Miracle-dz/UniFAR-FTUs huggingface dataset:
Components of the Calcium-Calcineurin Signaling Pathway in Fungal Cells and Their Potential as Antifungal Targets

ABSTRACT In recent years, the emergence of fungal resistance has become frequent, partly due to the widespread clinical use of fluconazole, which is minimally toxic and effective in the prevention and treatment of Candida albicans infections. The limited selection of antifungal drugs for clinical fungal infection therapy has prompted us to search for new antifungal drug targets. Calcium, which acts as the second messenger in both mammals and fungi, plays a direct role in controlling the expression patterns of its signaling systems and has important roles in cell survival. In addition, calcium and some of the components, mainly calcineurin, in the fungal calcium signaling pathway mediate fungal resistance to antifungal drugs. Therefore, an overview of the components of the fungal calcium-calcineurin signaling network and their potential roles as antifungal targets is urgently needed. The calcium-calcineurin signaling pathway consists of various channels, transporters, pumps, and other proteins or enzymes. Many transcriptional profiles have indicated that mutant strains that lack some of these components are sensitized to fluconazole or other antifungal drugs. In addition, many researchers have identified efficient compounds that exhibit antifungal activity by themselves or in combination with antifungal drugs by targeting some of the components in the fungal calcium-calcineurin signaling pathway. This targeting disrupts Ca2+ homeostasis, which suggests that this pathway contains potential targets for the development of new antifungal drugs.
Integrated surface model optimization for freehand three-dimensional echocardiography

The major obstacle of three-dimensional (3-D) echocardiography is that the ultrasound image quality is too low to reliably detect features locally. Almost all available surface-finding algorithms depend on decent quality boundaries to get satisfactory surface models. We formulate the surface model optimization problem in a Bayesian framework, such that the inference made about a surface model is based on the integration of both the low-level image evidence and the high-level prior shape knowledge through a pixel class prediction mechanism. We model the probability of pixel classes instead of making explicit decisions about them. Therefore, we avoid the unreliable edge detection or image segmentation problem and the pixel correspondence problem. An optimal surface model best explains the observed images such that the posterior probability of the surface model for the observed images is maximized. The pixel feature vector as the image evidence includes several parameters such as the smoothed grayscale value and the minimal second directional derivative. Statistically, we describe the feature vector by the pixel appearance probability model obtained by a nonparametric optimal quantization technique. Qualitatively, we display the imaging plane intersections of the optimized surface models together with those of the ground-truth surfaces reconstructed from manual delineations. Quantitatively, we measure the projection distance error between the optimized and the ground-truth surfaces. In our experiment, we use 20 studies to obtain the probability models offline. The prior shape knowledge is represented by a catalog of 86 left ventricle surface models. In another set of 25 test studies, the average epicardial and endocardial surface projection distance errors are 3.2 /spl plusmn/ 0.85 mm and 2.6 /spl plusmn/ 0.78 mm, respectively.
Efficient model-based quantification of left ventricular function in 3-D echocardiography

Quantitative functional analysis of the left ventricle plays a very important role in the diagnosis of heart diseases. While in standard two-dimensional echocardiography this quantification is limited to rather crude volume estimation, three-dimensional (3-D) echocardiography not only significantly improves its accuracy but also makes it possible to derive valuable additional information, like various wall-motion measurements. In this paper, we present a new efficient method for the functional evaluation of the left ventricle from 3-D echographic sequences. It comprises a segmentation step that is based on the integration of 3-D deformable surfaces and a four-dimensional statistical heart motion model. The segmentation results in an accurate 3-D + time left ventricle discrete representation. Functional descriptors like local wall-motion indexes are automatically derived from this representation. The method has been successfully tested both on electrocardiography-gated and real-time 3-D data. It has proven to be fast, accurate, and robust.
Candida albicans Induces Arginine Biosynthetic Genes in Response to Host-Derived Reactive Oxygen Species

