Miracle-dz/UniFAR-FTUs huggingface dataset:
An efficient wireless power link for implanted biomedical devices via resonant inductive coupling

This study presents a high efficiency inductive power link aiming for the implanted biomedical devices. Improving the efficiency of the inductive link is critical, since the overall efficiency of a remote powering system is dominated by the inductive link. Therefore, the proposed system utilizes the resonance phenomenon which enables maximum energy transfer between objects which are at resonance. In this study, the resonance is created between 4 spiral coils which are implemented on the internal and external units; each formed by two concentric coils. The system operates with 72% power efficiency at 10-12 MHz band at 10 mm distance which is a reasonable distance for powering implanted devices. Moreover, the characterization of the resonant inductive link with respect to distance and frequency is performed.
CD1-restricted adaptive immune responses to Mycobacteria in human group 1 CD1 transgenic mice

Group 1 CD1 (CD1a, CD1b, and CD1c)–restricted T cells recognize mycobacterial lipid antigens and are found at higher frequencies in Mycobacterium tuberculosis (Mtb)–infected individuals. However, their role and dynamics during infection remain unknown because of the lack of a suitable small animal model. We have generated human group 1 CD1 transgenic (hCD1Tg) mice that express all three human group 1 CD1 isoforms and support the development of group 1 CD1–restricted T cells with diverse T cell receptor usage. Both mycobacterial infection and immunization with Mtb lipids elicit group 1 CD1–restricted Mtb lipid–specific T cell responses in hCD1Tg mice. In contrast to CD1d-restricted NKT cells, which rapidly respond to initial stimulation but exhibit anergy upon reexposure, group 1 CD1–restricted T cells exhibit delayed primary responses and more rapid secondary responses, similar to conventional T cells. Collectively, our data demonstrate that group 1 CD1–restricted T cells participate in adaptive immune responses upon mycobacterial infection and could serve as targets for the development of novel Mtb vaccines.
Investigating ethnic differences in sexual health: focus groups with young people

Objectives: To compare normative beliefs about sexual health in young men and women from black Caribbean, black African, and white ethnic groups in order to better understand ethnic inequalities in sexual health. Methods: Focus group discussions with young people living in an area with known high prevalence of gonorrhoea and chlamydia. Groups were stratified by sex and self defined ethnicity. Results: 22 male and 20 female 16–25 year olds of black Caribbean, black African, and white ethnicity took part in eight discussions. Participants from black ethnic groups were more aware of gonorrhoea than white participants but all ethnic groups regarded these as being less important than unplanned pregnancy or HIV/AIDS. Most participants believed that they would have obvious symptoms if they had a sexually transmitted infection and could determine the cleanliness of sexual partners by visual or behavioural cues. Black Caribbean women were alone in acknowledging the likelihood of their partners having concurrent sexual relationships. Some black Caribbean women described negative attitudes of staff in genitourinary medicine clinics who were from the same ethnic background. Conclusion: In this focus group study we identified ethnic differences in terminology, awareness of sexually transmitted infections, non-exclusive sexual relationships, and experience of sexual health services but gender had a greater influence on normative beliefs. The similarities in norms for all ethnic groups might reflect common social and cultural exposures. The low priority given to sexually transmitted infections by young people from all ethnic groups needs to be addressed if they are to be tackled successfully.
Using a Network Model to Assess Risk of Forest Pest Spread via Recreational Travel

