Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial and Temporal Expression of Lactobacillus plantarum Genes in the Gastrointestinal Tracts of Mice

ABSTRACT Lactobacillus plantarum is a common inhabitant of mammalian gastrointestinal tracts, and L. plantarum strain WCFS1 is a human isolate with a known genome sequence. L. plantarum WCFS1 survives intestinal passage in an active form, and its transit time and transcriptional activities were monitored in 15 BALB/c mice at 2, 4, 6, 8, and 24 h after being fed a single intragastric dose of this organism. Enumeration of viable cells isolated from fecal material revealed that the majority of the L. plantarum inoculum transited the mouse intestine within 4 h after ingestion. Three mice were sacrificed at each time point, and total RNA was isolated from the mouse intestinal compartments (stomach through colon). Quantification of L. plantarum 16S rRNA by quantitative real-time reverse-transcription-PCR revealed that L. plantarum was present at elevated levels in the stomach and small intestine for at least 4 h following ingestion and for over 8 h in the cecum and colon. We also examined the expression of 9 L. plantarum housekeeping genes and 15 L. plantarum in vivo-inducible (ivi) genes previously identified by recombination-based in vivo expression technology to be induced in the mouse gastrointestinal tract. The relative expression levels of the ivi genes increased up to 350-fold in the mouse intestine compared to levels observed for L. plantarum WCFS1 cells grown in a rich laboratory medium. Moreover, several genes displayed intestinal compartment-specific (small intestine versus colon) activities. These results confirm that L. plantarum displays specific and differential responses at various sites along the mammalian intestine.
Algorithms for Integrated Routing and Scheduling for Aggregating Data from Distributed Resources on a Lambda Grid

In many e-science applications, there exists an important need to aggregate information from data repositories distributed around the world. In an effort to better link these resources in a unified manner, many lambda-grid networks, which provide end-to-end dedicated optical-circuit-switched connections, have been investigated. In this context, we consider the problem of aggregating files from distributed databases at a (grid) computing node over a lambda grid. The challenge is (1) to identify routes (that is, circuits) in the lambda-grid network, along which files should be transmitted, and (2) to schedule the transfers of these files over their respective circuits. To address this challenge, we propose a hybrid approach that combines offline and online scheduling. We define the Time-Path Scheduling Problem (TPSP) for offline scheduling. We prove that TPSP is NP-complete, develop a Mixed Integer Linear Program (MILP) formulation for TPSP, and then propose a greedy approach to solve TPSP because the MILP does not scale well. We compare the performance of the greedy approach on a few representative lambda-grid network topologies. One key input to the offline schedule is the file transfer time. Due to dynamics at the receiving end host, which is hard to model precisely, the actual file transfer time may vary. We first propose a model for estimating the file transfer time. Then, we propose online reconfiguration algorithms so that as files are transferred, the offline schedule may be modified online, depending on the amount of time that it actually took to transfer the file. This helps in reducing the total time to transfer all the files, which is an important metric. To demonstrate the effectiveness of our approach, we present results on an emulated lambda-grid network testbed.
Lysosomal Accumulation of Unesterified Cholesterol in Model Macrophage Foam Cells *

