Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene clustering by Latent Semantic Indexing of MEDLINE abstracts

MOTIVATION A major challenge in the interpretation of high-throughput genomic data is understanding the functional associations between genes. Previously, several approaches have been described to extract gene relationships from various biological databases using term-matching methods. However, more flexible automated methods are needed to identify functional relationships (both explicit and implicit) between genes from the biomedical literature. In this study, we explored the utility of Latent Semantic Indexing (LSI), a vector space model for information retrieval, to automatically identify conceptual gene relationships from titles and abstracts in MEDLINE citations. RESULTS We found that LSI identified gene-to-gene and keyword-to-gene relationships with high average precision. In addition, LSI identified implicit gene relationships based on word usage patterns in the gene abstract documents. Finally, we demonstrate here that pairwise distances derived from the vector angles of gene abstract documents can be effectively used to functionally group genes by hierarchical clustering. Our results provide proof-of-principle that LSI is a robust automated method to elucidate both known (explicit) and unknown (implicit) gene relationships from the biomedical literature. These features make LSI particularly useful for the analysis of novel associations discovered in genomic experiments. AVAILABILITY The 50-gene document collection used in this study can be interactively queried at http://shad.cs. utk.edu/sgo/sgo.html.
Pelvic floor muscle functioning in women with vulvar vestibulitis syndrome

Vaginal sEMG biofeedback and pelvic floor physical therapists' manual techniques are being increasingly included in the treatment of vulvar vestibulitis syndrome (VVS). Successful treatment outcomes have generated hypotheses concerning the role of pelvic floor pathology in the etiology of VVS. However, no data on pelvic floor functioning in women with VVS compared to controls are available. Twenty-nine women with VVS were matched to 29 women with no pain with intercourse. Two independent, structured pelvic floor examinations were carried out by physical therapists blind to the diagnostic status of the participants. Results indicated that therapists reached almost perfect agreement in their diagnosis of pelvic floor pathology. A series of significant correlations demonstrated the reliability of assessment results across muscle palpation sites. Women with VVS demonstrated significantly more vaginal hypertonicity, lack of vaginal muscle strength, and restriction of the vaginal opening, compared to women with no pain with intercourse. Anal palpation could not confirm generalized hypertonicity of the pelvic floor. We suggest that pelvic floor pathology in women with VVS is reactive in nature and elicited with palpations that result in VVS-type pain. Treatment interventions need to recognize the critical importance of addressing the conditioned, protective muscle guarding response in women with VVS.
Two centered black holes and N = 4 dyon spectrum

The exact spectrum of dyons in a class of N = 4 supersymmetric string theories is known to change discontinuously across walls of marginal stability. We show that the change in the degeneracy across the walls of marginal stability can be accounted for precisely by the entropy of two centered small black holes which (dis)appear as we cross the walls of marginal stability.
Toxicological Characterization of Phthalic Acid

There has been growing concern about the toxicity of phthalate esters. Phthalate esters are being used widely for the production of perfume, nail varnish, hairsprays and other personal/cosmetic uses. Recently, exposure to phthalates has been assessed by analyzing urine for their metabolites. The parent phthalate is rapidly metabolized to its monoester (the active metabolite) and also glucuronidated, then excreted. The objective of this study is to evaluate the toxicity of phthalic acid (PA), which is the final common metabolic form of phthalic acid esters (PAEs). The individual PA isomers are extensively employed in the synthesis of synthetic agents, for example isophthalic acid (IPA), and terephthalic acid (TPA), which have very broad applications in the preparation of phthalate ester plasticizers and components of polyester fiber, film and fabricated items. There is a broad potential for exposure by industrial workers during the manufacturing process and by the general public (via vehicle exhausts, consumer products, etc). This review suggests that PA shows in vitro and in vivo toxicity (mutagenicity, developmental toxicity, reproductive toxicity, etc.). In addition, PA seems to be a useful biomarker for multiple exposure to PAEs in humans.
Comparing Factors from Different Studies

