Miracle-dz/UniFAR-FTUs huggingface dataset:
HP1 modulates the transcription of cell-cycle regulators in Drosophila melanogaster

Heterochromatin protein 1 (HP1) was originally described as a non-histone chromosomal protein and is required for transcriptional gene silencing and the formation of heterochromatin. Although it is localized primarily at pericentric heterochromatin, a scattered distribution over a large number of euchromatic loci is also evident. Here, we provide evidence that Drosophila HP1 is essential for the maintenance of active transcription of euchromatic genes functionally involved in cell-cycle progression, including those required for DNA replication and mitosis. Depletion of HP1 in proliferating embryonic cells caused aberrant progression of the cell cycle at S phase and G2/M phase, linked to aberrant chromosome segregation, cytokinesis, and an increase in apoptosis. The chromosomal distribution of Aurora B, and the level of phosphorylation of histone H3 serine 10 were also altered in the absence of HP1. Using chromatin immunoprecipitation analysis, we further demonstrate that the promoters of a number of cell-cycle regulator genes are bound to HP1, supporting a direct role for HP1 in their active transcription. Overall, our data suggest that HP1 is essential for the maintenance of cell-cycle progression and the transcription of cell-cycle regulatory genes. The results also support the view that HP1 is a positive regulator of transcription in euchromatin.
Slc15a4, a Gene Required for pDC Sensing of TLR Ligands, Is Required to Control Persistent Viral Infection

Plasmacytoid dendritic cells (pDCs) are the major producers of type I IFN in response to viral infection and have been shown to direct both innate and adaptive immune responses in vitro. However, in vivo evidence for their role in viral infection is lacking. We evaluated the contribution of pDCs to acute and chronic virus infection using the feeble mouse model of pDC functional deficiency. We have previously demonstrated that feeble mice have a defect in TLR ligand sensing. Although pDCs were found to influence early cytokine secretion, they were not required for control of viremia in the acute phase of the infection. However, T cell priming was deficient in the absence of functional pDCs and the virus-specific immune response was hampered. Ultimately, infection persisted in feeble mice. We conclude that pDCs are likely required for efficient T cell priming and subsequent viral clearance. Our data suggest that reduced pDC functionality may lead to chronic infection.
Detection of KRAS Oncogene in Peripheral Blood as a Predictor of the Response to Cetuximab Plus Chemotherapy in Patients with Metastatic Colorectal Cancer

Purpose: Previously we developed membrane-arrays as a promising tool to detect circulating tumor cells (CTC) with KRAS oncogene in patients with malignancies. This study was conducted to determinate the predictive values of CTCs with KARS mutation by membrane-arrays for metastatic colorectal cancer patients treated with cetuximab plus chemotherapy. Experimental Design: Seventy-six metastatic colorectal cancer patients receiving cetuximab plus FOLFIRI or FOLFOX-4 chemotherapy were enrolled. KRAS mutation status in the peripheral blood of these patients was analyzed using membrane-arrays, and KRAS mutation status in tumors was analyzed by DNA sequencing. Results: Among 76 metastatic colorectal cancer patients, KRAS mutations in tumors and in peripheral blood were identified in 33 (43.4%) and 30 (39.5%) patients, respectively. The detection sensitivity, specificity, and accuracy of membrane-arrays for CTCs with KRAS oncogene were 84.4%, 95.3%, and 90.8%, respectively, and indeed a highly significant correlation to KRAS mutations in tumors (P < 0.0001) was observed. Forty-five (59.2%) patients responded to cetuximab plus chemotherapy, and 41 and 40 were wild-type KRAS in tumors and peripheral blood, respectively (both P < 0.0001). Patients with tumors that harbor wild-type KRAS are more likely to have a better progression-free survival and overall survival when treated with cetuximab plus chemotherapy (P < 0.0001). Likewise, patients with CTCs of wild-type KRAS in peripheral blood express a better progression-free survival and overall survival when treated with cetuximab plus chemotherapy (P < 0.0001). Conclusions: These findings provide evidence that detection of KRAS mutational status in CTCs, by gene expression array, has potential for clinical application in selecting metastatic colorectal cancer patients most likely to benefit from cetuximab therapy.
Polymorphisms of Catechol-O-Methyltransferase in Men with Renal Cell Cancer