Lysosomal accumulation of unesterified (free) cholesterol, following the phagocytic incorporation of cholesteryl oleate lipid droplets, was quantitatively characterized in a murine 5774 macrophage foam cell model. The induction of phagocytic incorporation by the macrophages, using an inverted culture technique, allowed the rapid delivery of large amounts of cholesteryl ester droplets to the lysosomes, leading to the subsequent generation of free cholesterol. The lysosomally generated free cholesterol was differentiated from the membrane cholesterol by a double radiolabeling procedure. Free cholesterol accumulation was quantitated in a population of low density lipid-filled lysosomes prepared by ultracentrifugal isolation of a floating lipid fraction from a homogenate of the cholesteryl ester-loaded cells. About 10% of the total N-acetyl-&glucosaminidase activity, a lysosomal marker, was recovered in the lipid fraction. Negligible amounts of alkaline phosphodiesterase1, a plasma membrane marker, or membrane cholesterol were present in this fraction. Electron microscopic and cytochemical analysis of the isolated lipid fraction revealed the presence of lysosomes in the fraction with a diameter ranging from 1.5 to 4 Gm. Continued hydrolysis of incorporated cholesteryl ester over a 24-h incubation resulted in approximately 30% of the generated free cholesterol in lipid-filled lysosomes. The accumulation of free cholesterol occurred whether or not the cholesterol esterifying enzyme, acyl-CoA: cholesterol acyltransferase, was inhibited. In addition, substantial amounts of free cholesterol accumulated even in the presence of efficient cholesterol acceptor particles, apolipoprotein high density lipoproteinphosphatidylcholine complexes which stimulate cholesterol efflux. Also, increased accumulation of free cholesterol in the lipid fraction was observed when cholesteryl ester-loaded cells were treated with the compound U-18666A which blocks the movement of lysosomal cholesterol. The data demonstrate that the phagocytic incorporation and hydrolysis of cholesteryl ester lipid droplets by macrophage foam cells lead to a substantial accumulation of free cholesterol in the
A Multi-Modal Face Recognition Method Using Complete Local Derivative Patterns and Depth Maps

In this paper, we propose a multi-modal 2D + 3D face recognition method for a smart city application based on a Wireless Sensor Network (WSN) and various kinds of sensors. Depth maps are exploited for the 3D face representation. As for feature extraction, we propose a new feature called Complete Local Derivative Pattern (CLDP). It adopts the idea of layering and has four layers. In the whole system, we apply CLDP separately on Gabor features extracted from a 2D image and depth map. Then, we obtain two features: CLDP-Gabor and CLDP-Depth. The two features weighted by the corresponding coefficients are combined together in the decision level to compute the total classification distance. At last, the probe face is assigned the identity with the smallest classification distance. Extensive experiments are conducted on three different databases. The results demonstrate the robustness and superiority of the new approach. The experimental results also prove that the proposed multi-modal 2D + 3D method is superior to other multi-modal ones and CLDP performs better than other Local Binary Pattern (LBP) based features.
Long-Range Activation of Systemic Immunity through Peptidoglycan Diffusion in Drosophila

The systemic immune response of Drosophila is known to be induced both by septic injury and by oral infection with certain bacteria, and is characterized by the secretion of antimicrobial peptides (AMPs) into the haemolymph. To investigate other possible routes of bacterial infection, we deposited Erwinia carotovora (Ecc15) on various sites of the cuticle and monitored the immune response via expression of the AMP gene Diptericin. A strong response was observed to deposition on the genital plate of males (up to 20% of a septic injury response), but not females. We show that the principal response to genital infection is systemic, but that some AMPs, particularly Defensin, are induced locally in the genital tract. At late time points we detected bacteria in the haemolymph of immune deficient RelishE20 flies, indicating that the genital plate can be a route of entry for pathogens, and that the immune response protects flies against the progression of genital infection. The protective role of the immune response is further illustrated by our observation that RelishE20 flies exhibit significant lethality in response to genital Ecc15 infections. We next show that a systemic immune response can be induced by deposition of the bacterial elicitor peptidoglycan (PGN), or its terminal monomer tracheal cytotoxin (TCT), on the genital plate. This immune response is downregulated by PGRP-LB and Pirk, known regulators of the Imd pathway, and can be suppressed by the overexpression of PGRP-LB in the haemolymph compartment. Finally, we provide strong evidence that TCT can activate a systemic response by crossing epithelia, by showing that radiolabelled TCT deposited on the genital plate can subsequently be detected in the haemolymph. Genital infection is thus an intriguing new model for studying the systemic immune response to local epithelial infections and a potential route of entry for naturally occurring pathogens of Drosophila.
Accessible telephone directories

Abstract We reduce to a standard circuit-size complexity problem a relativisation of the P=NP question that we believe to be connected with the same question in the model for computation over the reals defined by L. Blum. M. Shub, and S. Smale. On this occasion, we set the foundations of a general theory for computation over an arbitrary structure, extending what these three authors did in the case of rings.
Stent and artery geometry determine intimal thickening independent of arterial injury.

