Miracle-dz/UniFAR-FTUs huggingface dataset:
Early renal abnormalities in autosomal dominant polycystic kidney disease.

BACKGROUND AND OBJECTIVES Potential therapeutic interventions are being developed for autosomal dominant polycystic kidney disease (ADPKD). A pivotal question will be when to initiate such treatment, and monitoring disease progression will thus become more important. Therefore, the prevalence of renal abnormalities in ADPKD at different ages was evaluated. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Included were 103 prevalent ADPKD patients (Ravine criteria). Measured were mean arterial pressure (MAP), total renal volume (TRV), GFR, effective renal plasma flow (ERPF), renal vascular resistance (RVR), and filtration fraction (FF). Twenty-four-hour urine was collected. ADPKD patients were compared with age- and gender-matched healthy controls. RESULTS Patients and controls were subdivided into quartiles of age (median ages 28, 37, 42, and 52 years). Patients in the first quartile of age had almost the same GFR when compared with controls, but already a markedly decreased ERPF and an increased FF (GFR 117 +/- 32 versus 129 +/- 17 ml/min, ERPF 374 +/- 119 versus 527 +/- 83 ml/min, FF 32% +/- 4% versus 25% +/- 2%, and RVR 12 (10 to 16) versus 8 (7 to 8) dynes/cm(2), respectively). Young adult ADPKD patients also had higher 24-hour urinary volumes, lower 24-hour urinary osmolarity, and higher urinary albumin excretion (UAE) than healthy controls, although TRV in these young adult patients was modestly enlarged (median 1.0 L). CONCLUSIONS Already at young adult age, ADPKD patients have marked renal abnormalities, including a decreased ERPF and increased FF and UAE, despite modestly enlarged TRV and near-normal GFR. ERPF, FF, and UAE may thus be better markers for disease severity than GFR.
Roll motion control by stretch reflex in a continuously jumping musculoskeletal biped robot

Human's spinal reflexes response rapidly to the change of states of muscles, therefore, they are supposed to play an important role for dynamic motion. In order to realize three dimensional stable jumping, rapid control system is indispensable. In this paper, we investigate contribution of the stretch reflex for stabilizing roll motion of continuous jumping by constructing a musculoskeletal biped robot. By conducting numerical simulation and robot experiments, we show that the stretch reflex in the Soleus muscle effectively stabilizes the roll motion of the robot. Through investigation, we confirmed that roll motion was partially stabilized by implementation of the stretch reflex in the soleus muscle. This study may lead to understanding the role of spinal reflexes in human jumping and to realization of robust jumping of bipedal robots.
AthaMap: From in silico Data to Real Transcription Factor Binding Sites

AthaMap generates a map for cis-regulatory sequences for the whole Arabidopsis thaliana genome. AthaMap was initially developed by matrix-based detection of putative transcription factor binding sites (TFBS) mostly determined from random binding site selection experiments. Now, also experimentally verified TFBS have been included for 48 different Arabidopsis thaliana transcription factors (TF). Based on these sequences, 89,416 very similar putative TFBS were determined within the genome of A. thaliana and annotated to AthaMap. Matrix- and single sequence-based binding sites can be included in colocalization analysis for the identification of combinatorial cis-regulatory elements. As an example, putative target genes of the WRKY18 transcription factor that is involved in plant-pathogen interaction were determined. New functions of AthaMap include descriptions for all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR and MIPS. Transcription factors used in the binding site determination are linked to TAIR and TRANSFAC databases. AthaMap is freely available at http://www.athamap. de.
Activity of Carbapenems Combined with Clavulanate against Murine Tuberculosis

