Miracle-dz/UniFAR-FTUs huggingface dataset:
Nosocomial Yeast Infections Among Cancer Patients in Egypt: Species Distribution and Antifungal Susceptibility Profile

Background: The frequency of nosocomial yeast infections has increased dramatically in the recent years. They are considered an important cause of morbidity and mortality in immunocompromised cancer patients. The majority of yeast infections are caused by Candida species. However, species like Trichosporon and Rhodotorula should be considered as possible infectious agents as well. Objectives: This study aimed at determining the prevalence of yeast species, their distribution among patients and the antifungal susceptibility proﬁle at Oncology Center, Mansoura, Egypt. Methods: From December 2016 till November 2017, cancer patients who developed infective episodes two days or more following hospital admission were included in the study. Clinical samples were collected according to the site of infection using standard sterileprocedures. BloodsampleswereculturedusingtheBACT-ALERTsystem. Fungalidentiﬁcationandsusceptibilitytestingwere performed by Vitek 2 system. Results: Eighty-seven fungal strains were obtained from our patients. A higher isolation rate was observed in urine samples (47.1%) followed by oropharyngeal (24.1%) and blood (21.8%) samples. The majority of the yeast species were Candida albicans (40.2%), C. tropicalis (14.9%), C. parapsilosis (9.2%), C. famata (6.9%) and C. guilliermondii (6.9%). Out of the 87 samples, 8 (9.2%) were resistant to ﬂuconazole, 7 (8.0%) were resistant to ﬂucytosine, 5 (5.7%) were resistant to voriconazole and amphotericin B, and no sample was resistant to caspofungin or micafungin. Conclusions: Vitek 2 system oﬀers a novel method for the early identiﬁcation and susceptibility testing of diﬀerent yeast species. It helps to minimize the risk for emergence of resistant species and reduce mortality rates, particularly in cancer patients.
The whole process cost management based on BIM

The-whole-process cost management is the overall process of engineering construction from feasibility study through preliminary design, construction preparation, contracting, construction, completion and post-evaluation. All organizational activities and business behaviors centering on engineering cost can ensure the investment benefits of construction projects. this paper introduces how the cost management of BIM technology plays a role in the project construction.
Early changes in immune cell metabolism and function are a hallmark of sleeve gastrectomy: a prospective human study

Objective To characterize longitudinal changes in blood biomarkers, leukocyte composition, and gene expression following laparoscopic sleeve gastrectomy (LSG). Background LSG is an effective treatment for obesity, leading to sustainable weight loss and improvements in obesity-related co-morbidities and inflammatory profiles. However, the effects of LSG on immune function and metabolism remain uncertain. Methods Prospective data was collected from 23 enrolled human subjects from a single institution. Parameters of weight, co-morbidities, and trends in blood biomarkers and leukocyte subsets were observed from pre-operative baseline to one year in three-month follow-up intervals. RNA-sequencing was performed on pairs of whole blood samples from the first six subjects of the study (baseline and three months post-surgery) to identify genome-wide gene expression changes associated with undergoing LSG. Results LSG led to a significant decrease in mean total body weight loss (18.1%) at three months and among diabetic subjects a reduction in HbA1c. Improvements in clinical inflammatory and hormonal biomarkers were demonstrated as early as three months after LSG. A reduction in neutrophil-lymphocyte ratio was observed, driven by a reduction in absolute neutrophil counts. Gene set enrichment analyses of differential whole blood gene expression demonstrated that after three months, LSG induced transcriptomic changes not only in inflammatory cytokine pathways but also in several key metabolic pathways related to energy metabolism. Conclusions LSG induces significant changes in the composition and metabolism of immune cells as early as three months post-operatively. Further evaluation is required of bariatric surgery's effects on immunometabolism and consequences for host defense and metabolic disease.
Management of Working Capital in IFFCO and KRIBHCO - A Comparative Study