Es who, in their research, are faced with the possibility of a factor analysis seem to be divisible into two groups. One is comprised of individuals who decry all factorial methods: the vehemence of their denunciation being roughly in proportion to their ignorance of the subject. The orher group, if we omit the few experts in this difficult field, is comprised largely of novices who assume an understanding of the subjecc after having worked through a few of its approximate arithmetic procedures. N o w it is ironic that the healthy development of factor analysis is probably more endangered by the latter group than by the former, and the time seems opportune to draw attention to one common danger point: it occurs when one desires to compare the results of one factor study with those of another. Despite numerous warnings (cf. Anderson, 1963) it is still not widely realized chat factor loadings ( o r weighcs) obtained by the principal component or centroid methods are not invariant under changes of scale in the variates. For instance, the loadings obtained for a set of variates from an analysis of their correlation matrix when multiplie'd by the standard deviations of these variaces, are not, in general, equal to the loadings obtained from an analysis of the parent covariance matrix. It follows that, should E wish to compare the factors derived from a sec of variates (whether before or after rotation) for a sample of boys (say) with those for a comparable sample of girls, he may be led astray if his analyses are based on the correlation matrices and the variances of some of the variates differ from sex to sex. EqualIy he will be confounded (cf. Thomson, 1948, ch. 11, 1 2 ) if he tries to compare results for samples of (say) the same sex if one sample is more highly selected than the other in a way that affects the variance of one or more of the variates involved. It is not sufficient to realize, as Thurstone was the first to do, that restriction of variance may cause corresponding factors to become more or less correlated (oblique) when results from two or more studies are compared. Basically, it is necessary to consider the variances of the underlying factors themselves, as well as the correlations between them, when a comparison of factors derived from different samples is undertaken. Lawley and Maxwell ( in press) attempt a solution of this problem.
Mesenchymal stem cell engraftment in lung is enhanced in response to bleomycin exposure and ameliorates its fibrotic effects

Previously we described a reliable method based on immunodepletion for isolating mesenchymal stem cells (MSCs) from murine bone marrow and showed that, after intracranial transplantation, the cells migrated throughout forebrain and cerebellum and adopted neural cell fates. Here we systemically administered MSCs purified by immunodepletion from male bleomycin (BLM)-resistant BALB/c mice into female BLM-sensitive C57BL/6 recipients and quantified engraftment levels in lung by real-time PCR. Male DNA accounted for 2.21 × 10-5% of the total lung DNA in control-treated mice but was increased 23-fold (P = 0.05) in animals exposed to BLM before MSC transplantation. Fluorescence in situ hybridization revealed that engrafted male cells were localized to areas of BLM-induced injury and exhibited an epithelium-like morphology. Moreover, purification of type II epithelial cells from the lungs of transplant recipients resulted in a 3-fold enrichment of male, donor-derived cells as compared with whole lung tissue. MSC administration immediately after exposure to BLM also significantly reduced the degree of BLM-induced inflammation and collagen deposition within lung tissue. Collectively, these studies demonstrate that murine MSCs home to lung in response to injury, adopt an epithelium-like phenotype, and reduce inflammation and collagen deposition in lung tissue of mice challenged with BLM.
Decentralized model predictive control of dynamically-coupled linear systems: tracking under packet loss

Abstract For large-scale processes whose dynamics can be represented as the interaction of several dynamically-coupled linear subsystems, this paper proposes a decentralized model predictive control (MPC) design approach for set-point tracking under input constraints and possible loss of information packets. Following earlier results in (Alessio and Bemporad, 2007, 2008), the global model of the process is approximated as the decomposition of several (possibly overlapping) smaller models used for local predictions. We present sufficient criteria for asymptotic tracking of output set-points and rejection of constant measured disturbances when the overall process is in closed loop with the set of decentralized MPC controllers, under possible intermittent lack of communication of measurement data between controllers. The effectiveness of the approach is shown in a simulation example on distributed temperature control in the passenger area of a railcar.
Antimicrobial and Antibiofilm Activity of Chitosan on the Oral Pathogen Candida albicans