ABSTRACT The interaction of Candida albicans with phagocytes of the host's innate immune system is highly dynamic, and its outcome directly impacts the progression of infection. While the switch to hyphal growth within the macrophage is the most obvious physiological response, much of the genetic response reflects nutrient starvation: translational repression and induction of alternative carbon metabolism. Changes in amino acid metabolism are not seen, with the striking exception of arginine biosynthesis, which is upregulated in its entirety during coculture with macrophages. Using single-cell reporters, we showed here that arginine biosynthetic genes are induced specifically in phagocytosed cells. This induction is lower in magnitude than during arginine starvation in vitro and is driven not by an arginine deficiency within the phagocyte but instead by exposure to reactive oxygen species (ROS). Curiously, these genes are induced in a narrow window of sublethal ROS concentrations. C. albicans cells phagocytosed by primary macrophages deficient in the gp91phox subunit of the phagocyte oxidase do not express the ARG pathway, indicating that the induction is dependent on the phagocyte oxidative burst. C. albicans arg pathway mutants are retarded in germ tube and hypha formation within macrophages but are not notably more sensitive to ROS. We also find that the ARG pathway is regulated not by the general amino acid control response but by transcriptional regulators similar to the Saccharomyces cerevisiae ArgR complex. In summary, phagocytosis induces this single amino acid biosynthetic pathway in an ROS-dependent manner.
Performance analysis in unstructured overlays

In this paper, we propose a performance analysis model to study the reach-ability in unstructured overlay networks. Given a node's degree distribution and a network size, n, the model describes the flooding query pattern in a P2P network accurately. Also, we prove that in such an overlay network, the average distance between any two hosts is limited by O(log N). This model is simple and accurate, and therefore is a very useful tool in exploring many properties of massive overlay networks. It can be applied to P2P based content distribution networks and ad hoc wireless networks, for example.
Novel Bilobe Components in Trypanosoma brucei Identified Using Proximity-Dependent Biotinylation

ABSTRACT The trypanosomes are a family of parasitic protists of which the African trypanosome, Trypanosoma brucei, is the best characterized. The complex and highly ordered cytoskeleton of T. brucei has been shown to play vital roles in its biology but remains difficult to study, in large part owing to the intractability of its constituent proteins. Existing methods of protein identification, such as bioinformatic analysis, generation of monoclonal antibody panels, proteomics, affinity purification, and yeast two-hybrid screens, all have drawbacks. Such deficiencies—troublesome proteins and technical limitations—are common not only to T. brucei but also to many other protists, many of which are even less well studied. Proximity-dependent biotin identification (BioID) is a recently developed technique that allows forward screens for interaction partners and near neighbors in a native environment with no requirement for solubility in nonionic detergent. As such, it is extremely well suited to the exploration of the cytoskeleton. In this project, BioID was adapted for use in T. brucei. The trypanosome bilobe, a discrete cytoskeletal structure with few known protein components, represented an excellent test subject. Use of the bilobe protein TbMORN1 as a probe resulted in the identification of seven new bilobe constituents and two new flagellum attachment zone proteins. This constitutes the first usage of BioID on a largely uncharacterized structure, and demonstrates its utility in identifying new components of such a structure. This remarkable success validates BioID as a new tool for the study of unicellular eukaryotes in particular and the eukaryotic cytoskeleton in general.
Cognitive Stimulation for Portuguese Older Adults With Cognitive Impairment

Although some studies point to cognitive stimulation as a beneficial therapy for older adults with cognitive impairments, this area of research and practice is still lacking dissemination and is underrepresented in many countries. Moreover, the comparative effects of different intervention durations remain to be established and, besides cognitive effects, pragmatic parameters, such as cost-effectiveness and experiential relevance to participants, are seldom explored. In this work, we present a randomized controlled wait-list trial evaluating 2 different intervention durations (standard = 17 vs brief = 11 sessions) of a cognitive stimulation program developed for older adults with cognitive impairments with or without dementia. 20 participants were randomly assigned to the standard duration intervention program (17 sessions, 1.5 months) or to a wait-list group. At postintervention of the standard intervention group, the wait-list group crossed over to receive the brief intervention program (11 sessions, 1 month). Changes in neuropsychological, functionality, quality of life, and caregiver outcomes were evaluated. Experience during intervention and costs and feasibility were also evaluated. The current cognitive stimulation programs (ie, standard and brief) showed high values of experiential relevance for both intervention durations. High adherence, completion rates, and reasonable costs were found for both formats. Further studies are needed to definitively establish the potential efficacy, optimal duration, cost-effectiveness, and experiential relevance for participants of cognitive intervention approaches.
Rosuvastatin: The Most Efficient Treatment Option For Patients With Dyslipidemia

