Miracle-dz/UniFAR-FTUs huggingface dataset:
The genetic and environmental basis of atopic diseases

The prevalence of atopic diseases has increased abruptly in recent years in most Westernized societies, making the question why this happened the topic of a heated debate. The best paradigm available to date to explain this steep rise, the ‘hygiene hypothesis’, supports that it is the excess ‘cleanliness’ of our environments that has led to the decline in the number of infectious stimuli that are necessary for the proper development of our immune system. Recent findings support that it is the combined effect that not only pathogenic, but also non-pathogenic microorganisms, and even their structural components, can exert on the immune system that deters from the development of atopic responses. Adding to these results are intriguing new findings on the effect different gene polymorphisms can have on an individual's predisposition to allergic diseases. The most important linkages produced, to date, include those among the genes for IL-4, IL-13, HLA-DRB, TNF, LTA, FCER1B, IL-4RA, ADAM33, TCR α/δ, PHF11, GPRA, TIM, p40, CD14, DPP10, T-bet, GATA-3, and FOXP3 and allergic disorders. The two parallel research efforts, epidemiologic and genetic, are only recently starting to converge, producing fascinating results on the effect particular gene-environment interactions might have in the development of atopy. The most important lesson learned through this tremendous research effort is that not only a small number but thousands and millions of separate risk factors act in concordance in the production of the allergic phenotype.
Successful treatment of thrombotic microangiopathy after haematopoietic stem cell transplantation with rituximab

Thrombotic microangiopathy (TMA) is a grave complication after haematopoietic stem cell transplantation (HSCT) and effective treatment is undefined. Five patients with postHSCT TMA, which was refractory to at least 1 week of plasma exchange and prednisolone, were treated with rituximab (375 mg/m2/week × 4). Remission was achieved in four patients, of whom three remained in remission and one had died of sepsis at a median follow‐up of 10 months. ADAMTS13 levels were low in all evaluable patients, and only one patient showed significant anti‐ADAMTS13 antibody. The levels of ADAMTS13 and anti‐ADAMTS13 antibody did not change significantly with rituximab‐induced remission.
Coral Reefs and Carbon Dioxide

Hajime Kayanne et al. (1) investigate diurnal changes in CO2 partial pressure (PC02) and community metabolism on Shiraho reef (Ishigaki Island, Japan) and conclude that "reefs might serve as a sink, not a source, for atmospheric CO2" because of high net organic production relative to net calcification (Table 1). This conclusion is at odds with recent reports (2, 3, 4) and data (5) suggesting that reefs are net sources of atmospheric C02, albeit of limited importance in the current carbon budget. Furthermore, it is well established that the value of gross primary production (Pg) is close to that of respiration (R) in most coral reef flats, and that the net production (Pn) is around zero (6). One would expect some reefs to depart from this general trend, but consideration of currents and community distributions suggests that the data in the report by Kayanne et al. (1) represent neither the whole Shiraho reef nor all coral reefs. The reef flat at Shiraho comprises five different benthic communities and is under strong tidal influence (1, 7). Because Kayanne et al. measured PCO2at a single station over several days, the water masses at hand had different origins and crossed different communities depending on the direction of the current. Therefore, the observed changes in PCO2 likely did not result from the metabolic activity of the entire reef flat but, rather, from a variable combination of the communities located around the study site. Also, Kayanne et al. calculated mean daytime and nighttime reef water Pco2 with the use of a predictive regression equation
Decomposition of the Visible and Dark Matter in the Einstein Ring 0047–2808 by Semilinear Inversion

We measure the mass density profile of the lens galaxy in the Einstein ring system 0047-2808 using our semilinear inversion method developed in an earlier paper. By introducing an adaptively gridded source plane, we are able to eliminate the need for regularization of the inversion. This removes the problem of a poorly defined number of degrees of freedom, encountered by inversion methods that employ regularization, and so allows a proper statistical comparison between models. We confirm previous results indicating that the source is double and that a power-law model gives a significantly better fit than the singular isothermal ellipsoid model. We measure a slope α = 2.11 ± 0.04. We find, furthermore, that a dual-component constant M/L baryonic+dark halo model gives a significantly better fit than the power-law model, at the 99.7% confidence level. The inner logarithmic slope of the dark halo profile is found to be 0.87 (95% CL), consistent with the predictions of cold dark matter simulations of structure formation. We determine an unevolved B-band mass-to-light ratio for the baryons (only) of 3.05 h65 M☉/LB☉ (95% CL). This is the first measurement of the baryonic M/L of a single galaxy by purely gravitational lens methods. The baryons account for 65% (95% CL) of the total projected mass, or, assuming spherical symmetry, 84% (95% CL) of the total three-dimensional mass within the mean radius of 1. ″16 (7.5 h kpc) traced by the ring. Finally, at the level of >3 σ, we find that the halo mass is rounder than the baryonic distribution and that the two components are offset in orientation from one another.
In vivo imaging of choroidal angiogenesis using fluorescence-labeled cationic liposomes