The Indian Fertiliser Industry entered into the hundredth year of its existence in the year 2006. The industry had a very humble beginning in 1906, when the manufacturing unit of Single Super Phosphate (SSP) was set up in Ranipet near Chennai with annual capacity of 600 MT. The Fertiliser&Chemicals Travancore of India Ltd. (FACT) at Cochin in Kerala and the Fertiliser Corporation of India (FCI) in Sindri in Bihar were the first large sized fertiliser plants set up in forties and fifties with a view to establish an industrial base to achieve self-sufficiency in food grains. Subsequently, green revolution in the late sixties gave an impetus to the growth of fertiliser industry in India. In seventies and eighties, a significant addition to the fertiliser production capacity was witnessed. There has been spectacular growth in the production capacity and production of fertilisers, particularly during eighties and early nineties to meet the rising demand of fertilisers. The Indian fertiliser industry is one of the best in the world in terms of capacity utilisation.
A Study of Recurrent and Convolutional Neural Networks in the Native Language Identification Task

A Study of Recurrent and Convolutional Neural Networks in the Native Language Identification Task Robert Werfelmann Native Language Identification (NLI) is the task of predicting the native language of an author from their text written in a second language. The idea is to find writing habits that transfer from an author’s native language to their second language. Many approaches to this task have been studied, from simple word frequency analysis, to analyzing grammatical and spelling mistakes to find patterns and traits that are common between different authors of the same native language. This can be a very complex task, depending on the native language and the proficiency of the author’s second language. The most common approach that has seen very good results is based on the usage of n-gram features of words and characters. In this thesis, we attempt to extract lexical, grammatical, and semantic features from the sentences of non-native English essays using neural networks. The training and testing data was obtained from a large corpus of publicly available essays written by authors of several countries around the world. The neural network models consisted of Long Short-Term Memory and Convolutional networks using the sentences of each document as the input. Additional statistical features were generated from the text to complement the predictions of the neural networks, which were then used as feature inputs to a Support Vector Machine, making the final prediction. Results show that Long Short-Term Memory neural network can improve performance over a naive bag of words approach, but with a much smaller feature set. With more fine-tuning of neural network hyperparamters, these results will likely improve significantly.
BNIP-2 retards breast cancer cell migration by coupling microtubule-mediated GEF-H1 and RhoA activation

BNIP-2 acts as a brake on cell migration by scaffolding Rho and GEFs. Microtubules display dynamic turnover during cell migration, leading to cell contractility and focal adhesion maturation regulated by Rho guanosine triphosphatase activity. This interplay between microtubules and actomyosin is mediated by guanine nucleotide exchange factor (GEF)–H1 released after microtubule depolymerization or microtubule disconnection from focal adhesions. However, how GEF-H1 activates Rho upon microtubule disassembly remains elusive. Here, we found that BNIP-2, a BCH domain–containing protein that binds both RhoA and GEF-H1 and traffics with kinesin-1 on microtubules, is important for GEF-H1–driven RhoA activation upon microtubule disassembly. Depletion of BNIP-2 in MDA-MB-231 breast cancer cells decreases RhoA activity and promotes cell migration. Upon nocodazole-induced microtubule disassembly, the interaction between BNIP-2 and GEF-H1 increases, while knockdown of BNIP-2 reduces RhoA activation and cell rounding via uncoupling RhoA-GEF-H1 interaction. Together, these findings revealed that BNIP-2 couples microtubules and focal adhesions via scaffolding GEF-H1 and RhoA, fine-tuning RhoA activity and cell migration.
Scala step-by-step: soundness for DOT with step-indexed logical relations in Iris

The metatheory of Scala’s core type system—the Dependent Object Types (DOT) calculus—is hard to extend, like the metatheory of other type systems combining subtyping and dependent types. Soundness of important Scala features therefore remains an open problem in theory and in practice. To address some of these problems, we use a semantics-first approach to develop a logical relations model for a new version of DOT, called guarded DOT (gDOT). Our logical relations model makes use of an abstract form of step-indexing, as supported by the Iris framework, to model various forms of recursion in gDOT. To demonstrate the expressiveness of gDOT, we show that it handles Scala examples that could not be handled by previous versions of DOT, and prove using our logical relations model that gDOT provides the desired data abstraction. The gDOT type system, its semantic model, its soundness proofs, and all examples in the paper have been mechanized in Coq.
Genomic heterogeneity and clinical characterization of SARS-CoV-2 in Oregon