Long-distance dispersal pathways, which frequently relate to human activities, facilitate the spread of alien species. One pathway of concern in North America is the possible spread of forest pests in firewood carried by visitors to campgrounds or recreational facilities. We present a network model depicting the movement of campers and, by extension, potentially infested firewood. We constructed the model from US National Recreation Reservation Service data documenting more than seven million visitor reservations (including visitors from Canada) at campgrounds nationwide. This bi-directional model can be used to identify likely origin and destination locations for a camper-transported pest. To support broad-scale decision making, we used the model to generate summary maps for 48 US states and seven Canadian provinces that depict the most likely origins of campers traveling from outside the target state or province. The maps generally showed one of two basic spatial patterns of out-of-state (or out-of-province) origin risk. In the eastern United States, the riskiest out-of-state origin locations were usually found in a localized region restricted to portions of adjacent states. In the western United States, the riskiest out-of-state origin locations were typically associated with major urban areas located far from the state of interest. A few states and the Canadian provinces showed characteristics of both patterns. These model outputs can guide deployment of resources for surveillance, firewood inspections, or other activities. Significantly, the contrasting map patterns indicate that no single response strategy is appropriate for all states and provinces. If most out-of-state campers are traveling from distant areas, it may be effective to deploy resources at key points along major roads (e.g., interstate highways), since these locations could effectively represent bottlenecks of camper movement. If most campers are from nearby areas, they may have many feasible travel routes, so a more widely distributed deployment may be necessary.
Cerebrospinal Fluid Glucose and Lactate: Age-Specific Reference Values and Implications for Clinical Practice

Cerebrospinal fluid (CSF) analysis is an important tool in the diagnostic work-up of many neurological disorders, but reference ranges for CSF glucose, CSF/plasma glucose ratio and CSF lactate based on studies with large numbers of CSF samples are not available. Our aim was to define age-specific reference values. In 1993 The Nijmegen Observational CSF Study was started. Results of all CSF samples that were analyzed between 1993 and 2008 at our laboratory were systematically collected and stored in our computerized database. After exclusion of CSF samples with an unknown or elevated erythrocyte count, an elevated leucocyte count, elevated concentrations of bilirubin, free hemoglobin, or total protein 9,036 CSF samples were further studied for CSF glucose (n = 8,871), CSF/plasma glucose ratio (n = 4,516) and CSF lactate values (n = 7,614). CSF glucose, CSF/plasma glucose ratio and CSF lactate were age-, but not sex dependent. Age-specific reference ranges were defined as 5–95th percentile ranges. CSF glucose 5th percentile values ranged from 1.8 to 2.9 mmol/L and 95th percentile values from 3.8 to 5.6 mmol/L. CSF/plasma glucose ratio 5th percentile values ranged from 0.41 to 0.53 and 95th percentile values from 0.82 to 1.19. CSF lactate 5th percentile values ranged from 0.88 to 1.41 mmol/L and 95th percentile values from 2.00 to 2.71 mmol/L. Reference ranges for all three parameters were widest in neonates and narrowest in toddlers, with lower and upper limits increasing with age. These reference values allow a reliable interpretation of CSF results in everyday clinical practice. Furthermore, hypoglycemia was associated with an increased CSF/plasma glucose ratio, whereas hyperglycemia did not affect the CSF/plasma glucose ratio.
Genome-Wide Association Studies of Asthma in Population-Based Cohorts Confirm Known and Suggested Loci and Identify an Additional Association near HLA

Rationale Asthma has substantial morbidity and mortality and a strong genetic component, but identification of genetic risk factors is limited by availability of suitable studies. Objectives To test if population-based cohorts with self-reported physician-diagnosed asthma and genome-wide association (GWA) data could be used to validate known associations with asthma and identify novel associations. Methods The APCAT (Analysis in Population-based Cohorts of Asthma Traits) consortium consists of 1,716 individuals with asthma and 16,888 healthy controls from six European-descent population-based cohorts. We examined associations in APCAT of thirteen variants previously reported as genome-wide significant (P<5x10−8) and three variants reported as suggestive (P<5×10−7). We also searched for novel associations in APCAT (Stage 1) and followed-up the most promising variants in 4,035 asthmatics and 11,251 healthy controls (Stage 2). Finally, we conducted the first genome-wide screen for interactions with smoking or hay fever. Main Results We observed association in the same direction for all thirteen previously reported variants and nominally replicated ten of them. One variant that was previously suggestive, rs11071559 in RORA, now reaches genome-wide significance when combined with our data (P = 2.4×10−9). We also identified two genome-wide significant associations: rs13408661 near IL1RL1/IL18R1 (P Stage1+Stage2 = 1.1x10−9), which is correlated with a variant recently shown to be associated with asthma (rs3771180), and rs9268516 in the HLA region (P Stage1+Stage2 = 1.1x10−8), which appears to be independent of previously reported associations in this locus. Finally, we found no strong evidence for gene-environment interactions with smoking or hay fever status. Conclusions Population-based cohorts with simple asthma phenotypes represent a valuable and largely untapped resource for genetic studies of asthma.
Photodynamic therapy: Combined modality approaches targeting the tumor microenvironment