ABSTRACT Although beta-lactam antibiotics are not considered as antituberculous drugs, it has been recently shown that the combination of carbapenems and clavulanate is bactericidal in vitro. We evaluated in a murine model of tuberculosis the activity of carbapenems alone and combined with clavulanate against Mycobacterium tuberculosis. Swiss mice infected intravenously with 3 × 105 M. tuberculosis H37Rv were treated for 4 weeks with clavulanate alone or imipenem, meropenem, and ertapenem alone or combined with clavulanate, whereas a positive control group was treated with isoniazid, and a negative control group was held without treatment. The combination of imipenem or meropenem plus clavulanate significantly improved survival. Among groups of mice with 100% survival, only isoniazid reduced lung CFU counts; the carbapenem-clavulanate combinations did not prevent bacterial growth. Although less active than isoniazid, the combinations of imipenem or meropenem plus clavulanate improved the survival of mice infected with M. tuberculosis and should be further evaluated.
Use of a SCID mouse/human lymphoma model to evaluate cytokine-induced killer cells with potent antitumor cell activity

C.B-17 severe combined immune deficient (SCID) mice, which lack functional B and T lymphocytes, allow xenografts and, therefore, can be used to study the biology of human malignancies. Two different human B cell lymphoma cell lines, SU-DHL-4 and OCI-Ly8, which both harbor the t(14;18) chromosomal translocation, were injected into C.B-17 SCID mice. Mice injected intravenously or intraperitoneally developed tumors and died in a dose-dependent manner. The presence of tumor cells in various murine tissues could be demonstrated by a clonogenic tumor assay, staining of frozen sections with a monoclonal antibody (mAb) against a human B cell antigen (CD19), and with the polymerase chain reaction technique. A protocol using cytotoxic effector cells was developed and used to selectively deplete the tumor cells from bone marrow. These cells were developed by growing peripheral blood mononuclear cells in the presence of interferon gamma (IFN-gamma), anti- CD3 mAb, and interleukin 2 (IL-2). The timing of IFN-gamma treatment was critical and optimal if IFN-gamma was added before IL-2 treatment. The cells that were stimulated by IFN-gamma, followed by IL-2, could be expanded by treatment with a mAb directed against CD3. These cells could be further activated by IL-1, but not by tumor necrosis factor alpha. With this protocol, a tumor cell kill of 3 logs was obtained as measured by a clonogenic assay. Interestingly, despite their high cytotoxic activity against lymphoma cells, these cells had little toxicity against a subset of normal human hematopoietic precursor cells (granulocyte/macrophage colony-forming units). These cells were further tested by treating murine bone marrow contaminated with the human lymphoma cell line SU-DHL-4, and injecting these cells into SCID mice to assay for tumor growth in vivo. The animals injected with bone marrow contaminated with SU-DHL-4 cells had enhanced survival if the bone marrow was treated with the cytokine-induced killer cells before infusion. The SCID mouse provides a useful in vivo model for evaluation of new therapeutic approaches for lymphoma treatment. The cytokine- induced killer cells generated as described here could have an important impact on bone marrow purging for autologous bone marrow transplantation as well as for adoptive immunotherapy.
Warm autoimmune hemolytic anemia associated with an IgM autoanti-Ge

A 28-year-old male with a prior history of Hodgkin's disease and a recent upper respiratory tract infection presented with autoimmune hemolytic anemia (AIHA). The patient's red blood cells (RBCs) were spontaneously agglutinated after room temperature and 37 degrees C washes. Dithiothreitol-treated RBCs reacted strongly with anti-C3 and were nonreactive with anti-IgG, -IgM, and -IgA; they reacted with anti-IgM (kappa light chains only) by flow cytometry. The patient's serum was nonreactive. An acid eluate was only weakly reactive, but a 56 degrees C heat eluate strongly agglutinated untreated RBCs (3+). Ficin-treated RBCs were nonreactive. En(a-) RBCs were strongly reactive, but Ge- RBCs were nonreactive. The anti-Ge in the eluate was IgM. The patient's untreated RBCs were shown, by flow cytometry, to be weakly Ge+. This is the first report of IgM-mediated warm AIHA associated with autoanti-Ge.
Sizing Optimization of Sandwich Panels Having Prismatic Core Using Water Cycle Algorithm

