Miracle-dz/UniFAR-FTUs huggingface dataset:
Fitness consequences of a regulatory polymorphism in a seasonal environment

Gene regulation is commonly assumed to have evolved in response to environmental variability. Although tightly regulated in Escherichia coli strain K12, transcriptional control of arginine biosynthesis is deregulated in strain B. Caused by a single amino acid replacement in the arginine repressor, these contrasting regulatory strategies result in a fitness tradeoff. The K12 repressor is selectively favored in the presence of arginine and disfavored in its absence. In environments that cycle between high and low arginine, short seasons favor the K12 allele, whereas long seasons favor the B allele. Unexpectedly then, deregulated expression is adaptive in some seasonal habitats.
Thiol Peroxidase Protects Salmonella enterica from Hydrogen Peroxide Stress In Vitro and Facilitates Intracellular Growth

ABSTRACT At present, Salmonella is considered to express two peroxiredoxin-type peroxidases, TsaA and AhpC. Here we describe an additional peroxiredoxin, Tpx, in Salmonella enterica and show that a single tpx mutant is susceptible to exogenous hydrogen peroxide (H2O2), that it has a reduced capacity to degrade H2O2 compared to the ahpCF and tsaA mutants, and that its growth is affected in activated macrophages. These results suggest that Tpx contributes significantly to the sophisticated defense system that the pathogen has evolved to survive oxidative stress.
Tamoxifen therapy benefit predictive signature coupled with prognostic signature of post-operative recurrent risk for early stage ER+ breast cancer

Two types of prognostic signatures for predicting recurrent risk of ER+ breast cancer patients have been developed: one type for patients accepting surgery only and another type for patients receiving post-operative tamoxifen therapy. However, the first type of signature cannot distinguish high-risk patients who cannot benefit from tamoxifen therapy, while the second type of signature cannot identify patients who will be at low risk of recurrence even if they accept surgery only. In this study, we proposed to develop two coupled signatures to solve these problems based on within-sample relative expression orderings (REOs) of gene pairs. Firstly, we identified a prognostic signature of post-operative recurrent risk using 544 samples of ER+ breast cancer patients accepting surgery only. Then, applying this drug-free signature to 840 samples of patients receiving post-operative tamoxifen therapy, we recognized 553 samples of patients who would have been at high risk of recurrence if they had accepted surgery only and used these samples to develop a tamoxifen therapy benefit predictive signature. The two coupled signatures were validated in independent data. The signatures developed in this study are robust against experimental batch effects and applicable at the individual levels, which can facilitate the clinical decision of tamoxifen therapy.
Identification and Visualization of Corporate Structure: A Preliminary Investigation

Interpreting corporate reports has largely remained the domain of accountants, corporate lawyers and analysts. As we have unfortunately witnessed, even the best representatives of these groups can be mislead by opacity in reporting and corporate structures. As mergers and acquisitions, foreign investment and other activities complicate the corporate landscape, constituents of all skill levels should be entitled to clear explanations of events and decisions that potentially affect shareholder value. We are actively in the process of developing several approaches and tools to automate the extraction of certain types of corporate information and to present this data in a useful fashion. In this paper we will outline the major steps involved in automating the extraction of corporate subsidiary information and will demonstrate several approaches for visualizing subsidiaries and their relationships.
Increasing the Diagnostic Value of Evoked Potentials in Multiple Sclerosis by Quantitative Topographic Analysis of Multichannel Recordings