Oral candidiasis is particularly evident, not only in cancer patients receiving chemotherapy, but also in elderly people with xerostomy. In general, Candida is an opportunistic pathogen, causing infections in immunocompromised people and, in some cases, when the natural microbiota is altered. Chitosan, a natural derivative of chitin, is a polysaccharide that has been proven to possess a broad spectrum of antimicrobial activity that encompasses action against fungi, yeast and bacteria. While recent studies have revealed a significant antibiofilm activity upon several microorganisms, including C. albicans, little is known regarding the impact of chitosan upon the adhesive process or mature biofilms. With that in mind, the purpose of this work was to evaluate, in vitro, the capability of chitosan to inhibit C. albicans growth and biofilm formation. The results obtained showed that chitosan is capable of inhibiting C. albicans planktonic growth (HMW, 1 mg/mL; LMW, 3 mg/mL). Regarding biofilm growth, chitosan inhibited C. albicans adhesion (ca. 95%), biofilm formation (percentages above 90%) and reduced mature biofilms by ca. 65% and dual species biofilms (C. albicans and S. mutans) by ca. 70%. These results display the potential of this molecule to be used as an effective anti-Candida agent capable of acting upon C. albicans infections.
Salmonella Typhimurium Type III Secretion Effectors Stimulate Innate Immune Responses in Cultured Epithelial Cells

Recognition of conserved bacterial products by innate immune receptors leads to inflammatory responses that control pathogen spread but that can also result in pathology. Intestinal epithelial cells are exposed to bacterial products and therefore must prevent signaling through innate immune receptors to avoid pathology. However, enteric pathogens are able to stimulate intestinal inflammation. We show here that the enteric pathogen Salmonella Typhimurium can stimulate innate immune responses in cultured epithelial cells by mechanisms that do not involve receptors of the innate immune system. Instead, S. Typhimurium stimulates these responses by delivering through its type III secretion system the bacterial effector proteins SopE, SopE2, and SopB, which in a redundant fashion stimulate Rho-family GTPases leading to the activation of mitogen-activated protein (MAP) kinase and NF-κB signaling. These observations have implications for the understanding of the mechanisms by which Salmonella Typhimurium induces intestinal inflammation as well as other intestinal inflammatory pathologies.
Towards a Taxonomical Consensus: Diversity and Richness Inference from Large Scale rRNA gene Analysis

Population analysis is persistently challenging but important, leading to the determination of diversity and function prediction of microbial community members. Here we detail our bioinformatics methods for analyzing population distribution and diversity in large microbial communities. This was achieved via (i) a homology based method for robust phylotype determination, equaling the classification accuracy of the Ribosomal Database Project (RDP) classifier, but providing improved associations of closely related sequences; (ii) a comparison of different clustering methods for achieving more accurate richness estimations. Our methodology, which we developed using the RDP vetted 16S rRNA gene sequence set, was validated by testing it on a large 16S rRNA gene dataset of approximately 2300 sequences, which we obtained from a soil microbial community study. We concluded that the best approach to obtain accurate phylogenetics profile of large microbial communities, based on 16S rRNA gene sequence information, is to apply an optimized blast classifier. This approach is complemented by the grouping of closely related sequences, using complete linkage clustering, in order to calculate richness and evenness indices for the communities.
Sevoflurane but Not Propofol Preserves Myocardial Function During Minimally Invasive Direct Coronary Artery Bypass Surgery