Photodynamic therapy causes direct cytotoxicity to malignant cells within a tumor. Photodynamic therapy (PDT) can also have both direct and indirect effects upon various non‐malignant components of the tumor microenvironment. This action can lead to PDT‐mediated angiogenesis and inflammation, which are emerging as important determinants of PDT responsiveness.
Multiaccess Channels with State Known to Some Encoders and Independent Messages

We consider a state-dependent multiaccess channel (MAC) with state noncausally known to some encoders. For simplicity of exposition, we focus on a two-encoder model in which one of the encoders has noncausal access to the channel state. The results can in principle be extended to any number of encoders with a subset of them being informed. We derive an inner bound for the capacity region in the general discrete memoryless case and specialize to a binary noiseless case. In binary noiseless case, we compare the inner bounds with trivial outer bounds obtained by providing the channel state to the decoder. In the case of maximum entropy channel state, we obtain the capacity region for binary noiseless MAC with one informed encoder. For a Gaussian state-dependent MAC with one encoder being informed of the channel state, we present an inner bound by applying a slightly generalized dirty paper coding (GDPC) at the informed encoder and a trivial outer bound by providing channel state to the decoder also. In particular, if the channel input is negatively correlated with the channel state in the random coding distribution, then GDPC can be interpreted as partial state cancellation followed by standard dirty paper coding. The uninformed encoders benefit from the state cancellation in terms of achievable rates, however, it seems that GDPC cannot completely eliminate the effect of the channel state on the achievable rate region, in contrast to the case of all encoders being informed. In the case of infinite state variance, we provide an inner bound and also provide a nontrivial outer bound for this case which is better than the trivial outer bound.
Application of the shsp Gene, Encoding a Small Heat Shock Protein, as a Food-Grade Selection Marker for Lactic Acid Bacteria

ABSTRACT Plasmid pSt04 of Streptococcus thermophilus contains a gene encoding a protein with homology to small heat shock proteins (A. Geis, H. A. M. El Demerdash, and K. J. Heller, Plasmid 50:53-69, 2003). Strains cured from the shsp plasmids showed significantly reduced heat and acid resistance and a lower maximal growth temperature. Transformation of the cloned shsp gene into S. thermophilus St11 lacking a plasmid encoding shsp resulted in increased resistance to incubation at 60°C or pH 3.5 and in the ability to grow at 52°C. A food-grade cloning system for S. thermophilus, based on the plasmid-encoded shsp gene as a selection marker, was developed. This approach allowed selection after transfer of native and recombinant shsp plasmids into different S. thermophilus and Lactococcus lactis strains. Using a recombinant plasmid carrying an erythromycin resistance (Emr) gene in addition to shsp, we demonstrated that both markers are equally efficient in selecting for plasmid-bearing cells. The average transformation rates in S. thermophilus (when we were selecting for heat resistance) were determined to be 2.4 × 104 and 1.0 × 104 CFU/0.5 μg of DNA, with standard deviations of 0.54 × 104 and 0.32 × 104, for shsp and Emr selection, respectively. When we selected for pH resistance, the average transformation rates were determined to be 2.25 × 104 and 3.8 × 103 CFU/0.5 μg of DNA, with standard deviations of 0.63 × 104 and 3.48 × 103, for shsp and Emr selection, respectively. The applicability of shsp as a selection marker was further demonstrated by constructing S. thermophilus plasmid pHRM1 carrying the shsp gene as a selection marker and the restriction-modification genes of another S. thermophilus plasmid as a functional trait.
Plasma Soluble CD 30 as a Possible Marker of Adult T-cell Leukemia in HTLV-1 Carriers : a Nested Case-Control Study