Summary: This study presents a method to record and analyze multichannel visual-evoked potential (VEP) and somatosensory-evoked potential (SEP) in an objective, automatic, and quantitative manner. The intention of this study was to assess their diagnostic value in multiple sclerosis (MS). A 256-channel VEP and SEP were recorded in 44 healthy subjects, 26 patients with MS, and 20 patients with other neurologic diseases. Topographic pattern recognition methods were applied and a normative database was established. Z-score statistics allowed identifying the number of subjects with significant abnormal values in each group. These values were compared with conventional single-channel waveform analysis. The diagnostic value of the new measures for MS reached a sensitivity of 72% and a specificity of 100% for the VEP, which was significantly higher than the conventional analysis. For the SEP, the specificity was also high (93%) but the sensitivity remained low as in the conventional analysis (30%). The quantitative topographic analysis of multichannel VEP revealed high-diagnostic sensitivity and specificity for MS. Moreover, the method reliably identified the most dominant VEP and SEP components in the healthy subject group. The results indicate that objective topographic analysis of multichannel recordings increase the value of VEP as surrogate marker for MS.
Multi-layer perceptron training algorithms for pattern recognition of myoelectric signals

A challenge in using myoelectric signals in control of motorised prostheses is achieving effective signal pattern recognition and robust classification of intended motions. In this paper, the performance of Matlab's Multi-layer Perceptron (MLP) backpropogation training algorithms in motion classification were assessed. The test and evaluation platform used was “BioPatRec”, a Matlab-based open-source prosthetic control development environment, together with algorithms sourced from Matlab's neural network toolbox. The algorithms were used to interpret multielectrode myoelectric signals for motion classification, with the aim of finding the best performing algorithm and network model. The results showed that Matlab's trainlm and trainrp algorithms could achieve a higher accuracy than other tested MLP training algorithms (94.13 ± 0.037% and 91.09 ± 0.047%, respectively). Discussion of these results investigates significant features to obtain the highest performance.
Intimate Partner Sexual Assault: Traumatic Injuries, Psychological Symptoms, and Perceived Social Reactions

OBJECTIVE: To compare the consequences of sexual assault based on the relationship of the woman to her named assailant. METHODS: From January 2008 to March 2011, we conducted an observational and prospective study of females older than age 15 years who were examined at a sexual assault referral center. Data were collected and comparisons made between groups based on the victim's relationship to her named assailant: a current or former intimate partner (grouped as intimate partner), stranger, or acquaintance. Data were collected regarding the patients, assailants, and type of assault. At a 1-month follow-up examination, we evaluated clinical findings and reported reactions by the victim's friends, family, and acquaintances. We conducted descriptive analyses and searched for overall and pairwise differences among groups. RESULTS: There were 797 individuals seen during this time period. Thirty of the victims were male and were excluded from the study, leaving 767 females older than 15 years of age, 294 (38%) of whom attended the follow-up consultation. Simultaneous physical and sexual assaults were more frequent in intimate partner assaults than in assaults by unknown individuals or acquaintances: 55% (95% confidence interval [CI] 49–61) compared with 31% (95% CI 26–36) and 32% (95% CI 26–38; P<.001). One month after the initial examination, psychological trauma was noted in 92% of the patients and was evenly distributed among the three groups. Reactions from family members were similar for victims assaulted by intimate partners and other victims. CONCLUSION: Sexual assault by an intimate partner is associated with higher rates of extragenital trauma and similar rates of psychologic trauma and disrupted other relationships as that associated with assaults by strangers or acquaintances. Sexual assaults by intimate partners should be viewed as serious as assault by other assailants by law enforcement, the judiciary, and the public.
A probabilistic method for the operation of three-phase unbalanced active distribution networks

This study proposes a probabilistic multi-objective optimisation method for the operation of three-phase distribution networks incorporating active network management (ANM) schemes including coordinated voltage control and adaptive power factor control. The proposed probabilistic method incorporates detailed modelling of three-phase distribution network components and considers different operational objectives. The method simultaneously minimises the total energy losses of the lines from the point of view of distribution network operators and maximises the energy generated by photovoltaic (PV) cells considering ANM schemes and network constraints. Uncertainties related to intermittent generation of PVs and load demands are modelled by probability density functions (PDFs). Monte Carlo simulation method is employed to use the generated PDFs. The problem is solved using ɛ-constraint approach and fuzzy satisfying method is used to select the best solution from the Pareto optimal set. The effectiveness of the proposed probabilistic method is demonstrated with IEEE 13- and 34-bus test feeders.
Design of low density parity check codes for turbo multiuser detection