The estrogen metabolite, 4-hydroxy-estrogen, has been shown to play a role in malignant transformation of male kidneys. To counteract the effects of this catechol-estrogen, the catechol-O-methyltransferase (COMT) enzyme is capable of neutralizing the genotoxic effects of this compound. A polymorphic variant of COMT has been shown to have a reduced enzyme activity, and thus, we hypothesize that single nucleotide polymorphisms of the COMT gene can be a risk factor for renal cell cancer (RCC). To determine this hypothesis, a study of a Japanese male population was used and the genetic distributions of COMT polymorphisms at codons 62 (C→T), 72 (G→T), and 158 (G→A) were analyzed in 157 normal healthy subjects and 123 sporadic RCC (clear cell type) samples by using a sequence-specific PCR technique. These experiments show that the variant genotype (P = 0.025) and allele (P = 0.011) at codon 62 is a risk factor for RCC. The odds ratio and 95% confidence interval for cancer were 3.16 and 1.29 to 7.73, respectively, for the T/T genotype as compared with wild-type. No associations for renal cancer were found at either codons 72 or 158 in this Japanese male population. However, codons 62 and 158 were observed to be in linkage disequilibrium, and haplotype analysis shows the combined forms of T-A, T-G, and C-A to be associated with RCC as compared with C-G (P < 0.001). When evaluating the risk of COMT polymorphisms with grade of cancer, no associations were observed for any of the genotypes. This study is the first to report COMT polymorphism to be associated with RCC. These results are important in understanding the role of COMT polymorphisms in the pathogenesis of RCC. (Cancer Epidemiol Biomarkers Prev 2007;16(1):92–7)
Dwarf shrub hydraulics: two Vaccinium species (Vaccinium myrtillus, Vaccinium vitis‐idaea) of the European Alps compared

Vaccinium myrtillus and Vaccinium vitis‐idaea are two dwarf shrubs widespread in the European Alps. We studied the hydraulics of these species hypothesizing that (1) the hydraulic architecture of dwarf shrubs differs from trees, (2) hydraulic properties reflect the species' ecological amplitude and (3) hydraulic properties vary spatially and seasonally. Key hydraulic parameters (osmotic potential, turgor loss point, xylem hydraulic conductivity, vulnerability to drought‐induced embolism, stomata closure, drought‐induced cell damage and embolism repair) and related wood anatomical traits (conduit diameter and conduit wall reinforcement) were analyzed at four sites in Tyrol, Austria. Both species exhibited low hydraulic safety as well as low hydraulic efficiency. Fifty percentage embolism accumulated at −2.08 (V. myrtillus) and −1.97 MPa (V. vitis‐idaea), 88% stomata closure was at −2.19 and −2.35 MPa, respectively. After drought, both species showed embolism repair on re‐watering. Site‐specific variation within species was low, while seasonal changes in embolism resistance and turgor loss point were observed. Results indicate that studied Vaccinium species have a high risk for embolism formation. This is balanced by refilling capacities, which are probably based on the small growth height of dwarf shrubs. V. vitis‐idaea, which occurs on drier sites, showed more efficient repair and a lower turgor loss point than V. myrtillus.
Developmental Study of a Lamellar Body Fraction Isolated From Human Amniotic Fluid