Adult T-cell leukemia (ATL) is a highly aggressive T-cell malignancy that was first proposed as a new disease entity in 1977 (Uchiyama et al., 1977) and that was closely followed by the discovery of the human T-cell leukemia virus type 1 (HTLV-1) as the causative agent (Yoshida et al., 1982). ATL has a broad clinical spectrum (Takatsuki et al., 1985) and is classified into four clinical subtypes: smoldering, chronic, acute, and lymphoma (Shimoyama, 1991). Most HTLV-1-infected people remain asymptomatic, i.e., not diagnosed as having HTLV1-related diseases, such as ATL, HTLV-1-associated myelopathy, and others (Yamaguchi 1994). However, approximately 5% of asymptomatic HTLV-1 carriers develop ATL after a long period of latent infection, with the average age of the onset of 67 years (Yamaguchi 1994). For the long-term latency between initial HTLV-1 infection and ATL development, a multistage carcinogenesis theory where five or more genetic changes may be accumulated in HTLV-1-infected cells before the clinical onset of ATL is widely accepted (Okamoto et al., 1989; Franchini, 1995). Although a large number of reports have been published to date, genetic abnormalities involved in the
Phylogenetic inference under recombination using Bayesian stochastic topology selection

Motivation: Conventional phylogenetic analysis for characterizing the relatedness between taxa typically assumes that a single relationship exists between species at every site along the genome. This assumption fails to take into account recombination which is a fundamental process for generating diversity and can lead to spurious results. Recombination induces a localized phylogenetic structure which may vary along the genome. Here, we generalize a hidden Markov model (HMM) to infer changes in phylogeny along multiple sequence alignments while accounting for rate heterogeneity; the hidden states refer to the unobserved phylogenic topology underlying the relatedness at a genomic location. The dimensionality of the number of hidden states (topologies) and their structure are random (not known a priori) and are sampled using Markov chain Monte Carlo algorithms. The HMM structure allows us to analytically integrate out over all possible changepoints in topologies as well as all the unknown branch lengths. Results: We demonstrate our approach on simulated data and also to the genome of a suspected HIV recombinant strain as well as to an investigation of recombination in the sequences of 15 laboratory mouse strains sequenced by Perlegen Sciences. Our findings indicate that our method allows us to distinguish between rate heterogeneity and variation in phylogeny caused by recombination without being restricted to 4-taxa data. Availability: The method has been implemented in JAVA and is available, along with data studied here, from http://www.stats.ox.ac.uk/~webb. Contact: cholmes@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Hedgehog Shape Priors for Multi-Object Segmentation

Star-convexity prior is popular for interactive single object segmentation due to its simplicity and amenability to binary graph cut optimization. We propose a more general multi-object segmentation approach. Moreover, each object can be constrained by a more descriptive shape prior, "hedgehog". Each hedgehog shape has its surface normals locally constrained by an arbitrary given vector field, e.g. gradient of the user-scribble distance transform. In contrast to star-convexity, the tightness of our normal constraint can be changed giving better control over allowed shapes. For example, looser constraints, i.e. wider cones of allowed normals, give more relaxed hedgehog shapes. On the other hand, the tightest constraint enforces skeleton consistency with the scribbles. In general, hedgehog shapes are more descriptive than a star, which is only a special case corresponding to a radial vector field and weakest tightness. Our approach has significantly more applications than standard single star-convex segmentation, e.g. in medical data we can separate multiple non-star organs with similar appearances and weak edges. Optimization is done by our modified -expansion moves shown to be submodular for multi-hedgehog shapes.
COMMENT: Comment on energy level statistics in the mixed regime

We comment on the recent paper by Abul-Magd (1996 29 1) concerning the energy level statistics in the mixed regime, i.e. such having the mixed classical dynamics where regular and chaotic regions coexist in the phase space. We point out that his basic assumption on the additive property of the level-repulsion function r(S) (conditional probability density) in the sense of dividing it linearly into the regular and chaotic part in proportion to the classical fractional phase space volumes and is not justified, since among other things, it relies on the type of Berry's ergodic assumption, which, however, is only correct in a homogeneous ensemble of ergodic systems, not in the neighbourhood of an integrable system. Thus, his resulting distribution cannot be regarded as a theoretically well-founded object. We point out that the semiclassical limiting energy level spacing distribution must be of Berry - Robnik (1984) type, and explain what transitional behaviour of the Brody-type (with fractional power-law energy level repulsion) we observe in the near semiclassical regime where effective is not yet small enough. Thus we refer to the derivation, arguments and conclusions in our previous paper (Prosen and Robnik 1994 26 8059), and explain again the behaviour in this double transition region.
Cellular and Molecular Mechanism Underlying the Effect of Low-magnitude, High-frequency Vibration on Bone