Due to possessing unique structure, sandwich panels have special characteristics which the most important is having high strength to weight ratio. Sandwich panels having diverse prismatic cores have been investigated and comparisons have been carried out for finding the best design. For this reason, the importance of optimization techniques particularly metaheuristics is understood. Water cycle algorithm (WCA), as a recently developed optimizer, is inspired from water cycle process. The optimum dimensions and the minimum weight have been calculated in order to design ultra-light weight sandwich panels. The imposed constraints in this problem are buckling load and yield stress. The obtained figures and results conclude that the diamond prismatic topology (having corrugation order of 4) is the most weight efficient among other existing designs under specific loading direction.
The Redistribution of Power: Neurocardiac Signaling, Alcohol and Gender

Human adaptability involves interconnected biological and psychological control processes that determine how successful we are in meeting internal and environmental challenges. Heart rate variability (HRV), the variability in consecutive R-wave to R-wave intervals (RRI) of the electrocardiogram, captures synergy between the brain and cardiovascular control systems that modulate adaptive responding. Here we introduce a qualitatively new dimension of adaptive change in HRV quantified as a redistribution of spectral power by applying the Wasserstein distance with exponent 1 metric (W1) to RRI spectral data. We further derived a new index, D, to specify the direction of spectral redistribution and clarify physiological interpretation. We examined gender differences in real time RRI spectral power response to alcohol, placebo and visual cue challenges. Adaptive changes were observed as changes in power of the various spectral frequency bands (i.e., standard frequency domain HRV indices) and, during both placebo and alcohol intoxication challenges, as changes in the structure (shape) of the RRI spectrum, with a redistribution towards lower frequency oscillations. The overall conclusions from the present study are that the RRI spectrum is capable of a fluid and highly flexible response, even when oscillations (and thus activity at the sinoatrial node) are pharmacologically suppressed, and that low frequency oscillations serve a crucial but less studied role in physical and mental health.
Distributed clustering approach for UAV integrated wireless sensor networks

Wireless sensor networks (WSNs) consist of battery–limited sensor nodes which have the ability of sensing the environment, communicating with other nodes and processing the data. Large number of sensor node deployment over a geographical area imposes some constraints on the retrieval of the data. The use of mobile sinks (e.g., unmanned aerial vehicle, UAV) is an effective solution method for such large–scale networks. However, depending on the path and altitude of the UAV, and the type of radios in use, coverage problem arises where some nodes cannot get connected to the UAV. In this paper, the coverage problem is examined where UAV is used as mobile sink node. On the basis of our analysis, a dynamic and distributed clustering approach is proposed. Evaluations are performed with a realistic simulation environment. Performance results show that proposed approach reduces the energy–consumption and construct more stable and well balanced clusters that connect the uncovered nodes to the UAV.
From Stock Bottle to Vaccine: Elucidating the Particle Size Distributions of Aluminum Adjuvants Using Dynamic Light Scattering

The physicochemical properties of aluminum salts are key determinants of their resultant adjuvanticity in vivo when administered as part of a vaccine. While there are links between particle size and the efficacy of the immune response, the limited literature directly characterizing the PSD of aluminum adjuvants has stymied the elucidation of such a relationship for these materials. Hence, this comparative study was undertaken to monitor the PSD of aluminum adjuvants throughout the process of vaccine formulation using DLS. A significant proportion of the stock suspensions was highly agglomerated (>9 μm) and Alhydrogel® exhibited the smallest median size (2677 ± 120 nm) in comparison to Adju-Phos® or Imject alum® (7152 ± 308 and 7294 ± 146 nm respectively) despite its large polydispersity index (PDI). Dilution of these materials induced some degree of disaggregation within all samples with Adju-Phos® being the most significantly affected. The presence of BSA caused the median size of Alhydrogel® to increase but these trends were not evident when model vaccines were formulated with either Adju-Phos® or Imject alum®. Nevertheless, Alhydrogel® and Adju-Phos® exhibited comparable median sizes in the presence of this protein (4194 ± 466 and 4850 ± 501 nm respectively) with Imject alum® being considerably smaller (2155 ± 485 nm). These results suggest that the PSD of aluminum adjuvants is greatly influenced by dilution and the degree of protein adsorption experienced within the vaccine itself. The size of the resultant antigen-adjuvant complex may be important for its immunological recognition and subsequent clearance from the injection site.
Business process similarity metric supporting one-to-many relationship