BACKGROUND Clinical trials show that larger immediate postdeployment stent diameters provide greater ultimate luminal size, whereas animal data show that arterial injury and stent design determine late neointimal thickening. At deployment, a stent stretches a vessel, imposing a cross-sectional polygonal luminal shape that depends on the stent design, with each strut serving as a vertex. We asked whether this design-dependent postdeployment luminal geometry affects late neointimal thickening independently of the extent of strut-induced injury. METHODS AND RESULTS Stainless steel stents of 3 different configurations were implanted in rabbit iliac arteries for 3 or 28 days. Stents designed with 12 struts per cross section had 50% to 60% less mural thrombus and 2-fold less neointimal area than identical stents with only 8 struts per cross section. Sequential histological sectioning of individual stents showed that immediate postdeployment luminal geometry and subsequent neointimal area varied along the course of each stent subunit. Mathematical modeling of the shape imposed by the stent on the artery predicted late neointimal area, based on the re-creation of a circular vessel lumen within the confines of the initial stent-imposed polygonal luminal shape. CONCLUSIONS Immediate postdeployment luminal geometry, dictated by stent design, determines neointimal thickness independently of arterial injury and may be useful for predicting patterns of intimal growth for novel stent designs.
Pax5 Activates Immunoglobulin Heavy Chain V to DJ Rearrangement in Transgenic Thymocytes

Mice deficient for the B cell–restricted transcription factor Pax5 show a defect in the VH to DJH rearrangement step of immunoglobulin heavy chain gene assembly even though the expression of the V(D)J recombinase is not diminished in Pax5 −/− pro–B cells. To investigate whether Pax5 is limiting for VH to DJH rearrangement, we generated transgenic mice which express Pax5 in developing thymocytes. We show that enforced expression of Pax5 in thymocytes results in a partial block in T cell development due to defective pre-TCR signaling in β-selection. Moreover, our results demonstrate that expression of Pax5 in early thymocytes is sufficient to induce VH to DJH rearrangements in CD4+CD8+ T cells and lead us to suggest that Pax5 may play a direct role in the lineage-specific regulation of immunoglobulin heavy chain gene rearrangement.
Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression

We propose a new method for constructing genetic network from gene expression data by using Bayesian networks. We use nonparametric regression for capturing nonlinear relationships between genes and derive a new criterion for choosing the network in general situations. In a theoretical sense, our proposed theory and methodology include previous methods based on Bayes approach. We applied the proposed method to the S. cerevisiae cell cycle data and showed the effectiveness of our method by comparing with previous methods.
The proverbial chicken or the egg? Dissection of the role of cell-free hemoglobin versus reactive oxygen species in sickle cell pathophysiology.

SICKLE CELL PATHOPHYSIOLOGY comprises a complex interplay of episodic vasoocclusive events, ischemia-reperfusion injury, overproduction of reactive oxygen species (ROS), inflammation, endothelial activation, and hemolysis, all somehow driven by a single amino acid substitution in the -globin chain of hemoglobin. Hemolysis and oxidative stress act synergistically to promote vascular dysfunction in sickle cell disease (SCD). As a result of chronic hemolysis, levels of free plasma hemoglobin are increased at baseline and nitric oxide (NO) bioavailability is diminished, producing endothelial dysfunction that has been linked to chronic vasculopathic complications of SCD such as pulmonary hypertension, cutaneous leg ulceration, priapism, and sudden death (14, 18, 19, 22, 23, 25). NO regulates vasorelaxation and also possesses antioxidant, antiadhesive, and antithrombotic properties (33). NO is produced from the substrate L-arginine by endothelial nitric oxide synthase (eNOS) and mediates vasorelaxation through a paracrine action on vascular smooth muscle cells underlying the endothelium. Endothelial dysfunction, characterized by impaired vascular responsiveness resulting from decreased NO bioavailability, is associated with atherosclerosis, diabetes mellitus, hypertension, hypercholesterolemia, smoking, and obesity, illustrating the central importance of NO in the physiological regulation of vasomotor activity (3, 6).
MiR-487a Promotes TGF-β1-induced EMT, the Migration and Invasion of Breast Cancer Cells by Directly Targeting MAGI2