We consider the analysis and design of low density parity check (LDPC) codes for turbo multiuser detection in multipath code-division multiple-access (CDMA) channels. We develop techniques to compute the probability density function (pdf) of the extrinsic information at the output of the multiuser detector. We show that the output pdf can be modeled as symmetric Gaussian for synchronous CDMA in additive white Gaussian noise (AWGN) channel and as a mixture of symmetric Gaussian densities for asynchronous CDMA system over fading channel. The expectation-maximization (EM) algorithm can be used to compute the parameters of this mixture. Using these techniques, we are able to accurately compute the thresholds for LDPC codes and design good irregular LDPC codes. Simulation results are in good agreement with the computed thresholds and the designed irregular LDPC codes outperform regular ones significantly.
Cybersemiotics: a New Interdisciplinary Development Applied to the Problems of Knowledge Organisation and Document Retrieval in Information Science

This article is a contribution to the development of a comprehensive interdisciplinary theory of LIS in the hope of giving a more precise evaluation of its current problems. The article describes an interdisciplinary framework for lis, especially information retrieval (IR), in a way that goes beyond the cognitivist ‘information processing paradigm’. The main problem of this paradigm is that its concept of information and language does not deal in a systematic way with how social and cultural dynamics set the contexts that determine the meaning of those signs and words that are the basic tools for the organisation and retrieving of documents in LIS. The paradigm does not distinguish clearly enough between how the computer manipulates signs and how librarians work with meaning in practice when they design and run document mediating systems. The ‘cognitive viewpoint’ of Ingwersen and Belkin makes clear that information is not objective, but rather only potential, until it is interpreted by an individual mind with its own internal mental world view and purposes. It facilitates further study of the social pragmatic conditions for the interpretation of concepts. This approach is not yet fully developed. The domain analytic paradigm of Hjorland and Albrechtsen is a conceptual realisation of an important aspect of this area. In the present paper we make a further development of a non‐reductionistic and interdisciplinary view of information and human social communication by texts in the light of second‐order cybernetics, where information is seen as ‘a difference which makes a difference’ for a living autopoietic (self‐organised, self‐creating) system. Other key ideas are from the semiotics of Peirce and also Warner. This is the understanding of signs as a triadic relation between an object, a representation and an interpretant. Information is the interpretation of signs by living, feeling, self‐organising, biological, psychological and social systems. Signification is created and con‐trolled in a cybernetic way within social systems and is communicated through what Luhmann calls generalised media, such as science and art. The modern socio‐linguistic concept ‘discourse communities’ and Wittgenstein's ‘language game’ concept give a further pragmatic description of the self‐organising system's dynamic that determines the meaning of words in a social context. As Blair and Liebenau and Backhouse point out in their work it is these semantic fields of signification that are the true pragmatic tools of knowledge organ‐isation and document retrieval. Methodologically they are the first systems to be analysed when designing document mediating systems as they set the context for the meaning of concepts. Several practical and analytical methods from linguistics and the sociology of knowledge can be used in combination with standard methodology to reveal the significant language games behind document mediation.
Sterol transfer, PI4P consumption, and control of membrane lipid order by endogenous OSBP

The network of proteins that orchestrate the distribution of cholesterol among cellular organelles is not fully characterized. We previously proposed that oxysterol‐binding protein (OSBP) drives cholesterol/PI4P exchange at contact sites between the endoplasmic reticulum (ER) and the trans‐Golgi network (TGN). Using the inhibitor OSW‐1, we report here that the sole activity of endogenous OSBP makes a major contribution to cholesterol distribution, lipid order, and PI4P turnover in living cells. Blocking OSBP causes accumulation of sterols at ER/lipid droplets at the expense of TGN, thereby reducing the gradient of lipid order along the secretory pathway. OSBP consumes about half of the total cellular pool of PI4P, a consumption that depends on the amount of cholesterol to be transported. Inhibiting the spatially restricted PI4‐kinase PI4KIIIβ triggers large periodic traveling waves of PI4P across the TGN. These waves are cadenced by long‐range PI4P production by PI4KIIα and PI4P consumption by OSBP. Collectively, these data indicate a massive spatiotemporal coupling between cholesterol transport and PI4P turnover via OSBP and PI4‐kinases to control the lipid composition of subcellular membranes.
Intestinal carriage of P fimbriated Escherichia coli and the susceptibility to urinary tract infection in young children.