Purpose Precise monitoring of active angiogenesis in neovascular eye diseases such as age-related macular degeneration (AMD) enables sensitive use of antiangiogenic drugs and reduces adverse side effects. So far, no in vivo imaging methods are available to specifically label active angiogenesis. Here, we report such a technique using fluorophore-labeled cationic liposomes (CL) detected with a standard clinical in vivo scanning laser ophthalmoscope (SLO). Methods C57Bl/6 mice underwent laser coagulations at day 0 (d0) to induce choroidal neovascularization (CNV). Liposomes labeled with Oregon green, rhodamine (Rh), or indocyanine green (ICG) were injected into the tail vein at various time points after laser coagulation, and their fluorescence was observed in vivo 60 min later using an SLO, or afterwards in choroidal flatmounts or cryosections. Results SLO detected accumulated fluorescence only in active CNV lesions with insignificant background noise. The best signal was obtained with CL-ICG. Choroidal flatmounts and cryosections of the eye confirmed the location of retained CL in CNV lesions. Neutral liposomes, in contrast, showed no accumulation. Conclusions These results establish fluorophore-labeled CL as high affinity markers to selectively stain active CNV. This novel, non-invasive SLO imaging technique could improve risk assessment and indication for current intraocular antiangiogenic drugs in neovascular eye diseases, as well as monitor therapeutic outcomes. Labeling of angiogenic vessels using CL can be of interest not only for functional imaging in ophthalmology but also for other conditions where localization of active angiogenesis is desirable.
The Effect of Neighborhood Disadvantage on the Racial Disparity in Ovarian Cancer-Specific Survival in a Large Hospital-Based Study in Cook County, Illinois

This paper examines the effect of neighborhood disadvantage on racial disparities in ovarian cancer-specific survival. Despite treatment advances for ovarian cancer, survival remains shorter for African-American compared to White women. Neighborhood disadvantage is implicated in racial disparities across a variety of health outcomes and may contribute to racial disparities in ovarian cancer-specific survival. Data were obtained from 581 women (100 African-American and 481 White) diagnosed with epithelial ovarian cancer between June 1, 1994, and December 31, 1998 in Cook County, IL, USA, which includes the city of Chicago. Neighborhood disadvantage score at the time of diagnosis was calculated for each woman based on Browning and Cagney’s index of concentrated disadvantage. Cox proportional hazard models measured the association of self-identified African-American race with ovarian cancer-specific survival after adjusting for age, tumor characteristics, surgical debulking, and neighborhood disadvantage. There was a statistically significant negative association (−0.645) between ovarian cancer-specific survival and neighborhood disadvantage (p = 0.008). After adjusting for age and tumor characteristics, African-American women were more likely than Whites to die of ovarian cancer (HR = 1.59, p = 0.003). After accounting for neighborhood disadvantage, this risk was attenuated (HR = 1.32, p = 0.10). These findings demonstrate that neighborhood disadvantage is associated with ovarian cancer-specific survival and may contribute to the racial disparity in survival.
Metabolic Features of Protochlamydia amoebophila Elementary Bodies – A Link between Activity and Infectivity in Chlamydiae

The Chlamydiae are a highly successful group of obligate intracellular bacteria, whose members are remarkably diverse, ranging from major pathogens of humans and animals to symbionts of ubiquitous protozoa. While their infective developmental stage, the elementary body (EB), has long been accepted to be completely metabolically inert, it has recently been shown to sustain some activities, including uptake of amino acids and protein biosynthesis. In the current study, we performed an in-depth characterization of the metabolic capabilities of EBs of the amoeba symbiont Protochlamydia amoebophila. A combined metabolomics approach, including fluorescence microscopy-based assays, isotope-ratio mass spectrometry (IRMS), ion cyclotron resonance Fourier transform mass spectrometry (ICR/FT-MS), and ultra-performance liquid chromatography mass spectrometry (UPLC-MS) was conducted, with a particular focus on the central carbon metabolism. In addition, the effect of nutrient deprivation on chlamydial infectivity was analyzed. Our investigations revealed that host-free P. amoebophila EBs maintain respiratory activity and metabolize D-glucose, including substrate uptake as well as host-free synthesis of labeled metabolites and release of labeled CO2 from 13C-labeled D-glucose. The pentose phosphate pathway was identified as major route of D-glucose catabolism and host-independent activity of the tricarboxylic acid (TCA) cycle was observed. Our data strongly suggest anabolic reactions in P. amoebophila EBs and demonstrate that under the applied conditions D-glucose availability is essential to sustain metabolic activity. Replacement of this substrate by L-glucose, a non-metabolizable sugar, led to a rapid decline in the number of infectious particles. Likewise, infectivity of Chlamydia trachomatis, a major human pathogen, also declined more rapidly in the absence of nutrients. Collectively, these findings demonstrate that D-glucose is utilized by P. amoebophila EBs and provide evidence that metabolic activity in the extracellular stage of chlamydiae is of major biological relevance as it is a critical factor affecting maintenance of infectivity.
An innovative ultrasound foot scanner system for measuring the change in biomechanical properties of plantar tissue from sitting to standing