Tumor metastasis is a complex and multistep process and its exact molecular mechanisms remain unclear. We attempted to find novel microRNAs (miRNAs) contributing to the migration and invasion of breast cancer cells. In this study, we found that the expression of miR-487a was higher in MDA-MB-231breast cancer cells with high metastasis ability than MCF-7 breast cancer cells with low metastasis ability and the treatment with transforming growth factor β1 (TGF-β1) significantly increased the expression of miR-487a in MCF-7 and MDA-MB-231 breast cancer cells. Subsequently, we found that the transfection of miR-487a inhibitor significantly decreased the expression of vimentin, a mesenchymal marker, while increased the expression of E-cadherin, an epithelial marker, in both MCF-7 cells and MDA-MB-231 cells. Also, the inactivation of miR-487a inhibited the migration and invasion of breast cancer cells. Furthermore, our findings demonstrated that miR-487a directly targeted the MAGI2 involved in the stability of PTEN. The down-regulation of miR-487a increased the expression of p-PTEN and PTEN, and reduced the expression of p-AKT in both cell lines. In addition, the results showed that NF-kappaB (p65) significantly increased the miR-487a promoter activity and expression, and TGF-β1 induced the increased miR-487a promoter activity via p65 in MCF-7 cells and MDA-MB-231 cells. Moreover, we further confirmed the expression of miR-487a was positively correlated with the lymph nodes metastasis and negatively correlated with the expression of MAGI2 in human breast cancer tissues. Overall, our results suggested that miR-487a could promote the TGF-β1-induced EMT, the migration and invasion of breast cancer cells by directly targeting MAGI2.
Expansion of the Tonotopic Area in the Auditory Cortex of the Blind

A part of the core area of the auditory cortex was examined in nine blind and10 sighted individuals by magnetic source imaging and was found to be enlarged by a factor of 1.8 in the blind compared with the sighted humans. Moreover, the latency of the N1m component of the auditory-evoked magnetic response was significantly decreased in the blind. The development of use-dependent cortical reorganization may be a consequence of the absence of visual input in combination with enhanced auditory activity generated by the long-term concentration by blind individuals on nonvisual cues to interact appropriately with the environment. It is consistent with and well suited to mediate the demonstrated increased ability of the blind to accurately localize acoustic sources in peripheral auditory fields and to decode speech.
A tale of two parasites: the comparative epidemiology of cryptosporidiosis and giardiasis

SUMMARY New Zealand has a higher reported incidence of cryptosporidiosis and giardiasis than most other developed countries. This study aimed to describe and compare the epidemiology of these infections in New Zealand, to better understand their impact on public health and to gain insight into their probable modes of transmission. We analysed cryptosporidiosis and giardiasis notification data for a 10-year period (1997–2006). Highest rates for both diseases were in Europeans, children aged 0–5 years, and those living in low-deprivation areas. Cryptosporidiosis distribution was consistent with mainly farm animal (zoonotic) reservoirs. There was a dose–response relationship with increasing grades of rurality, marked spring seasonality, and positive correlation with farm animal density. Giardiasis distribution was consistent with predominantly human (anthroponotic) reservoirs, with an important contribution from overseas travel. Further research should focus on methods to reduce transmission of Cryptosporidium in rural areas and on reducing anthroponotic transmission of Giardia.
Hyperbaric oxygen does not improve outcome in patients with necrotizing soft tissue infection.