In many areas graph match techniques are used to compare and identify common characteristics. In this paper we apply graph similarity techniques on the business processes used inside organizations and extracted with process mining techniques. The scope is to identify if an organization uses a similar process for a specific business case as another organization. However as the existence of exact matching is less probable, error tolerant graph matching techniques are more suitable for real life data. Business processes could have a different granularity level; one business process is more detailed in specific areas than the business process subject of the comparison. The custom algorithm for business process match presented in this paper takes into consideration a one-to-many relation for activities: one activity is matched with a set of activities in the other graph. Such information is important in extracting the common characteristics of organizations and could represent an input for choosing a collaborator. Business processes if not available are extracted with process mining techniques and are reduced to directed graph format. A custom graph similarity algorithm extended for multivalent nodes is applied and a business process similarity factor is retrieved.
Interval reverse nearest neighbor queries on uncertain data with Markov correlations

Nowadays, many applications return to the user a set of results that take the query as their nearest neighbor, which are commonly expressed through reverse nearest neighbor (RNN) queries. When considering moving objects, users would like to find objects that appear in the RNN result set for a period of time in some real-world applications such as collaboration recommendation and anti-tracking. In this work, we formally define the problem of interval reverse nearest neighbor (IRNN) queries over moving objects, which return the objects that maintain nearest neighboring relations to the moving query objects for the longest time in the given interval. Location uncertainty of moving data objects and moving query objects is inherent in various domains, and we investigate objects that exhibit Markov correlations, that is, each object's location is only correlated with its own location at previous timestamp while being independent of other objects. There exists the efficiency challenge for answering IRNN queries on uncertain moving objects with Markov correlations since we have to retrieve not only all the possible locations of each object at current time but also its historically possible locations. To speed up the query processing, we present a general framework for answering IRNN queries on uncertain moving objects with Markov correlations in two phases. In the first phase, we apply space pruning and probability pruning techniques, which reduce the search space significantly. In the second phase, we verify whether each unpruned object is an IRNN of the query object. During this phase, we propose an approach termed Probability Decomposition Verification (PDV) algorithm which avoid computing the probability of any object being an RNN of the query object exactly and thus improve the efficiency of verification. The performance of the proposed algorithm is demonstrated by extensive experiments on synthetic and real datasets, and the experimental results show that our algorithm is more efficient than the Monte-Carlo based approximate algorithm.
Notch signaling controls hepatoblast differentiation by altering the expression of liver-enriched transcription factors

Hepatoblasts give rise to both mature hepatocytes and cholangiocytes. While Notch signaling has been implicated in the formation of bile ducts composed of cholangiocytes, little is known about the mechanism of lineage commitment of hepatoblasts. Here we describe the role of the Notch pathway in hepatoblast differentiation. Immunohistochemical analysis showed that Jagged1 was expressed in the cells surrounding the portal veins and Notch2 was expressed in most hepatic cells at mid gestation when ductal plates are formed surrounding the portal veins. Interestingly, the Jagged1+ cells were adjacent to ductal plates, suggesting that the Notch signaling is activated in hepatoblasts that undergo differentiation into cholangiocytes. In fact, expression of the Notch intracellular domain in Dlk+ hepatoblasts inhibited hepatic differentiation and significantly reduced the expression of albumin, a marker of both hepatoblasts and hepatocytes. Furthermore, the addition of Matrigel to the hepatoblast culture upregulated the expression of cytokeratin 7 and 19, integrin β4, and HNF1β, which are known to be expressed in cholangiocytes. By contrast, downregulation of the Notch signaling by siRNA specific for Notch2 mRNA as well as by the γ-secretase inhibitor L-685,458 promoted the hepatic differentiation. Consistent with the previous finding that mature cholangiocytes strongly express HNF1β, but barely express HNF1α, HNF4, and C/EBPα, activation of the Notch signaling upregulated HNF1β expression, whereas it downregulated the expression of HNF1α, HNF4, and C/EBPα. These results suggest that the Notch signaling contributes to form a network of these transcription factors suitable for cholangiocyte differentiation.
Concerted Up-regulation of Aldehyde/Alcohol Dehydrogenase (ADHE) and Starch in Chlamydomonas reinhardtii Increases Survival under Dark Anoxia*

