Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural and Biochemical Characterization of Chlamydia trachomatis Hypothetical Protein CT263 Supports That Menaquinone Synthesis Occurs through the Futalosine Pathway*

Background: Specific pathways and components for respiration in Chlamydia are poorly understood. Results: The C. trachomatis hypothetical protein CT263 crystal structure displays strong structural similarity with 5′-methylthioadenosine nucleosidase enzymes. Conclusion: Bioinformatic analyses and enzymatic characterization of CT263 suggest menaquinone biosynthesis proceeds through the futalosine pathway in Chlamydiaceae. Significance: Unique structural aspects of the CT263 active site can be leveraged to modify existing transition state inhibitors. The obligate intracellular human pathogen Chlamydia trachomatis is the etiological agent of blinding trachoma and sexually transmitted disease. Genomic sequencing of Chlamydia indicated this medically important bacterium was not exclusively dependent on the host cell for energy. In order for the electron transport chain to function, electron shuttling between membrane-embedded complexes requires lipid-soluble quinones (e.g. menaquionone or ubiquinone). The sources or biosynthetic pathways required to obtain these electron carriers within C. trachomatis are poorly understood. The 1. 58Å crystal structure of C. trachomatis hypothetical protein CT263 presented here supports a role in quinone biosynthesis. Although CT263 lacks sequence-based functional annotation, the crystal structure of CT263 displays striking structural similarity to 5′-methylthioadenosine nucleosidase (MTAN) enzymes. Although CT263 lacks the active site-associated dimer interface found in prototypical MTANs, co-crystal structures with product (adenine) or substrate (5′-methylthioadenosine) indicate that the canonical active site residues are conserved. Enzymatic characterization of CT263 indicates that the futalosine pathway intermediate 6-amino-6-deoxyfutalosine (kcat/Km = 1.8 × 103 m−1 s−1), but not the prototypical MTAN substrates (e.g. S-adenosylhomocysteine and 5′-methylthioadenosine), is hydrolyzed. Bioinformatic analyses of the chlamydial proteome also support the futalosine pathway toward the synthesis of menaquinone in Chlamydiaceae. This report provides the first experimental support for quinone synthesis in Chlamydia. Menaquinone synthesis provides another target for agents to combat C. trachomatis infection.
MatchPad: Interactive Glyph‐Based Visualization for Real‐Time Sports Performance Analysis

Today real‐time sports performance analysis is a crucial aspect of matches in many major sports. For example, in soccer and rugby, team analysts may annotate videos during the matches by tagging specific actions and events, which typically result in some summary statistics and a large spreadsheet of recorded actions and events. To a coach, the summary statistics (e.g., the percentage of ball possession) lacks sufficient details, while reading the spreadsheet is time‐consuming and making decisions based on the spreadsheet in real‐time is thereby impossible. In this paper, we present a visualization solution to the current problem in real‐time sports performance analysis. We adopt a glyph‐based visual design to enable coaching staff and analysts to visualize actions and events “at a glance”. We discuss the relative merits of metaphoric glyphs in comparison with other types of glyph designs in this particular application. We describe an algorithm for managing the glyph layout at different spatial scales in interactive visualization. We demonstrate the use of this technical approach through its application in rugby, for which we delivered the visualization software, MatchPad, on a tablet computer. The MatchPad was used by the Welsh Rugby Union during the Rugby World Cup 2011. It successfully helped coaching staff and team analysts to examine actions and events in detail whilst maintaining a clear overview of the match, and assisted in their decision making during the matches. It also allows coaches to convey crucial information back to the players in a visually‐engaging manner to help improve their performance.
Matrix metalloproteinase-7 expression in colorectal cancer liver metastases: evidence for involvement of MMP-7 activation in human cancer metastases.

PURPOSE Matrix metalloproteinase-7 (MMP-7) is a member of the MMP family, which is overexpressed by some tumor cells and is thought to enhance the tumor metastatic potential. The aim of this study is to examine the MMP-7 expression in the human colorectal cancer (CRC) liver metastases and normal liver tissue using multiple techniques and to determine its association with liver metastases formation. EXPERIMENTAL DESIGN MMP-7 mRNA, protein, and enzymatic levels were determined by reverse transcription-PCR, Western blot analysis, and casein zymography in the specimens of human CRC liver metastases and paired normal liver tissue from 44 patients. The cellular localization of MMP-7 was analyzed by immunohistochemistry. RESULTS Our data reveal that all of the investigated liver metastases samples overexpressed MMP-7 mRNA and protein compared with the normal liver tissue. By zymogram, higher levels of the latent form of MMP-7 were found in 88.6% (39 of 44) liver metastases samples, whereas normal liver tissue exhibited only trace amounts. The activated form of MMP-7 was only found in those in which the pro-MMP-7 was present (n = 39); in contrast, it was not detected in the normal liver tissues. Immunohistochemically, MMP-7 is localized to the cytoplasm of tumor cells, and the strong signal is concentrated in the tumor front areas. CONCLUSIONS Our observations emphasize the important role of MMP-7 production and activation in human CRC liver metastases formation.
Differential gene expression in the pig limbal side population: implications for stem cell cycling, replication, and survival.