The first reported case of COVID-19 in the State of Oregon occurred in late February 2020, with subsequent outbreaks occurring in the populous Portland metro area but also with significant outbreaks in less-populous and rural areas. Here we report viral sequences from 188 patients across the hospitals and associated clinics in the Providence Health System in the State of Oregon dating back to the early days of the outbreak. We show a significant shift in dominant clade lineages over time in Oregon, with the rapid emergence and dominance of Spike D614G-positive variants. We also highlight significant diversity in SARS-CoV-2 sequences in Oregon, including a large number of rare mutations, indicative that these genomes could be utilized for outbreak tracing. Lastly, we show that SARS-CoV-2 genomic information may offer additional utility in combination with clinical covariates in the prediction of acute disease phenotypes.
Late Quaternary history of North Eurasian Norway spruce (Picea abies) and Siberian spruce (Picea obovata) inferred from macrofossils, pollen and cytoplasmic DNA variation

We used combined palaeobotanical and genetic data to assess whether Norway spruce (Picea abies) and Siberian spruce (Picea obovata), two major components of the Eurasian boreal forests, occupied separate glacial refugia, and to test previous hypotheses on their distinction, geographical delimitation and introgression.
The Nutritional Potential of Poultry Offal

Abstract RAPID expansion of the poultry industry and changes in consumer preference from “New York” dressed to eviscerated poultry have developed increased needs for profitable disposal of poultry byproducts. Rendering plants process a large proportion of the poultry heads, feet, viscera, blood and feathers used in feeds today (Kahle and Gray, 1957; Lortscher et al., 1957). Blood is heat-dried for use as a supplement in feeds. Wet feathers may be hydrolyzed under high steam pressure, dried and ground for use in feeds (McKerns and Rittersporn, 1958). In recent years, poultry offal, including heads, feet, and viscera, has become increasingly valuable as a feed or feed supplement in the diets of fur-bearing animals (Bassett and Wilke, 1948), and household pets (Morris, 1946). In cooked form, offal may be used to advantage as a feed for hogs (Kahle and Gray, 1957). Little information is available concerning the nutrient composition of poultry offal. Partial …
Investigating the effect of several determinative factors on gastric cancer morbidity in Aghbulagh Village, Meshgin Shahr –Ardabil Province: A case control study

Background & Aim : Gastric cancer is the most common gastrointestinal cancer in Iran, especially in the northwestern part of the country. The purpose of this study was to investigate the factors affecting gastric cancer in the village of Aghbolagh MeshginShahr, Ardebil . Methods : This study was carried out in the village of Agbolagh located in Meshginshahr, Ardebil province in which gastric cancer was considered as a highly prioritized concern. Hence, a case-control study was designed on 21 patients with gastric cancer diagnosed during 2013-2015. This study included 63 control subjects who were randomly and purposefully selected from the adjacent villages and matched for age and sex. Odds ratio and logistic regression were calculated for probable risk factors . Results : The mean age in the case group was 64.7 years and in control group was 61.1 years. In multivariate analysis, using logistic regression, educational level variables (OR = 0.38, CI = 0.15-0.88), family history (OR = 12.9, CI =2.5-72.5) and low fruit consumption (OR =3.06, = 0.49-9.89) were significantly different compared to control cases. Also, single-variable analysis revealed a significant difference for the . intervals between meals (OR =3.5, CI =1.2-9.9). Conclusion : Given the high odds ratio for family history variables, genetic studies are recommended to identify the involved genes and their interactions with the environmental factors in this region
Understanding the microbial ecosystem on the grape berry surface through numeration and identification of yeast and bacteria