This prospective study analyzed the intestinal carriage of P fimbriated Escherichia coli as a host susceptibility factor in urinary tract infection (UTI). P fimbriation was defined by the pap and G adhesin (papG1A2, prsGJ96) genotypes. Children with UTI carried pap+ E. coli in the fecal flora more often than healthy controls both at diagnosis (86% vs. 29%) and during infection-free intervals (approximately 40%; P < .01). P1 blood group-positive children carried pap+ E. coli in the fecal flora more often (88%) than those with P2 blood group (40%; P < .05). A pap+ E. coli strain caused UTI in 53 of 55 patients who carried both pap+ and pap- strains in their fecal flora. These results suggest that persons who develop UTI have an increased tendency to carry pap+ E. coli in the large intestine and that these pap+ E. coli cause UTI more often than pap E. coli strains in the fecal flora of the same host.
Evaluation of effect of laser etching on shear bond strength between maxillofacial silicone and acrylic resin subjected to accelerated aging process

Objective: Maxillofacial prosthesis are supported by implants, require a retentive matrix to retain the suprastructure. The retentive matrix is made up of acrylic resin to which the silicone prostheses are anchored by micro-mechanical bond. The delamination of silicone away from the retentive matrix is a persisting problem in implant-supported maxillofacial prosthesis. Aim: This study aimed to evaluate the effect of laser etching on the shear bond strength (BS) between acrylic resin and maxillofacial silicone, after 24 h of fabrication and after 200 h of accelerated aging. Materials and Methods: The samples were prepared according to ISO/TR 11405:1994 in maxillofacial silicone and polymethyl methacrylate resin. The untreated samples were Group A (control), Group B (silicon carbide [SiC] paper abrasion 80 grit size), and Group C (erbium-doped yttrium aluminum garnet laser etching). Then, the samples were coated with primer and bonded to maxillofacial silicone. The samples were subjected to shear BS test in an universal testing machine after 24 h of fabrication and after 200 h of accelerated aging. Results: The results were statistically analyzed using one-way ANOVA and Tukey's HSD post hoc test. The shear BS test after 24 h of fabrication showed better BS in SiC paper abrasion. The shear BS test after 200 h of accelerated aging showed better BS in laser etching compared to SiC abrasion. Conclusion: Laser etching produced better shear BS compared to conventional SiC paper abrasion after 200 h of accelerated aging process.
Automated Data Extraction from Scholarly Line Graphs

Line graphs are ubiquitous in scholarly papers. They are usually generated from a data table and often used to compare performances of various methods. The data in these figures can not be accessed. Manual extraction of this data is hard and not scalable. On the other hand, automated systems for such data extraction task is not yet available. We report an analysis of line graphs to explain the challenges of building a fully automated data extraction system. Next, we describe a system for automated data extraction from color line graphs. Our system has multiple components: image classification for identifying line graphs; text extraction from the figures and curve extraction. For the classification, we show that unsupervised feature learning outperforms traditional low-level image descriptors by 10%. For the text extraction, our heuristics outperforms the accuracy of the previous method by 29%. We also propose a novel curve extraction method that has an average accuracy of 82%. A large partially annotated dataset for future research is described.
Cloning, sequencing, and use as a molecular probe of a gene encoding an aminoglycoside 6'-N-acetyltransferase of broad substrate profile