PURPOSE To define the molecular signature of limbal SP cells and identify signaling pathways associated with the phenotype of these putative stem cells. METHODS Primary cultures of pig limbal epithelial cells stained with Hoechst 33342 were sorted by flow cytometry into SP and non-SP cells, and purified RNA was processed for microarray analysis with an oligonucleotide spotted array. Expressed transcripts for which SP and non-SP expressions differed by more that 1.5-fold in each paired set and by twofold overall were considered to be differentially expressed. Differential expression was validated by quantitative PCR and immunostaining. Data-mining methods were used to identify cellular processes that are either salient or depressed in the SP cells. RESULTS The microarray identified approximately 9000 distinct, expressed, and identifiable genes. Of those, 382 and 296 were either over- or underexpressed in the SP cells, respectively. Overrepresentation analysis indicated that SP cells are in a low metabolic and biosynthetic state. In addition, a pattern of elevated MXD1, MAXI2, DUSP5, p27/KIP1, and p57/KIP2 and decreased Cyclin D and CDK genes can be expected to slow intrinsic and mitogen-induced G(1)-to-S cell cycle transition. SP cells were also rich in genes associated with stem cell phenotype and genes providing protection against oxidative and/or xenobiotic damage. CONCLUSIONS Microarray analysis of pig limbal SP cells yielded a molecular signature underscoring a phenotype characterized by slow cycling and low metabolic activity. The results provide valuable insights for the preservation and/or replication of epithelial stem cells.
Web Application Development and Quality - Observations from Interviews with Companies in Norway

In this paper we present our findings from a series of interviews with companies developing web applications, investigating how quality issues are managed when developing web applications in a rush-to-market and competitive environment. Our findings suggest that requirement practises are communication intensive, that companies perceive quality attributes related to a good user experience important, and that companies don’t have a clear trade-off situation.
Diversified occupation and communication program versions for persons with acquired neurological damage and multiple disabilities

Abstract Background: Persons with acquired neurological damage and multiple disabilities can be largely dependent on their caregivers, unless technology-aided programs are available to support them. Objective: This study extended the assessment of a technology-aided program recently developed to help these persons achieve independent occupations and communicate effectively. Subjects: Seven participants were involved in the study. Method: The program relied on: (a) a computer for presenting the occupation and communication options (e.g. songs, television, and text messaging); and (b) microswitches for helping the participants access those options with small responses. The program was diversified (in terms of options available and responses/microswitches used) according to the participants’ characteristics and interests, and thus multiple program versions were set up and assessed. Results: The participants successfully used the individualized versions of the program and, accordingly, managed independent occupation and communication (i.e. remaining engaged for means of about 60%–90% of the session times). Conclusion: A technology-aided program can be adapted to persons with acquired neurological damage and multiple disabilities to support their independent occupations and communication engagements.
Regulation of the serotonin transporter in the pathogenesis of irritable bowel syndrome

Serotonin (5-HT) and the serotonin transporter (SERT) have earned a tremendous amount of attention regarding the pathogenesis of irritable bowel syndrome (IBS). Considering that enteric 5-HT is responsible for the secretion, motility and perception of the bowel, the involvement of altered enteric 5-HT metabolism in the pathogenesis of IBS has been elucidated. Higher 5-HT availability is commonly associated with depressed SERT mRNA in patients with IBS compared with healthy controls. The expression difference of SERT between IBS patients and healthy controls might suggest that SERT plays an essential role in IBS pathogenesis, and SERT was expected to be a novel therapeutic target for IBS. Progress in this area has begun to illuminate the complex regulatory mechanisms of SERT in the etiology of IBS. In this article, current insights regarding the regulation of SERT in IBS are provided, including aspects of SERT gene polymorphisms, microRNAs, immunity and inflammation, gut microbiota, growth factors, among others. Potential SERT-directed therapies for IBS are also described. The potential regulators of SERT are of clinical importance and are important for better understanding IBS pathophysiology and therapeutic strategies.
Using test case metrics to predict code quality and effort

This paper reports on an investigation into the use of a design metric (the number of test cases) to predict code quality, development and testing time during the production of functional and object-oriented programs. We report on whether a significant difference exists in the number of test cases for equivalent functional and object-oriented programs as well as determining whether these test cases metrics are correlated with various development and design metrics for the different paradigms. The results of this investigation suggest that test case metrics could be used both as indicators of code quality and to predict the development and testing effort required for functional and object-oriented programs.
HMM Tagging on Coherent vs. Nonsense Text