Volatile anesthetics exert cardioprotective properties in experimental and clinical studies. We designed this study to investigate the effects of sevoflurane on left ventricular (LV) performance during minimally invasive direct coronary artery bypass grafting (MIDCAB) without cardiopulmonary bypass. Fifty-two patients scheduled for MIDCAB surgery were randomly assigned to a propofol or a sevoflurane group. Apart from the anesthetics used, there was no difference in surgical and anesthetic management. After determination of cardiac troponin T, creatine kinase, and creatine kinase MB, electrocardiographic (ECG) data and echocardiography variables (myocardial performance index and early to atrial filling velocity ratio) the left anterior descending coronary artery (LAD) was clamped until anastomosis with the left internal mammary artery was completed. During LAD occlusion and during reperfusion, echocardiography measurements were repeated. Blood samples were obtained repeatedly for up to 72 h. After LAD occlusion, myocardial performance index and early to atrial filling velocity ratio in the propofol group deteriorated significantly from 0.40 ± 0.12 and 1.29 ± 0.35 to 0.49 ± 0.10 and 1.13 ± 0.22, respectively, whereas there was no change in the sevoflurane group. In the propofol group myocardial performance index remained increased (0.47 ± 0.11) compared with baseline during reperfusion. There were no significant differences in ECG and laboratory values between groups. In conclusion, during a brief period of ischemia in patients undergoing MIDCAB surgery, sevoflurane preserved myocardial function better than propofol.
What a high prevalence of white coat hypertension in society!

BACKGROUND There are many patients in society using antihypertensive medication, which has been initiated just after a single office measurement but actually they are normotensive and in contrast, there are many patients not using any antihypertensive medication because of a normal blood pressure (BP) at the doctor's office but they are actually hypertensive. MATERIALS AND METHODS We randomly took 438 consecutive patients. Clinical BP was measured by the same physician, and a 10-day twice daily home blood pressure measurement (HBPM) and 24-hour ambulatory blood pressure measurement (ABPM) were obtained. RESULTS Among 438 patients, 170 (38%) normotension (NT), 190 (43%) white coat hypertension (WCHT), 10 (2%) masked hypertension (MHT), and 68 (15%) sustained hypertension (HT) cases were detected. Although the prevalences of sustained HT and MHT increased by decade, the prevalence of WCHT was much higher in all decades until the eighth decade. Even in the second decade, its prevalence was 33% and higher than 45% in the third, fourth, and fifth decades of life. No statistically significant difference was found for number of WCHT, MHT, and sustained HT cases between ABPM and HBPMs. CONCLUSION HBPM should be the preferred method of diagnosis of WCHT, MHT, and sustained HT against conventional BPM at the doctor's office and even ABPM due to its simplicity and equal effectiveness with ABPM. It should be applied to every patient above the age of 40 years once a year due to high prevalences of sustained and masked HT cases. Additionally, due to the very high prevalences of WCHT even in the very early decades, WCHT should be thought of as a normal response of the body against various stresses and its management should be limited to annual follow-up with HBPMs.
Bandwidth choice for nonparametric classification

It is shown that, for kernel-based classification with univariate distributions and two populations, optimal bandwidth choice has a dichotomous character. If the two densities cross at just one point, where their curvatures have the same signs, then minimum Bayes risk is achieved using bandwidths which are an order of magnitude larger than those which minimize pointwise estimation error. On the other hand, if the curvature signs are different, or if there are multiple crossing points, then bandwidths of conventional size are generally appropriate. The range of different modes of behavior is narrower in multivariate settings. There, the optimal size of bandwidth is generally the same as that which is appropriate for pointwise density estimation. These properties motivate empirical rules for bandwidth choice.
Development of chicks and predispersal behaviour of young in the Eagle Owl Bubo bubo