Microbial species present on the surface of grape berries at harvest play an important role in winemaking, thus counting and identifying them is of great importance. The use of conventional microbial techniques and molecular methods allowed a quantitative and qualitative inventory of the different microbial species present on the grape berries. These experiments were carried out in several areas of the Bordeaux region on the red grape varieties Merlot, Cabernet Sauvignon and Cabernet Franc. Populations and species clearly varied according to berry development stage. The most widespread yeast species at berry set, Aureobasidium pullulans was never detected at harvest. Fermentative yeasts were detected at harvest and not in the first stage of grape growth. Oenoccocus oeni was detected on immature as well as on mature berries. Gluconobacter oxydans was detected mainly at harvest. Detection of Pediococcus parvulus, was dependent on the vineyard. Veraison appeared to be a key stage for yeast colonisation and the increase in population involved a change in the proportion of each species. The number of A. pullulans fell significantly at veraison as it was superseded by fermentative yeasts. Microbial populations peaked at harvest when the berry surface available for adhesion was largest and no agrochemical treatments had been applied for some weeks. Soil, grape variety and grapegrowing practices may also influence this microbial ecosystem. Based on these and published data, we formulated hypotheses to describe this microbial ecosystem, thus enabling us to develop the concept of a microbial biofilm.
Cost-Effective App Data Distribution in Edge Computing

Edge computing, as an extension of cloud computing, distributes computing and storage resources from centralized cloud to distributed edge servers, to power a variety of applications demanding low latency, e.g., IoT services, virtual reality, real-time navigation, etc. From an app vendor's perspective, app data needs to be transferred from the cloud to specific edge servers in an area to serve the app users in the area. However, according to the pay-as-you-go business model, distributing a large amount of data from the cloud to edge servers can be expensive. The optimal data distribution strategy must minimize the cost incurred, which includes two major components, the cost of data transmission between the cloud to edge servers and the cost of data transmission between edge servers. In the meantime, the delay constraint must be fulfilled - the data distribution must not take too long. In this article, we make the first attempt to formulate this Edge Data Distribution (EDD) problem as a constrained optimization problem from the app vendor's perspective and prove its <inline-formula><tex-math notation="LaTeX">$\mathcal {NP}$</tex-math><alternatives><mml:math><mml:mi mathvariant="script">NP</mml:mi></mml:math><inline-graphic xlink:href="xia-ieq1-3010521.gif"/></alternatives></inline-formula>-hardness. We propose an optimal approach named EDD-IP to solve this problem exactly with the Integer Programming technique. Then, we propose an <inline-formula><tex-math notation="LaTeX">$O(k)$</tex-math><alternatives><mml:math><mml:mrow><mml:mi>O</mml:mi><mml:mo>(</mml:mo><mml:mi>k</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="xia-ieq2-3010521.gif"/></alternatives></inline-formula>-approximation algorithm named EDD-A for finding approximate solutions to large-scale EDD problems efficiently. EDD-IP and EDD-A are evaluated on a real-world dataset and the results demonstrate that they significantly outperform three representative approaches.
Adaptation Modulates Spike-Phase Coupling Tuning Curve in the Rat Primary Auditory Cortex

Adaptation is an important mechanism that causes a decrease in the neural response both in terms of local field potentials (LFP) and spiking activity. We previously showed this reduction effect in the tuning curve of the primary auditory cortex. Moreover, we revealed that a repeated stimulus reduces the neural response in terms of spike-phase coupling (SPC). In the current study, we examined the effect of adaptation on the SPC tuning curve. To this end, employing the phase-locking value (PLV) method, we estimated the spike-LFP coupling. The data was obtained by a simultaneous recording from four single-electrodes in the primary auditory cortex of 15 rats. We first investigated whether the neural system may use spike-LFP phase coupling in the primary auditory cortex to encode sensory information. Secondly, we investigated the effect of adaptation on this potential SPC tuning. Our data showed that the coupling between spikes’ times and the LFP phase in beta oscillations represents sensory information (different stimulus frequencies), with an inverted bell-shaped tuning curve. Furthermore, we showed that adaptation to a specific frequency modulates SPC tuning curve of the adapter and its neighboring frequencies. These findings could be useful for interpretation of feature representation in terms of SPC and the underlying neural mechanism of adaptation.
MR Imaging of SCA3/MJD