Linguists would very much like to know whether the two are the same or at least whether the latter subsumes the former. A partial answer, no, is given by the fact that HMM-taggers have not yet been found that tag 100%. The discrepancy could be non-existent (but not yet shown) or could be due to inherent limitations in HMM:s (a question which could in principle be resolved by intractable amounts of brute force). But, the discrepancy could also be due to a wrong understanding part-of-speech tagging in language, or the necessity of semantics. We will look at it from this angle. If it can be shown that taggers perform just as well on text when there is no semantic coherence, this is a good argument that the discrepancy is due to semantics. Tagging is an art over three kinds of data: text, lexicon and tag sequence. Normally, a tagger is given a (semantically coherent) text annotated with a tag sequence. The tag lexicon is either given independently or extracted from the annotated text. In our case, we have done tests varying the said parametres away from what is normally the case.
From States to Secretariats: Delegation in the African Union Peace and Security Council

ABSTRACT African Union member states are formally responsible for deciding on peace operation mandates, yet evidence from the African Union Peace and Security Council indicates that states informally delegate some decision-making autonomy to the commission. Given the commission’s formal responsibilities in implementation, why have member states delegated any decision-making in international security? This article argues that, faced with resource limitations, African Union states surrender some decision-making autonomy to access relevant information, make informed decisions, and strengthen mandates. The argument challenges assertions that delegation does not occur in security decision-making. Findings draw on interviews with African Union ambassadors, commission staff, and other regional organization elites.
Magnetic resonance spectroscopy and gliomas

In vivo proton magnetic resonance spectroscopy (1HMRS) can substantially improve the non-invasive categorization of human brain tumors, especially for gliomas. It provides greater information concerning tumor activity and characterization of the tumor tissue than is possible with MRI techniques alone. Moreover, 1HMRS may ultimately prove to be a highly beneficial modality in the post-irradiation care of patients with brain gliomas. This paper reviews the current status of 1HMRS with the emphasis on its clinical utility in the diagnosis of active tumor processes of gliomas, and its use in planning surgical and radiation therapy interventions and monitoring tumor treatment paradigms.
Children With Medical Complexity: An Emerging Population for Clinical and Research Initiatives

Children with medical complexity (CMC) have medical fragility and intensive care needs that are not easily met by existing health care models. CMC may have a congenital or acquired multisystem disease, a severe neurologic condition with marked functional impairment, and/or technology dependence for activities of daily living. Although these children are at risk of poor health and family outcomes, there are few well-characterized clinical initiatives and research efforts devoted to improving their care. In this article, we present a definitional framework of CMC that consists of substantial family-identified service needs, characteristic chronic and severe conditions, functional limitations, and high health care use. We explore the diversity of existing care models and apply the principles of the chronic care model to address the clinical needs of CMC. Finally, we suggest a research agenda that uses a uniform definition to accurately describe the population and to evaluate outcomes from the perspectives of the child, the family, and the broader health care system.
Precise Torque Control in Flux-Weakening Operation of Surface-Mounted PM Motor with Magnetic Saliencies

Magnetic saliency effect in surface-mounted permanent-magnet (SMPM) motors on the torque control at high speeds is first presented and analyzed in this paper. Measurement of the d- and q-axes impedance difference is performed to prove the existence of the magnetic saliency. Then, the saliency effects on the torque control performance in the flux weakening region are discussed. Based on the developed motor modeling with the reluctance torque, the proposed control adjusts the d- and q-axis current toward the operating point to track the commanded torque. The feasibility of the presented idea is verified by experimental results on a commercial 600-W SMPM motor.
Detection of tumor progression in optic pathway glioma with and without neurofibromatosis type 1.

BACKGROUND We wanted to determine the sensitivity and specificity of serial changes in visual acuity and visual evoked potentials (VEPs) to detect radiological progression of tumor volume in children with optic pathway gliomas. METHODS From a retrospective review of a cohort of 69 patients, 54 patients met inclusion criteria (31 with primary chemotherapy, 4 with primary radiotherapy, and 19 with stable tumor volume and no treatment). Age at presentation ranged from 0.3 to 13 years. Patients were serially followed by MRI, age-corrected visual acuity in log minimum angle of resolution (logMAR), and pattern VEP. Longitudinal data averaged 7.9 years (range 0.5-16 y). Visual assessments were aligned with MRI data within 6-month intervals. Tumor progression was defined by 25% or greater increase in volume. RESULTS Visual acuity in the better eye had poor sensitivity and specificity for detecting tumor volume progression (0.5 and 0.5, respectively). Visual acuity in the worse eye showed worse sensitivity and specificity because false positives (visual decline without tumor progression) were more frequent than true positives (visual decline with tumor progression). VEPs showed slightly better sensitivity and specificity (0.69 and 0.58, respectively). In patients with stable tumors, visual acuity fluctuated ±0.55 logMAR (SD = 0.15) between examinations. VEP amplitude fluctuated -0.74 to 0.48 log units (SD = 0.19) between examinations. CONCLUSIONS Serial changes in visual function do not reliably detect tumor progression. Conversely, tumor progression does not reliably indicate decreased visual function. Objective visual function and serial MRIs are complementary in management of optic pathway gliomas.
Ödül Eksikliği Sendromu