It has been unequivocally proven that lowering serum cholesterol reduces the risk of cardiovascular disease. For every 1% reduction in serum total cholesterol, the risk of coronary heart disease is lowered by 2%, and with a 1 mmol/l reduction in low-density lipoprotein cholesterol (LDL-C), the 5-year incidence of major coronary events, coronary revascularization and stroke, is reduced by approximately one fifth. The risk of cardiovascular disease increases linearly with increasing serum cholesterol. Thus, people with high cholesterol levels have the highest risk, but in any population the largest number of cardiovascular events and deaths will occur in people whose serum cholesterol is only marginally elevated, as they form the largest pool of the background population. Unfortunately, a significant number of patients requiring lipid-modifying therapy remain untreated or suboptimally treated, with almost half failing to reach current guideline targets for LDL-C, and therefore remaining at unacceptably high.
SPM1 Stabilizes Subpellicular Microtubules in Toxoplasma gondii

ABSTRACT We have identified two novel proteins that colocalize with the subpellicular microtubules in the protozoan parasite Toxoplasma gondii and named these proteins SPM1 and SPM2. These proteins have basic isoelectric points and both have homologs in other apicomplexan parasites. SPM1 contains six tandem copies of a 32-amino-acid repeat, whereas SPM2 lacks defined protein signatures. Alignment of Toxoplasma SPM2 with apparent Plasmodium SPM2 homologs indicates that the greatest degree of conservation lies in the carboxy-terminal half of the protein. Analysis of Plasmodium homologs of SPM1 indicates that while the central 32-amino-acid repeats have expanded to different degrees (7, 8, 9, 12, or 13 repeats), the amino- and carboxy-terminal regions remain conserved. In contrast, although the Cryptosporidium SPM1 homolog has a conserved carboxy tail, the five repeats are considerably diverged, and it has a smaller amino-terminal domain. SPM1 is localized along the full length of the subpellicular microtubules but does not associate with the conoid or spindle microtubules. SPM2 has a restricted localization along the middle region of the subpellicular microtubules. Domain deletion analysis indicates that four or more copies of the SPM1 repeat are required for localization to microtubules, and the amino-terminal 63 residues of SPM2 are required for localization to the subpellicular microtubules. Gene deletion studies indicate that neither SPM1 nor SPM2 is essential for tachyzoite viability. However, loss of SPM1 decreases overall parasite fitness and eliminates the stability of subpellicular microtubules to detergent extraction.
Escherichia coli and Salmonella 2000 : the View From Here MOSELIO SCHAECHTER AND THE VIEW FROM HERE

In 1995, an editorial in Science (267:1575) commented that predictions made some 25 years previously regarding “Biology and the Future of Man” were largely fulfilled but that “the most revolutionary and unexpected findings were not predicted. ” We would be glad to do as well! As we stated at the beginning, our work as editors of the Escherichia coli and Salmonella book did not endow us with special powers of prophecy but it does permit us to express our excitement for the future. In our opinion, E. coli and S. enterica will continue to play a central role in biological research. This is not because they are intrinsically more interesting than any other bacteria, as we believe that all bacteria are equally interesting. However, knowledge builds on knowledge, and it is here that these two species continue to have a large edge not only over other microorganisms but also, for some time to come, over all other forms of life. It is interesting in this connection that biotechnology, having made detours through other microorganisms, always seems to return to E. coli.
Packet Scheduling Algorithm for Non-real-time Service with Soft QoS Requirement in Mobile Broadband Wireless Access System