An emerging non-pharmacological treatment for bone degenerative diseases is whole body vibration (WBV), a mechanical signal composed of low-magnitude, high-frequency (LMHF) vibrations that when applied to bone, have osteogenic and anti-resorptive effects. Currently, the cellular and molecular mechanism underlying the effect of WBV on bone is unclear. In this study, we investigated the response of osteocytes, the putative mechanosensor in bone, under LMHF vibration. As bone cells differentiate from mesenchymal stromal cells (MSCs), we also studied the osteogenic differentiation of rat MSCs in the presence of vibration loading. We found that vibrated osteocytes show gene and protein expression changes suggestive of an antiosteoclastogenic response, and secrete soluble factors that inhibit osteoclast formation and activity. In contrast, rat MSCs showed moderate to no response to LMHF vibration during osteogenic differentiation. Our data suggest that in vivo effects of LMHF vibration are mediated through mechanosensing and biochemical responses by osteocytes.
Ulcerative Colitis and Immunoglobulin G4

Background/Aims Ulcerative colitis (UC) is sometimes associated with autoimmune pancreatitis (AIP). Infiltration of immunoglobulin G4 (IgG4)-positive plasma cells is sometimes detected in the colonic mucosa of AIP or UC patients. This study aimed to clarify the relation between UC and IgG4. Methods Associations with UC were reviewed in 85 AIP patients. IgG4 immunostaining was performed on biopsy specimens from the colonic mucosa of 14 AIP and 32 UC patients. Results UC was confirmed in two cases (type 1 AIP, n=1; suspected type 2 AIP, n=1). Abundant infiltration of IgG4-positive plasma cells in the colonic mucosa was detected in the case of suspected type 2 AIP with UC and two cases of type 1 AIP without colitis. Abundant infiltration of IgG4-positive plasma cells was detected in 10 UC cases (IgG4-present, 31%). Although 72% of IgG4-absent UC patients showed mild disease activity, 70% of IgG4-present patients showed moderate to severe disease activity (p<0.05). Conclusions UC is sometimes associated with AIP, but it seems that UC is not a manifestation of IgG4-related disease. Infiltration of IgG4-positive plasma cells is sometimes detectable in the colonic mucosa of UC patients and is associated with disease activity.
Definition, measurement, and correlates of quality of life in nursing homes: toward a reasonable practice, research, and policy agenda.

PURPOSE This article identifies challenges in defining, measuring, and studying quality of life of nursing home residents. DESIGN AND METHOD A theoretical analysis was conducted based on literature and the author's own large-scale studies of quality of life of nursing home residents. RESULTS Measuring quality of life is a relatively low priority in nursing homes because of focus on markers of poor quality of care, pervasive sense that nursing homes are powerless to influence quality of life, and impatience with research among those dedicated to culture change. The research argues that the resident voice must be sought in reaching operational definitions for quality of life and as reporters on the quality of their own lives, and that resident burden is a spurious concern that should not deter direct interviews with residents. Five challenges in measuring quality of life were identified: (a) designing questions with appropriate response categories and time frames, (b) developing a sampling strategy, (c) aggregating information at the individual and facility level, (d) validating what are ultimately subjective constructs, and (e) developing an approach using observations and proxies to assess quality of life for approximately the 40% of the residents who will be impossible to interview. IMPLICATIONS Although residents' perceived quality of life is partly a product of their health, social supports, and personalities, nursing homes can directly influence quality of life through their policies, practices, and environments, and, indirectly, through their approaches to family and community. A research agenda is needed, which includes both methodological research and studies of the correlates of quality of life.