Odul eksikligi sendromu (OES), beynin odullendirme sureclerinde meydana gelen kimyasal dengesizlikler sonucunda bircok davranissal bozukluklarin ortaya ciktigi bir tablo olarak tanimlanmistir. Beyindeki odul sistemi 1950’lerde tesadufen Olds tarafindan kesfedilmistir. Beyindeki odul sisteminin temelini limbik sistem olusturmaktadir. OES’nin bazal gangliyonlar, basta NAC olmak uzere mezolimbik beyin bolgeleri, prefrontal korteks, hipotalamus ve amigadala gibi limbik sistemin onemli parcalarini da kapsayan genis bir beyin alaninda meydana gelen cesitli bozukluklarla iliskili oldugu artik bilinmektedir. Limbik sistem, temel duygulari ve davranislari kontrol etmekte ve haz algisina temel olusturmaktadir. Ayrica hafiza ve ogrenme, cinsel davranis, motivasyon ve beslenme gibi onemli davranislari da kontrol etmektedir. Dopamin basta olmak uzere bircok norotransmitterin OES patogenezinde rol aldigi belirtilmektedir. OES’nin alkol bagimliligi, madde kotuye kullanimi, sigara kullanimi, kompulsif asiri yeme, obezite, dikkat eksikligi hiperaktivite bozuklugu, Tourette bozuklugu, kontrolsuz internet kullanimi ve patolojik kumar oynama gibi bozukluklar ile iliskisi ve norobiyolojik ortak yollari da calismalarla gosterilmistir. Bu makalede, OES ile ilgili bilgilerin ve calismalarin literatur esliginde tartisilmasi amaclandi.Anahtar Kelimeler: Odul eksikligi sendromu, odul yolagi, bagimlilik.Baginti beyani: Yazarlar bu makale ile ilgili olarak herhangi bir cikar catismasi bildirmemislerdir.Reward deficiency syndrome (RDS) has been described as a statement resulted in many behavioral disorders due to chemical imbalances in the brain’s reward system. This system has been incidentally discovered by Olds in 1950. Limbic system is the basis of that system. It is now known that RDS is associated with a variety of disorders occur in a wide area of the brain covering the important parts of the limbic-system as basal ganglia, including the mesolimbic regions of the brain; particularly NAC, the prefrontal cortex, hypothalamus and amygdala. The limbic system, the basis for the perception of pleasure, controls basic emotions and behaviors. It is stated that many neurotransmitters, especially dopamine play a role in the pathogenesis of RDS. Furthermore, it also controls important behaviors including memory and learning, sexual behavior, motivation and nutrition. It is reported that RDS has neurobiological common paths and relation with alcohol addiction, substance abuse, smoking, compulsive overeating, obesity, attention deficit and hyperactivity, Tourette’s disorder, uncontrolled internet usage and pathological gambling. RDS-related information and studies discussed in the literature were evaluated in this article.Key Words: Reward deficiency syndrome, reward cascade, dependenceDeclaration of interest: The authors reported no conflict of interest related to this article.
Exploiting response models: optimizing cross-sell and up-sell opportunities in banking

The banking industry regularly mounts campaigns to improve customer value by offering new products to existing customers. In recent years this approach has gained significant momentum because of the increasing availability of customer data and the improved analysis capabilities in data mining. Typically, response models based on historical data are used to estimate the probability of a customer purchasing an additional product and the expected return from that additional purchase. Even with these computational improvements and accurate models of customer behavior, the problem of efficiently using marketing resources to maximize the return on marketing investment is a challenge. This problem is compounded because of the capability to launch multiple campaigns through several distribution channels over multiple time periods. The combination of alternatives creates a complicated array of possible actions. This paper presents a solution that answers the question of what products, if any, to offer to each customer in a way that maximizes the marketing return on investment. The solution is an improvement over the usual approach of picking the customers that have the largest expected value for a particular product because it is a global maximization from the viewpoint of the bank and allows for the effective implementation of business constraints across customers and business units. The approach accounts for limited resources, multiple sequential campaigns, and other business constraints. Furthermore, the solution provides insight into the cost of these constraints, in terms of decreased profits, and thus is an effective tool for both tactical campaign execution and strategic planning.