In this paper, a packet scheduling algorithm for non-real-time service is considered, with a soft QoS requirements, which allows for degrading the QoS level, e.g., typically the packet delay, whenever necessary, in mobile broadband wireless internet access systems. This is designed to optimally trade off system throughput and delay performance, depending on soft QoS requirements, as opposed to most existing packet scheduling algorithms for non-real-time service, which are simply designed to maximize the system throughput without a delay constraint in any sense. The proposed adaptive exponential scheduling algorithm intentionally introduces additional delay to some users under bad channel conditions, allowing for serving users only under good channel conditions, as long as the resulting QoS degradation is acceptable for non-real-time service users. The results from system-level simulation demonstrate that the system capacity can be significantly increased, over existing algorithms, by as much as 65%, using the adaptive exponential scheduling algorithm, and satisfying the given QoS level requirements.
Incremental Learning With Selective Memory (ILSM): Towards Fast Prostate Localization for Image Guided Radiotherapy

Image-guided radiotherapy (IGRT) requires fast and accurate localization of the prostate in 3-D treatment-guided radiotherapy, which is challenging due to low tissue contrast and large anatomical variation across patients. On the other hand, the IGRT workflow involves collecting a series of computed tomography (CT) images from the same patient under treatment. These images contain valuable patient-specific information yet are often neglected by previous works. In this paper, we propose a novel learning framework, namely incremental learning with selective memory (ILSM), to effectively learn the patient-specific appearance characteristics from these patient-specific images. Specifically, starting with a population-based discriminative appearance model, ILSM aims to “personalize” the model to fit patient-specific appearance characteristics. The model is personalized with two steps: backward pruning that discards obsolete population-based knowledge and forward learning that incorporates patient-specific characteristics. By effectively combining the patient-specific characteristics with the general population statistics, the incrementally learned appearance model can localize the prostate of a specific patient much more accurately. This work has three contributions: 1) the proposed incremental learning framework can capture patient-specific characteristics more effectively, compared to traditional learning schemes, such as pure patient-specific learning, population-based learning, and mixture learning with patient-specific and population data; 2) this learning framework does not have any parametric model assumption, hence, allowing the adoption of any discriminative classifier; and 3) using ILSM, we can localize the prostate in treatment CTs accurately (DSC ~ 0.89) and fast ( ~ 4 s), which satisfies the real-world clinical requirements of IGRT.
Beneficial Effect of Anti-obese Herbal Medicine Mixture with Chitosan in High Fat Diet-induced Obese Rats

This study was carried out to investigate the dietary effects of chitosan mixture (CM), an herbal medicine mixture with Sukjihwang (HS), and CM containing HS (CHS) on obesity in an induced obese model of rats fed high-fat only (HF), in which supplemented diets of 5% CM (HCM), 5% HS (HHS), or 2.5% CM-2.5% HS (HCH) was tested for 6 weeks. Body weight gains, obesity indexes, and body fat contents in the experimental groups (HCM, HHS, HCH) were decreased compared with HF group. The levels of serum triglyceride, total lipid, total cholesterol and LDL-cholesterol in the experimental groups were markedly decreased, however HDL-cholesterol levels in the experimental groups were slightly increased compared with HF group. In addition, although serum ALT and AST activity, and relative organ weights were lower than those of HF group, serum albumin contents were not significantly different in all experimental groups including the normal control group (NC). In conclusion, there are improved effects on obesity in the obese model of animals with all experimental diets supplementations, and the improvement degrees on obesity depend on the content and compositions of the herbal medicine mixture. Further study is needed on the anti-obesity mechanism of these diets.
Nebi-Musa: A Therapeutic Communuity for Drug Addicts in a Muslim Context

'Maqam Al-Nebi Musa' an eight-centuries old Muslim religious site located between Jerusalem and Jericho, is analyzed as a drug rehabilitation therapeutic community (TC). Male recovering addicts visit the site for upwards of 6 months, and follow a five-stage therapeutic program. The TC was initiated by, and is led by, five Sufi mystics, themselves former addicts. Its therapeutic significance is analyzed in the context of Muslim religious teaching and rituals, traditional Arab culture, and community and familial support systems.
New Genome Sequence of an Echinacea purpurea Endophyte, Arthrobacter sp. Strain EpSL27, Able To Inhibit Human-Opportunistic Pathogens