The present study investigated the reliability of an innovative ultrasound foot scanner system in assessing the thickness and stiffness of plantar soft tissue and the comparison of stiffness and thickness in sitting and standing. Fifteen young healthy individuals were examined. The target sites on the foot sole for investigation included the heel pad, the fifth metatarsal head, the second metatarsal head, the first metatarsal head, and the pulp of the hallux. The test (day 1) and retest (day 2) were performed 1 week apart at the exact time with humidity and temperature of the assessment room under control. The thickness and stiffness of the plantar soft tissue obtained in sitting and standing positions on day 1 were used for comparison. The results showed significant test–retest reliability [intraclass correlation coefficient(3,2)>0.90, P<0.001] at all five sites in both sitting and standing positions. When changing from sitting to standing, the plantar soft tissue became significantly thinner (with decrease ranging from 10 to 14% at various sites) and stiffer (with increase ranging from 123 to 164% at various sites, all P<0.05). The present innovative system is a reliable device for the measurement of the thickness and stiffness of plantar soft tissue in either the sitting or the standing position. The change in positions from sitting to standing resulted in a significant thinning and stiffening of plantar soft tissues. This system could be a potential clinical device to monitor the biomechanical properties of plantar tissue in the elderly or in patients with diseases such as diabetes to estimate the risk of developing foot ulcer or other foot complications.
Mechanism of Recurrent/Persistent Ischemic/Functional Mitral Regurgitation in the Chronic Phase After Surgical Annuloplasty: Importance of Augmented Posterior Leaflet Tethering

Background— Surgical annuloplasty can potentially hoist the posterior annulus anteriorly, exaggerate posterior leaflet (PML) tethering, and lead to recurrent ischemic/functional mitral regurgitation (MR). Characteristics of leaflet configurations in late postoperative MR were investigated. Methods and Results— In 30 patients with surgical annuloplasty for ischemic MR and 20 controls, the anterior leaflet (AML) and PML tethering angles relative to the line connecting annuli, posterior and apical displacement of the coaptation and the MR grade were measured by echocardiography before, early after, and late after surgery. Early after surgery, grade of MR and AML tethering generally decreased (P<0.01), whereas PML tethering significantly worsened (P<0.01). Nine of the 30 patients showed recurrent/persistent MR late after surgery. Compared with patients without late MR, those with the MR showed similar reduction in the annular area, significant re-increase in posterior displacement of the coaptation, and progressive worsening in PML tethering (P<0.05) late after surgery in comparison to the early phase. Both preoperative MR and late postoperative MR were significantly correlated with all tethering variables in univariate analysis. Although apical displacement of the coaptation was the primary determinant of preoperative MR (r2=0.60, P<0.0001), increased PML tethering was the primary determinant of late MR (r2=0.75, P<0.0001). Conclusions— Whereas both leaflets tethering is related to preoperative ischemic MR, both leaflets tethering but with predominant contribution from augmented and progressive PML tethering is related to recurrent/persistent ischemic/functional MR late after surgical annuloplasty.
On Concurrent Detection of Errors in Polynomial Basis Multiplication

The detection of errors in arithmetic operations is an important issue. This paper discusses the detection of multiple-bit errors due to faults in bit-serial and bit-parallel polynomial basis (PB) multipliers over binary extension fields. Our approach is based on multiple parity bits. Experimental results presented here show that due to an increase in the number of parity bits, the area overhead tends to increase linearly, but the probability of error detection approaches unity fairly quickly, e.g., for eight parity bits. In bit-serial implementation of a GF(2163) PB multiplier using eight parity bits, the area overhead and the probability of error detection are 10.29% and 0.996, respectively. This is achieved without any increase in the computation time of the GF(2163) PB multiplier
Latent semantic sentence clustering for multi-document summarization