Summary: Several properties of a pellet fraction obtained on centrifuging amniotic fluid at 10,000 x g for 20 min were investigated. From these analyses, we defined a developmental profile which appears to describe the maturational process of the fetal lung surfactant system. At 14 to 18 wk gestation, the pellet fraction consisted of membrane-bound vesicles without internal lamellae. The phospholipid composition did not resemble that of surfactant, the major phospholipid being sphingomyelin. This stage, designated as presurfactant, persisted until 30 to 32 wk gestation. After this time, the phospholipid concentration of the pellet fraction increased continuously throughout development, and gradual but continuous changes in phospholipid composition were observed. Lecithin and phosphatidylinositol increased between 39 and 35 wk gestation. Interruption of pregnancies at this stage, termed onset of surfactant synthesis, resulted in 100% incidence of respiratory distress syndrome. From 36 wk gestation to postterm, the pellet fraction contained structures with the characteristic morphology of the lamellar inclusion bodies. The presence of single membrane components in these preparations did not contribute to the phospholipid composition. Early formed lamellar bodies lacked phosphatidylglycerol and had a high content of phosphatidylinositol. Once phosphatidylglycerol appeared in the lamellar body fraction, it continued to increase, accompanied by a decrease in phosphatidylinositol with little change in lecithin. A phosphatidylglycerol value of greater than 1% of the total phospholipids appeared to represent the stage of maturity at which there was no risk of respiratory distress syndrome.Speculation: The characterization of a pellet fraction obtained from human amniotic fluid led to the description of a developmental profile which appears to define the individual stages involved in the biochemical maturation of the fetal lung surfactant system. The development of respiratory distress syndrome appears to be very much dependent on the stage at which this process is interrupted. It is expected that such analyses can be adapted to provide a simple, yet specific index of fetal pulmonary maturity.
Security architecture for wireless sensor networks using frequency hopping and public key management

The security aspect of wireless sensor networks has taken the attention of numerous researchers in the past several years. It has recently been proven that public keys are now feasible in wireless sensor networks but still consume a lot of processing time and memory. In this paper we propose the use of public keys based on ECC to exchange symmetric keys that will be used to encrypt communications. In addition, we propose a time segmentation approach that enables frequency hopping time slotted communications. Nodes secretly exchange frequency hopping sequences that enable them to fight against jamming and eavesdropping.
A comparison of the long‐term consequences of vaginal delivery versus caesarean section on the prevalence, severity and bothersomeness of urinary incontinence subtypes: a national cohort study in primiparous women

To study the effect of one vaginal delivery (VD) compared with one caesarean section (CS) on the prevalence, severity and bothersomeness of urinary incontinence (UI) subtypes—stress (SUI), urge (UUI) and mixed (MUI)—20 years after delivery.
Software botryology. Automatic clustering of software systems

It has long been recognized that the decomposition of a large software system into "meaningful" subsystems is essential for both the development and maintenance phases of a software project. We introduce the term "software botryology" for the area of research that attempts to automatically cluster a software system ("botrys" is the ancient Greek word for a cluster of grapes). In this paper, we survey approaches to the clustering problem from researchers in the software engineering community. We also present clustering techniques used in other disciplines and argue that their utilization in a software context could lead to better solutions to the software clustering problem. Finally, we outline research challenges and open problems of interest.
STUDIES ON THE SENSITIZATION OF ANIMALS WITH SIMPLE CHEMICAL COMPOUNDS

With the view of making new types of chemicals accessible for investigations on drug hypersensitiveness, methods have been devised for sensitizing animals with diazomethane and mustard oil, two non-aromatic compounds. Guinea pigs have been sensitized to diazomethane, a substance of high reactivity and known to cause severe allergic effects in man. With the second substance, allylisothiocyanate, likewise capable of forming conjugates with substances in the animal body, sensitization effects have been obtained in man and in hogs. Sensitization in human beings was successful with one out of six individuals treated. The observations indicate species and individual differences as regards the ability to become sensitized to various chemical compounds.
Detection of Contrast Agents: Plane Wave Versus Focused Transmission