A gene coding for an aminoglycoside 6'-N-acetyltransferase that was able to modify amikacin was cloned from a plasmid isolated from a clinical strain of Enterobacter cloacae. Sequencing of a 955-bp segment which mediates the modifying activity revealed a single open reading frame of 432 nucleotides that predicted a polypeptide of 144 amino acid residues with a molecular weight of 16,021. Putative ribosomal binding sites and -10 and -35 sequences were located at the 5' end of the gene. The size of the polypeptide was confirmed through minicell analysis of the expression products of plasmids containing the sequence. The use of the gene as a molecular probe revealed its specificity toward strains harboring genes coding for related enzymes. This probe is therefore useful for epidemiological studies.
The diagnosis of subclinical mastitis in lactating cows: a comparison of cytological methods and a monovalent radial immunodiffusion test.

GIESECKE, W. H. & VILJOEN, M. H . , 1974. The diagnosis of subclinical mastitis in lactating cows: a comparison of cytological methods and a monovalent radial immunodiffusion test. Onderstepoort J. vet. Res., 41(2) 51 74 (1974). The diagnostic accuracy of conventional methods for the diagnosis of subclinical mastitis, such as the direct microscopic count (DMC) and electronic cell count (ECC) either used alone or in combination with bacteriological examinations, according to international standards, were compared with DNA determinations and a radial immunodiffusion test (MMT). The latter is based on single radial immunodiffusion of bovine serum albumin (BSA) in agarose containing anti-BSA serum. This investigation was conducted on 1 008 foremilk samples, collected via the teat canal from 179 dairy cows, plus 56 samples obtained from 14 of them by means of cisternal puncture. It is concluded that BSA concentrations in milk causing an MMT diameter s 8mm are diagnostic for mastitis in lactating cows under the conditions existing in this experiment. The coefficient of variation of the MMT (14, 67%) is significantly smaller than that of the DMC (87, 78%), ECC (72,25%) and DNA content (37, 19%) respectively and lies within the 15% limit recommended for diagnostic methods. Diagnoses made by MMT, DMC and ECC over 3 successive days varied by 4,1~,-;;; 14,5 % or 28,4% respectively. The reduced repeatability of the MMT resulted from genuine changes in udder health whereas 10,1% and 24,3% of variance observed for the DMC and ECC respectively were due to other factors. In comparison to the MMT, mastitis diagnosis based on international standards resulted in 43,13 ± 20, 8% false positives. These are mainly due to teat canal infections simulating mastitis. When both the MMT and international mastitis standards were used it was possible to distinguish between quarters with irrelevant and relevant teat canal infections, non-specific cellular reactions and septic or aseptic mastitis without having to resort to cisternal puncture. Staphylococcal beta toxin inoculated into the teat canal, facilitated studies on the sequence of events leading to elevated BSA levels and cellular counts in the udder. A pre-inflammatory leucocytosis, resulting from passage of small amounts of toxin into the teat cistern was shown to occur in this investigation. The diagnosis of subclinical mastitis in dry cows and within the first week post parium is as inaccurate by means of the MMT as by conventional methods.
Design of Linearly Polarized Rectangular Microstrip Patch Antenna Using IE3D/PSO

In this project, a novel particle swarm optimization method based on IE3D is used to design an Inset Feed Linearly Polarized Rectangular Microstrip Patch Antenna. The aim of the thesis is to Design and fabricate an inset fed rectangular Microstrip Antenna and study the effect of antenna dimensions Length (L) , Width (W) and substrate parameters relative Dielectric constant (er) , substrate thickness on Radiation parameters of Band width. Low dielectric constant substrates are generally preferred for maximum radiation. The conducting patch can take any shape but rectangular and circular configurations are the most commonly used configuration. Other configurations are complex to analyze and require heavy numerical computations. The length of the antenna is nearly half wavelength in the dielectric; it is a very critical parameter, which governs the resonant frequency of the antenna. In view of design, selection of the patch width and length are the major parameters along with the feed line depth. Desired Patch antenna design is initially simulated by using IE3D simulator. And Patch antenna is realized as per design requirements.