BACKGROUND Patients with necrotizing soft tissue infections (NSTIs) require prompt surgical debridement, appropriate intravenous antibiotics, and intensive support. Despite aggressive treatment, their mortality and morbidity rates remain high. The benefit of hyperbaric oxygen (HBO) as an adjunctive treatment is controversial. We investigated the effect of HBO in treating NSTIs. METHODS We analyzed clinical data retrospectively for 78 patients with NSTIs: 30 patients at one center were treated with surgery, antibiotics, and supportive care; 48 patients at a different center received adjunctive HBO treatment. We compared the two groups in terms of demographic characteristics, risk factors, NSTI microbiology, and patient outcomes. To identify variables associated with higher mortality rates, we used logistic regression analysis. RESULTS Demographic characteristics and risk factors were similar in the HBO and non-HBO groups. The mean patient age was 49.5 years; 37% of the patients were female, and 49% had diabetes mellitus. Patients underwent a mean of 3.0 excisional debridements. The median hospital length of stay was 16.5 days; the median duration of antibiotic use was 15.0 days. In 36% of patients, cultures were polymicrobial; group A Streptococcus was the organism most commonly isolated (28%). We identified no statistically significant differences in outcomes between the two groups. The mortality rate for the HBO group (8.3%) was lower, although not significantly different (p = 0.48), than that observed for the non-HBO group (13.3%). The number of debridements was greater in the HBO group (3.0; p = 0.03). The hospital length of stay and duration of antibiotic use were similar for the two groups. Multivariable analysis showed that hypotension on admission and immunosuppression were significant independent risk factors for death. CONCLUSIONS Adjunctive use of HBO to treat NSTIs did not reduce the mortality rate, number of debridements, hospital length of stay, or duration of antibiotic use. Immunosupression and early hypotension were important risk factors associated with higher mortality rates in patients with NSTIs.
TRANSMITTING HUGE AMOUNTS OF DATA: DESIGN, IMPLEMENTATION AND PERFORMANCE OF THE BULK DATA TRANSFER MECHANISM IN ALMA ACS

We present and discuss the design, implementation and performance of the bulk data transfer mechanism developed in the framework of the ALMA (Atacama Large Millimeter Array) Common Software (ACS) [2][6]. ALMA will be the largest millimetre wavelength astronomical interferomete r in the world consisting of 64 12-meters antennas, and the need for transferring efficiently huge amounts of data arises consequently. For example, a typical output data rate expected from the correlator (the device responsible for the processing of raw digitized data from the antennas) will be of the order of 64 MB per second [1]. Since all subsystems in ALMA rely on a communication infrastructure (ACS), which is CORBA -based, this poses some problems to meet the stringent QoS (quality-of-service) requirements. It is well known in fact that DOC (Dis tributed Object Computing) middleware, such as CORBA, increases the packet latency due to marshalling/d e -marshalling, to usage of the IIOP protocol, etc. To cope with ALMA requirements and to overcome the CORBA potential bottleneck, we developed a transfer mechanism based on the ACE/TAO CORBA Audio/Video (A/V) Streaming service. This architecture uses CORBA for handshaking, but allows an efficient data transfer by creating out -of-bound stream(s) of data (i.e. bypassing the CORBA protocol), thus enabling ALMA applications to keep leveraging the inherent portability and flexibility benefits of the ACS middleware. Our infrastructure, which was put on the top of the ACE/TAO A/V Streaming service implementation, allows creating one or more out -of-bound flows in a simple way (a flow is a continuous sequence of frames in a clearly identified direction); each flow can be configured using different communication protocols (e.g. TCP, UDP) with a measured efficiency comparable to that of a raw socket connection. We designed and implemented also a Distributer model, which mimics a multicast behaviour. One or more receivers can subscribe to a common object (the Distributer) which receives data from one sender (e.g. the correlator), and dispatches them to all the subscribed receivers using out-of-bound connections.
J O U R N a L O F Veterinary Science Detection and Molecular Characterization of Infectious Bronchitis Virus Isolated from Recent Outbreaks in Broiler Flocks in Thailand

Thirteen field isolates of infectious bronchitis virus (IBV) were isolated from broiler flocks in Thailand between January and June 2008. The 878-bp of the S1 gene covering a hypervariable region was amplified and sequenced. Phylogenetic analysis based on that region revealed that these viruses were separated into two groups (I and II). IBV isolates in group I were not related to other IBV strains published in the GenBank database. Group 1 nucleotide sequence identities were less than 85% and amino acid sequence identities less than 84% in common with IBVs published in the GenBank database. This group likely represents the strains indigenous to Thailand. The isolates in group II showed a close relationship with Chinese IBVs. They had nucleotide sequence identities of 97-98% and amino acid sequence identities 96-98% in common with Chinese IBVs (strain A2, SH and QXIBV). This finding indicated that the recent Thai IBVs evolved separately and at least two groups of viruses are circulating in Thailand.