ABSTRACT We announce here the draft genome sequence of Arthrobacter sp. strain EpSL27, isolated from the stem and leaves of the medicinal plant Echinacea purpurea and able to inhibit human-pathogenic bacterial strains. The genome sequencing of this strain may lead to the identification of genes involved in the production of antimicrobial molecules.
HbA1c and Lower Extremity Amputation Risk in Patients With Diabetes

In this meta-analysis, we aimed to assess glycosylated hemoglobin (HbA1c) level and lower extremity amputation (LEA) risk in patients with diabetes. Systematic computerized searches of the PubMed and Web of Knowledge were performed. We compared HbA1c level between groups with LEA and without LEA by meta-analysis; we also examined the dose–response relationship between HbA1c level and LEA risk. Sixteen studies were included in the meta-analysis. Eleven studies with 43 566 patients compared HbA1c between groups with and without LEA. The mean HbA1c (%) ranged from 8.3 to 12.5 in the group with LEA and from 7.4 to 11.3 in the group without LEA. The pooled weighted mean difference was 1.110 (95% confidence interval = 0.510-1.709; Z = 3.63, P = .008). The funnel plot was symmetrical, and Begg’s test (z = 0.00, P = 1.000) and Egger’s test (t = −0.02, P = .984) suggested no significant publication bias. Six studies with 109 933 patients included in the dose–response meta-analysis. The LEA incidence ranged from 0.3% to 14.6% between different HbA1c levels. Dose–response meta-analysis showed statistically significant association between HbA1c and LEA risk (χ2 = 65.51, P = .000). In linear model, the odds ratio for LEA incidence was 1.229 (95% confidence interval = 1.169-1.292) for every 1% HbA1c increase. In the spline model, the odds ratio of LEA risk increased with HbA1c levels, especially when HbA1c ranged from 5% to 9%. Our meta-analysis indicates that high level of HbA1c is an important risk factor for LEA in patients with diabetes. This evidence supports the strategy for lowering glucose levels to reduce amputation in patients with diabetes.
Complete Genome Sequence of Xanthomonas citri pv. anacardii Strain IBSBF2579 from Brazil

ABSTRACT The bacterium Xanthomonas citri pv. anacardii is the agent of angular leaf spot of the cashew tree (Anacardium occidentale L.). The complete genome sequencing of the strain IBSBF2579 was done on an Illumina HiSeq 2500 platform. The de novo assembly of the X. citri pv. anacardii strain IBSBF2579 genome yielded 133 contigs, with a size of 5,329,247 bp and a G+C content of 64.03%. The prediction was performed by GeneMarkS and the automatic annotation by Rapid Annotations using Subsystems Technology (RAST), with 4,406 identified genes.
HOUDINI: make that urinary catheter disappear – nurse-led protocol

Urinary tract infections (UTI) are the most common healthcare associated infection in acute hospitals. The risk of developing a catheter associated urinary tract infection (CAUTI) increases the longer a urinary catheter remains in situ. Although criteria for insertion and continuation are known, there are few tools to aid with removal decision making. This pilot study evaluated the effectiveness of a nurse-led HOUDINI urinary catheter removal protocol in reducing the number of days of urinary catheter usage, thus potentially reducing the associated risk of a CAUTI.
Tumor Versus Tumor-Associated Macrophages: How Hot is the Link?

One of the functions of macrophages is to provide a defense mechanism against tumor cells. In contrast, tumor-associated macrophages (TAMs), which represent the major inflammatory component of the stroma of many tumors, are associated with tumor progression and metastasis. TAMs, in contrast with normal macrophages, exhibit the M2 phenotype, and thereby exhibit pro-tumoral functions, including angiogenesis and matrix remodeling. This review will discuss the role of TAMs in tumor progression and provide an overview of their significant part in tumor metastasis and angiogenesis.