. The indicator that we test in this study is a departure from the usual assumption of equal well-being from any nature, as it intends to approximate the ‘actual’ subjective quality of nature near people’s homes. International comparability of the indicator is enhanced by the use of a definition of cities as functional urban areas (FUAs), which can be done consistently across countries. Results demonstrate that the average ‘nearness’ of urban populations to high-amenity nature varies widely across the observed cities. Importantly, inhabitants of cities with high population densities are found to live, on average, closer to high-amenity nature than inhabitants of low density cities. The implication here is that living in high density cities may not come solely at the expense of living close to nature; this implication challenges the findings of currently used indicators that neglect to examine the subjective amenity-level of nature. 37 This chapter is based on: Daams, M.N. , & Veneri, P. How near are urban inhabitants to high-amenity nature? Exploring and testing a new indicator for Dutch, Danish, and German cities. Submitted to an ISI rated journal.
DESCRIPTION OF THE CONDITION Anastomotic leakage after construction of a colorectal anastomo-

2. DEFINITIONS Anastomotic leakage was defined according to the definitions made by the Surgical Infection Study Group [1]. They have defined anastomotic leakage as a leak of luminal contents from a surgical join between two hollow viscera, emerging through the wound or drain site, or collecting in relation to the anastomosis. The leakage may affect the clinical state of the patient, causing fever, abscess, septicemia, metabolic disturbances and/or multiple-organ failure. Any local anastomotic leakage in the absence of clinical symptoms may be regarded as a subclinical leakage [1]. Moreover, anastomotic leakage may be defined according to the degrees of severity. Radiological leakage is defined as leakage visualized upon radiological examination without the patient having clinical symptoms. Both minor and major clinical leakage are defined as clinical symptoms of anastomotic leakage as described above. However, when a change in surgical and/or medical management is necessary, the leakage is defined as major. For both conditions, radiological leakage may also be present [2].
Perception, prevalence and correlates of depression among females attending the Gynaecological Clinic of Usmanu Danfodiyo University Teaching Hospital, Sokoto, Nigeria

Background: Infertility is a global problem, particularly in developing countries, and it has been linked with emotional responses such as depression, anxiety, guilt, social isolation, and decreased self-esteem in both men and women. Aim: This study was conducted to assess the perception, prevalence and correlates of depression among females attending the Gynecological Clinic of Usmanu Danfodiyo University Teaching Hospital, Sokoto, Nigeria. Materials and Methods: A cross-sectional study was conducted among 156 females with infertility (selected by systematic sampling technique) in Sokoto, Nigeria. A structured interviewer-administered questionnaire was used to collect data on the research variables. Data were analyzed using IBM SPSS version 20 statistical computer software package. Results: The mean age of the respondents was 28.3 ± 6.4 years. Majority, 113 (72.4%) of the 156 respondents perceived the need to share their feelings concerning the delay they had in having a child with others, but close to half of them (48.7%) had fears of adverse consequences after doing so. About a fifth of respondents (21.8%) had depression and it was associated with being married for ≤ 3 years, having negative attitude to child adoption, and poor support from in-laws. Conclusion: This study showed high levels of perception of the benefits and consequences of sharing their feelings regarding their infertility with others, and high prevalence of depression among females with infertility in Sokoto, Nigeria. Care providers should promote child adoption among women undergoing fertility treatment, routinely screen them for depression and include their extended family members in the interventions for preventing depression among them.