Aldehyde/alcohol dehydrogenases (ADHEs) are bifunctional enzymes that commonly produce ethanol from acetyl-CoA with acetaldehyde as intermediate and play a key role in anaerobic redox balance in many fermenting bacteria. ADHEs are also present in photosynthetic unicellular eukaryotes, where their physiological role and regulation are, however, largely unknown. Herein we provide the first molecular and enzymatic characterization of the ADHE from the photosynthetic microalga Chlamydomonas reinhardtii. Purified recombinant ADHE catalyzed the reversible NADH-mediated interconversions of acetyl-CoA, acetaldehyde, and ethanol but seemed to be poised toward the production of ethanol from acetaldehyde. Phylogenetic analysis of the algal fermentative enzyme supports a vertical inheritance from a cyanobacterial-related ancestor. ADHE was located in the chloroplast, where it associated in dimers and higher order oligomers. Electron microscopy analysis of ADHE-enriched stromal fractions revealed fine spiral structures, similar to bacterial ADHE spirosomes. Protein blots showed that ADHE is regulated under oxic conditions. Up-regulation is observed in cells exposed to diverse physiological stresses, including zinc deficiency, nitrogen starvation, and inhibition of carbon concentration/fixation capacity. Analyses of the overall proteome and fermentation profiles revealed that cells with increased ADHE abundance exhibit better survival under dark anoxia. This likely relates to the fact that greater ADHE abundance appeared to coincide with enhanced starch accumulation, which might reflect ADHE-mediated anticipation of anaerobic survival.
Asymptotic density, computable traceability, and 1-randomness

Let r be a real number in the unit interval [0, 1]. A set A ⊆ ω is said to be coarsely computable at density r if there is a computable function f such that {n | f(n) = A(n)} has lower density at least r. Our main results are that A is coarsely computable at density 1/2 if A is computably traceable or truth-table reducible to a 1-random set. In the other direction, we show that if a degree a is hyperimmune or PA, then there is an a-computable set which is not coarsely computable at any positive density.
Comparative Analysis of FLC Homologues in Brassicaceae Provides Insight into Their Role in the Evolution of Oilseed Rape

We identified nine FLOWERING LOCUS C homologues (BnFLC) in Brassica napus and found that the coding sequences of all BnFLCs were relatively conserved but the intronic and promoter regions were more divergent. The BnFLC homologues were mapped to six of 19 chromosomes. All of the BnFLC homologues were located in the collinear region of FLC in the Arabidopsis genome except BnFLC.A3b and BnFLC.C3b, which were mapped to noncollinear regions of chromosome A3 and C3, respectively. Four of the homologues were associated significantly with quantitative trait loci for flowering time in two mapping populations. The BnFLC homologues showed distinct expression patterns in vegetative and reproductive organs, and at different developmental stages. BnFLC.A3b was differentially expressed between the winter-type and semi-winter-type cultivars. Microsynteny analysis indicated that BnFLC.A3b might have been translocated to the present segment in a cluster with other flowering-time regulators, such as a homologue of FRIGIDA in Arabidopsis. This cluster of flowering-time genes might have conferred a selective advantage to Brassica species in terms of increased adaptability to diverse environments during their evolution and domestication process.