This thesis investigates the applicability of Latent Semantic Analysis (LSA) to sentence clustering for Multi-Document Summarization (MDS). In contrast to more shallow approaches like measuring similarity of sentences by word overlap in a traditional vector space model, LSA takes word usage patterns into account. So far LSA has been successfully applied to different Information Retrieval (IR) tasks like information filtering and document classification (Dumais, 2004). In the course of this research, different parameters essential to sentence clustering using a hierarchical agglomerative clustering algorithm (HAC) in general and in combination with LSA in particular are investigated. These parameters include, inter alia, information about the type of vocabulary, the size of the semantic space and the optimal numbers of dimensions to be used in LSA. These parameters have not previously been studied and evaluated in combination with sentence clustering (chapter 4). This thesis also presents the first gold standard for sentence clustering in MDS. To be able to evaluate sentence clusterings directly and classify the influence of the different parameters on the quality of sentence clustering, an evaluation strategy is developed that includes gold standard comparison using different evaluation measures (chapter 5). Therefore the first compound gold standard for sentence clustering was created. Several human annotators were asked to group similar sentences into clusters following guidelines created for this purpose (section 5.4). The evaluation of the human generated clusterings revealed that the human annotators agreed on clustering sentences above chance. Analysis of the strategies adopted by the human annotators revealed two groups – hunters and gatherers – who differ clearly in the structure and size of the clusters they created (chapter 6). On the basis of the evaluation strategy the parameters for sentence clustering and LSA are optimized (chapter 7). A final experiment in which the performance of LSA in sentence clustering for MDS is compared to the simple word matching approach of the traditional Vector Space Model (VSM) revealed that LSA produces better quality sentence clusters for MDS than VSM.
CD4+ T cell effector commitment coupled to self-renewal by asymmetric cell divisions

Upon infection, an activated CD4+ T cell produces terminally differentiated effector cells and renews itself for continued defense. In this study, we show that differentiation and self-renewal arise as opposing outcomes of sibling CD4+ T cells. After influenza challenge, antigen-specific cells underwent several divisions in draining lymph nodes (LN; DLNs) while maintaining expression of TCF1. After four or five divisions, some cells silenced, whereas some cells maintained TCF1 expression. TCF1-silenced cells were T helper 1–like effectors and concentrated in the lungs. Cells from earliest divisions were memory-like and concentrated in nondraining LN. TCF1-expressing cells from later divisions in the DLN could self-renew, clonally yielding a TCF1-silenced daughter cell as well as a sibling cell maintaining TCF1 expression. Some TCF1-expressing cells in DLNs acquired an alternative, follicular helper-like fate. Modeled differentiation experiments in vitro suggested that unequal PI3K/mechanistic target of rapamycin signaling drives intraclonal cell fate heterogeneity. Asymmetric division enables self-renewal to be coupled to production of differentiated CD4+ effector T cells during clonal selection.
Node-density independent localization

This paper presents an enhanced version of a novel radio interferometric positioning technique for node localization in wireless sensor networks that provides both high accuracy and long range simultaneously. The ranging method utilizes two transmitters emitting radio signals at almost the same frequencies. The relative location is estimated by measuring the relative phase offset of the generated interference signal at two receivers. Here, we analyze how the selection of carrier frequencies affects the precision and maximum range. Furthermore, we describe how the interplay of RF multi-path and ground reflections degrades the ranging accuracy. To address these problems, we introduce a technique that continuously refines the range estimates as it converges to the localization solution. Finally, we present the results of a field experiment where our prototype achieved 4 cm average localization accuracy for a quasi-random deployment of 16 COTS motes covering the area of two football fields. The maximum range measured was 170 m, four times the observed communication range. Consequently, node deployment density is no longer constrained by the localization technique, but rather by the communication range
A framework for specifying, modeling, implementation and verification of SOC protocols

We are presenting a hybrid verification framework to design, verify and implement SOC protocols. The framework is based on the creation of specifications in terms of extended state transition tables, creation of templates for different phases of the design cycle and integration of these components in a design flow. The resultant design flow presents a tight integration of the debug/verification loop across different design stages that in turn reduce the time to market of the chip. This framework was applied to the design process of multiple SOC chips' production and the results have shown measurable enhancements.
Expressiveness of Two-Valued Semantics for Abstract Dialectical Frameworks

We analyse the expressiveness of Brewka and Woltran's abstract dialectical frameworks for two-valued semantics. By expressiveness we mean the ability to encode a desired set of two-valued interpretations over a given propositional vocabulary A using only atoms from A. We also compare ADFs' expressiveness with that of (the two-valued semantics of) abstract argumentation frameworks, normal logic programs and propositional logic. While the computational complexity of the two-valued model existence problem for all these languages is (almost) the same, we show that the languages form a neat hierarchy with respect to their expressiveness. We then demonstrate that this hierarchy collapses once we allow to introduce a linear number of new vocabulary elements. We finally also analyse and compare the representational succinctness of ADFs (for two-valued model semantics), that is, their capability to represent two-valued interpretation sets in a space-efficient manner.