Spinocerebellar ataxia type 3/Machado–Joseph disease (SCA3/MJD) is a progressive autosomal dominantly inherited cerebellar ataxia characterized by the aggregation of polyglutamine-expanded protein within neuronal nuclei in the brain, which can lead to brain damage that precedes the onset of clinical manifestations. Magnetic resonance imaging (MRI) techniques such as morphometric MRI, diffusion tensor imaging (DTI), functional magnetic resonance imaging (fMRI), and magnetic resonance spectroscopy (MRS) have gained increasing attention as non-invasive and quantitative methods for the assessment of structural and functional alterations in clinical SCA3/MJD patients as well as preclinical carriers. Morphometric MRI has demonstrated typical patterns of atrophy or volume loss in the cerebellum and brainstem with extensive lesions in some supratentorial areas. DTI has detected widespread microstructural alterations in brain white matter, which indicate disrupted brain anatomical connectivity. Task-related fMRI has presented unusual brain activation patterns within the cerebellum and some extracerebellar tissue, reflecting the decreased functional connectivity of these brain regions in SCA3/MJD subjects. MRS has revealed abnormal neurochemical profiles, such as the levels or ratios of N-acetyl aspartate, choline, and creatine, in both clinical cases and preclinical cases before the alterations in brain anatomical structure. Moreover, a number of studies have reported correlations of MR imaging alterations with clinical and genetic features. The utility of these MR imaging techniques can help to identify preclinical SCA3/MJD carriers, monitor disease progression, evaluate response to therapeutic interventions, and illustrate the pathophysiological mechanisms underlying the occurrence, development, and prognosis of SCA3/MJD.
Primary Spinal Extradural Hydatid Cyst Causing Spinal Cord Compression: A Case Report

Background: Hydatid disease of the spine is caused by the parasite Echinococcus granulosus, a helminth belonging to the cestode group. Usually located in lungs or liver, hydatidosis of the bone occurs in only 0.5-4% of all hydatid locations, and half of these cases are located in the spine. We report a case of a spinal primary location of a hydatid cyst operated at our department. Case presentation: The patient is a 52-year-old lady who was presenting a year before she consulted dorsalgia followed by a weakness of the lower limbs and urinary retention, spine MRI performed objectified an epidural cystic formation. The patient was operated and the lesion was removed without complications. The pathology study revealed the hydatid nature of the cyst. Conclusion: The spinal hydatid cyst is a rare condition leading to major complications once there is spinal cord compression; early management and total removal of the cyst without rupture are the factors with the best clinical outcome and less recurrence.
A Hybrid Optimization Approach to Design Optimally Tuned PID Controller for an AVR System

The Automatic Voltage Regulator (AVR) system is one of the main controls used in power systems to keep the terminal voltage within the specified range at the generator output. It is aimed to improve the dynamic performance and minimize the steady state error by using different controllers in the AVR system. Optimization algorithms are widely used to optimally tune the parameters of the controller. In this study, Symbiotic organism search (SOS), Particle swarm optimization (PSO) and Whale optimization (WO) algorithms are used to tune the parameters of a PID controller designed for an AVR system. For each algorithm, transient response analysis of the AVR system is examined and performance comparison is made. In addition, PSO-SOS hybrid optimization approach is proposed to reduce the time required for optimization while achieving the same transient response characteristics. The proposed hybrid structure is also compared with the optimization algorithms used alone in terms of both required time and transient response performance. It is concluded that the SOS algorithm provides better results than WO and PSO algorithms. In addition, with the proposed hybrid algorithm the same transient response characteristics are achieved in a shorter time than the SOS algorithm.