Ultrasound contrast agent (UCA) imaging provides a cost-effective diagnostic tool to assess tissue perfusion and vascular pathologies. However, excessive transmission (TX) levels may negatively impact both uniform diffusion and survival rates of contrast agents, limiting their density and thus their echogenicity. Contrast detection methods with both high sensitivity and low-contrast destruction rate are thus essential to maintain diagnostic capabilities. Plane-wave TX with a high number of compounding angles has been suggested to produce good quality images at pressure levels that do not destroy UCA. In this paper, we performed a quantitative evaluation of detection efficacy of flowing UCA with either traditional focused scanning or ultrafast plane-wave imaging. Amplitude modulation (AM) at nondestructive pressure levels was implemented in the ULA-OP ultrasound research platform. The influence of the number of compounding angles, peak-negative pressure, and flow speed on the final image quality was investigated. Results show that the images obtained by compounding multiple angled plane waves offer a greater contrast (up to a 12-dB increase) with respect to focused AM. This increase is attributed mainly to noise reduction caused by the coherent summation in the compounding step. Additionally, we show that highly sensitive detection is already achieved with a limited compounding number ($N <; 16$), thus suggesting the feasibility of continuous contrast monitoring at a high frame rate. This capability is essential to properly detect contrast agents flowing at high speed, as an excessive angle compounding is shown to be destructive for the contrast signal, as the UCA motion quickly causes loss of correlation between consecutive echoes.
GLOTTAL FLOW MODELS : WAVEFORMS, SPECTRA AND PHYSICAL MEASUREMENTS

Most of the main time-domain glottal flow models proposed in the literature can ultimately be described in a unified manner by a set of five parameters: the fundamental frequency f0, the amplitude of voicing Av, the open quotient Oq, the asymmetry coefficient αm and the return phase quotient Qa. Time and frequency-domain analytical formulations are given in the case of an abrupt closure. The two main spectral components (glottal formant and spectral slope) are detailed and related to the time-domain parameters. The use of signal models for voice source analysis is discussed with regards to the open quotient, on the basis of physical (electroglottographic and acoustic) measurements.
Viral load of the highly pathogenic avian influenza H5N1 virus in infected human tissues

The highly pathogenic avian influenza A (H5N1) virus is a virulent virus that causes an acute febrile respiratory disease with high mortality in humans. To gain a better insight of H5N1 viral distributions in infected human tissues, the levels of viral RNA were determined in the autopsy tissues from two patients who were infected with H5N1 virus by using real‐time reverse transcription‐polymerase chain reaction. In one patient who died on day 6 of the illness, the viral load in the lung was extremely high, whereas the levels of viral RNA in the other organs were more than 6 log lower. In the other patient who died on day 17 of the illness, the viral load was similar in the lung and other organs, and was comparable to the viral load in the extra‐pulmonary tissues of the first patient. These results suggested that while the H5N1 virus can cause disseminated infection in humans, the lung is still the major site of viral replication, and viral replication in the lung in the later stages may decrease as a result of the depletion of the available target cells. In addition, the mRNA levels of the tumor necrosis factor‐α (TNF‐α) were found to be associated with the viral titers. J. Med. Virol. 83:1418–1423, 2011. © 2011 Wiley‐Liss, Inc.
Effect of antisense microRNA targeting survivin on rectal cancer HRC-9698 cells and its mechanism.