Little quantitative information on the development and behaviour of chicks and young is available for many species, despite the crucial importance of such data and the sensitivity of this stage in a bird’s life. For Eagle Owls Bubo bubo, despite the large amount of scientific literature on this species, much basic information is lacking. This study provides a photographic and morphometric guide for age estimation of nestlings and fledglings, as well as data on the call behaviour of young, and patterns of movements during the post-fledging dependence period. The most remarkable event in chick development is the rapid increase in mass, and size gain, during the first 30 and 40‐45 days, respectively. Because after this time morphometric differences become less evident, young-feather development is more useful for ageing. Patterns of chick call behaviour showed that the time spent calling increased with age and, from 110 days of age, chick vocalizations were usually uniformly distributed through the whole night and most synchronized at sunset and sunrise (the maximum recorded number of vocalizations per chick and per night was 1106 calls). During the post-fledging dependence period, radiotagged Owls moved widely, up to 1500 m from the nest after the age of 80‐90 days. During such movements, the mean distance among siblings increased with age, from 168 m on average for juveniles less than 100 days old, to 489 m for those older than 100 days. Definitive dispersal started when young were about 150‐160 days old. Information on chick call behaviour and movements is crucial for unbiased census and nest checking, as well as for the definition of young post-fledging areas. Knowledge of the latter is very important in terms of conservation and management (especially for those species that move largely around their nest before dispersal) owing to the high mortality that can occur during this period.
Creating new visualization and human interface devices for theraputic video games

CREATING NEW VISUALIZATION AND HUMAN INTERFACE DEVICES FOR THERAPEUTIC VIDEO GAMES by Kunal Jayant Doshi Virtual reality (VR) gaming environment as a tool for rehabilitation of patients with upper extremity disorders is fast gaining momentum. VR based motor training systems provide an engaging, motivating and adaptable environment where the motion of the limb displayed in the virtual world is a replication of the motion produced in the real world by the patient's extremity. The goal of this thesis was to create a generic gaming system which can be interfaced to a number of different Human interface devices (HID) and produce rich graphics to create a virtual environment which closely resembles the real world. This would overcome the current limitations of the 'HANDS UP' game developed by the Neuromuscular lab which accepts only a web camera input and uses color marker detection to recreate the limb movements in simple two dimensional environment. Three dimensional worlds designed in Virtual Reality Modeling Language (VRML) were controlled using SIMROBOT and Virtual reality toolbox in MATLAB to create better visualization. The Human Interface devices currently used for Virtual Reality video games are expensive and cannot be afforded for home use. Various new HID's like the Flock of Birds, Nintendo Wiimote and IMU 6 DOF V3 were tested for their use in the virtual gaming environment. Each device presented their own set of advantages and problems. The thesis work involved understanding and resolving these problems and interfacing the devices with the gaming system. CREATING NEW VISUALIZATION AND HUMAN INTERFACE DEVICES FOR THERAPEUTIC VIDEO GAMES by Kunal Jayant Doshi A Thesis Submitted to the Faculty of New Jersey Institute of Technology in Partial Fulfillment of the Requirements for the Degree of Master of Science in Biomedical Engineering Department of Biomedical Engineering
Efficient Algorithms for Layer Assignment Problem

The layer assignment problem for interconnect is the problem of determining which layers should be used for wiring the signal nets. The objective of the layer assignment problem in general is to minimize the number of vias required. Thus, it is also referred to as the via minimization problem. In a via minimization problem, if the topology of the given layout is fixed, the problem is referred to as a constrained via minimization (CVM) problem. On the other hand, if both the topology of the layout and the layer assignment are to be decided, it is referred to as an unconstrained via minimization (UVM) problem. In this paper, both the CVM and UVM problems are studied. For the CVM problems, efficient algorithms which can be easily modified to take extra constraints into consideration are proposed. Experimental results show that the proposed algorithms for the CVM problem are time efficient compared with existing algorithms and generate better (near-optimal) results. For the UVM problems, a new heuristic approach is presented which generates better results but takes longer computing time. In the CVM problem, some vias are "essential" to the given layout. That is, they have to be selected and cannot be replaced by other possible vias. An efficient algorithm for identifying essential vias is also presented and discussed in this paper.