BACKGROUND Rectal cancer seriously threats to human health. Traditional chemotherapy drugs might kill rectal cancer cells while easy cause side effects and clinical complications. Therefore, it is necessary to explore possible new methods for rectal cancer treatment. Survivin is an important tumor-specific protein. Previous researches showed it may be closely related to nasopharyngeal carcinoma. Its role in rectal cancer remains unclear. METHODS Cultivate human rectal cancer HRC-9698 cells. Antisense microRNA targeting survivin and control miRNA were constructed and transfected to HRC-9698 cells. MTT assay was applied to detect cell growth. Flow cytometry was used to test cell apoptosis. Western blot was performed to detect Osteopontin expression level. Colony formation and transwell assay were used to test cell clone formation and invasion abilities. RESULTS Antisense microRNA targeting survivin can inhibit HRC-9698 cell proliferation and induce its apoptosis. Antisense microRNA targeting survivin decreased osteopontin expression level. Overexpressed osteopontin inhibited antisense microRNA targeting survivin induced cell apoptosis. Antisense microRNA targeting survivin suppressed HRC-9698 cells' colony formation and invasion abilities. CONCLUSION Antisense microRNA targeting survivin induced osteopontin participated HRC-9698 cell apoptosis. Antisense microRNA targeting survivin inhibited HRC-9698 cell colony formation and invasive abilities, indicating that survivin may play its anti-tumor effect through inducing cell apoptosis and inhibiting cell metastasis and invasion.
A Meta-Analytic Review of Stand-Alone Interventions to Improve Body Image

Objective Numerous stand-alone interventions to improve body image have been developed. The present review used meta-analysis to estimate the effectiveness of such interventions, and to identify the specific change techniques that lead to improvement in body image. Methods The inclusion criteria were that (a) the intervention was stand-alone (i.e., solely focused on improving body image), (b) a control group was used, (c) participants were randomly assigned to conditions, and (d) at least one pretest and one posttest measure of body image was taken. Effect sizes were meta-analysed and moderator analyses were conducted. A taxonomy of 48 change techniques used in interventions targeted at body image was developed; all interventions were coded using this taxonomy. Results The literature search identified 62 tests of interventions (N = 3,846). Interventions produced a small-to-medium improvement in body image (d + = 0.38), a small-to-medium reduction in beauty ideal internalisation (d + = -0.37), and a large reduction in social comparison tendencies (d + = -0.72). However, the effect size for body image was inflated by bias both within and across studies, and was reliable but of small magnitude once corrections for bias were applied. Effect sizes for the other outcomes were no longer reliable once corrections for bias were applied. Several features of the sample, intervention, and methodology moderated intervention effects. Twelve change techniques were associated with improvements in body image, and three techniques were contra-indicated. Conclusions The findings show that interventions engender only small improvements in body image, and underline the need for large-scale, high-quality trials in this area. The review identifies effective techniques that could be deployed in future interventions.
Impact of Perioperative Infarcts After Cardiac Surgery

Background and Purpose— Brain injury after cardiac surgery is a serious concern for patients and their families. The purpose of this study was to use 3-T fluid attenuated inversion recovery MRI to characterize new and preexisting cerebral ischemic lesions in patients undergoing cardiac surgery and to test whether the accumulation of new ischemic lesions adversely affects cognition. Methods— Digital comparison of before and after fluid attenuated inversion recovery MRI images was performed for 77 cardiac surgery patients. The burden of preexisting versus new ischemic lesions was quantified and compared with the results of baseline and postoperative neuropsychological testing. Results— After surgery, new lesions were identified in 31% of patients, averaging 0.5 lesions per patient (67 mm3 [0.004%] of brain tissue). Patients with preexisting lesions were 10× more likely to receive new lesions after surgery than patients without preexisting lesions. Preexisting ischemic lesions were observed in 64% of patients, averaging 19.4 lesions (1542 mm3 [0.1%] of brain tissue). New lesions in the left hemisphere were significantly smaller and more numerous (29 lesions; median volume, 44 mm3; volume range, 5–404 mm3) than those on the right (10 lesions; median volume, 128 mm3; volume range, 13–1383 mm3), which is consistent with a cardioembolic source of particulate emboli. Overall, the incidence of postoperative cognitive decline was 46% and was independent of whether new lesions were present. Conclusions— New lesions after cardiac surgery added a small (≈4%) contribution to the burden of preexisting cerebrovascular disease and did not seem to affect cognitive function. Clinical Trial Registration— URL: http://public.ukcrn. org.uk. Unique identifier: UKCRN ID: 11702.