Miracle-dz/UniFAR-FTUs huggingface dataset:
Variants in 6q25.1 Are Associated with Mammographic Density in Malaysian Chinese Women

Background: Mammographic density is an established risk factor for breast cancer and has a strong heritable component. Genome-wide association studies (GWAS) for mammographic density conducted in women of European descent have identified several genetic associations, but none of the studies have been tested in Asians. We sought to investigate whether these genetic loci, and loci associated with breast cancer risk and breast size, are associated with mammographic density in an Asian cohort. Methods: We conducted genotyping by mass spectrometry in 1,189 women (865 Chinese, 187 Indian, and 137 Malay). Quantitative measurements of mammographic density were performed using ImageJ, a fully automated thresholding technique. The associations of SNPs to densities were analyzed using linear regression models. Results: We successfully evaluated the associations of 36 SNPs with mammographic densities. After adjusting for age, body mass index, parity, and menopausal status, we found that in our cohort of 865 Malaysian Chinese, three SNPs in the 6q25.1 region near ESR1 (rs2046210, rs12173570, and rs10484919) that were associated with mammographic density, breast cancer risk, or breast size in previous GWAS were significantly associated with both percentage density and absolute dense area. We could not replicate the most significant association found previously in European women (rs10995190, ZNF365 gene) because the minor allele was absent for Asian women. Conclusion: We found that the directions of genetic associations were similar to those reported in Caucasian women. Impact: Our results show that even in Asian women with lower population risk to breast cancer, there is shared heritability between mammographic density and breast cancer risk. Cancer Epidemiol Biomarkers Prev; 25(2); 327–33. ©2015 AACR.
Evaluation of Newly Developed Immunoperoxidase Monolayer Assays for Detection of Antibodies against Bovine Herpesvirus 4

ABSTRACT This study describes the evaluation of immunoperoxidase monolayer assays (IPMAs) for detection of antibodies against bovine herpesvirus 4 (BHV4) DN-599 or BHV4 LVR 140 in sera of cattle. We compared the quality of these IPMAs with the quality of a BHV4 indirect enzyme-linked immunosorbent assay (ELISA). In addition, a preliminary serological survey of BHV4 antibodies was carried out to estimate the seroprevalence of BHV4 in Dutch cattle at different ages. The specificities of both BHV4 IPMAs were 1.00. The geometrical mean titers (detection limit) of the BHV4 IPMAs were twice as high as that of the BHV4 indirect ELISA. In experimentally infected cattle, BHV4 antibodies were detectable by IPMAs 16 to 18 days postinfection, which was almost 2 weeks earlier than in the indirect ELISA. The reproducibility of the BHV4 DN-599 IPMA (κD value, 0.92) and of the BHV4 LVR 140 IPMA (κD value, 0.87) were good. For field sera the overall agreement between the BHV4 indirect ELISA and the two BHV4 IPMAs, DN-599 and LVR 140, was 95 and 96%, respectively. The serological-survey study showed that the estimated seroprevalence of BHV4 in Dutch cattle was 16 to 18% and that the percentage of BHV4-positive animals varied by age category (between 6 and 43%). In summary, the two BHV4 IPMA formats have several advantages that make IPMA a useful alternative to the BHV4 indirect ELISA for detecting BHV4 antibodies in cattle.
Expressions of Nuclear Factor κB, Inducible Nitric Oxide Synthase, and Vascular Endothelial Growth Factor in Adenoid Cystic Carcinoma of Salivary Glands: Correlations with the Angiogenesis and Clinical Outcome

Objective: To evaluate the expressions of nuclear factor κB (NF-κB p65), inducible nitric oxide synthase enzyme (iNOS), and vascular endothelial growth factor (VEGF) in relation to angiogenesis (microvessel density, MVD) and clinical outcomes in adenoid cystic carcinoma (ACC) of salivary glands. Methods: Immunohistochemical staining was used to quantify the protein expression levels of NF-κB p65, iNOS, and VEGF in 80 surgically resected ACCs and 20 normal salivary tissues. In all cases of ACCs, MVD was evaluated by counting CD34-reactive endothelial cells or endothelial cell clusters. Results: The nuclear localization of NF-κB p65 was only detected in ACC cells. Both iNOS and VEGF staining activities in ACCs were more significant than those in normal gland tissues (P < 0.01). MVD had significant correlations with NF-κB p65, iNOS, and VEGF expressions (P < 0.01). In three histologic types of ACCs, the NF-κB, iNOS, VEGF expressions, and MVD were significantly higher in solid type than in cribriform and tubular types (P < 0.01). The NF-κB, iNOS, VEGF expressions, and MVD were significantly correlated with clinical stage, tumor size, vascular invasion, recurrence, and metastasis (P < 0.05). Multivariate analysis showed NF-κB, iNOS and VEGF expression, MVD, solid histotype, and perineural invasion had an independent prognostic effect on overall survival. Conclusion: The expressions of NF-κB p65, iNOS, and VEGF were related with MVD. Clinical outcomes raised the possibility that the overexpression of these cytokines might contribute to tumor angiogenesis and have prognostic value in ACCs.
Amnesia due to Lesions Confined to the Hippocampus: A Clinical-Pathologic Study

Reported here is the case of a 65-year-old man who suffered a burst of severe, repetitive generalized seizures (status epilepticus). On recovery of consciousness he was left with a profound impairment of memory, which remained unchanged for the subsequent 30 months of his life. During this period the cognitive defect was fully documented. Careful neuropathologic examination disclosed the presence of remarkably discrete lesions, confined to the hippocampus on each side. Because of the rarity of well-documented instances of this type and their importance in the study of memory function, we are reporting our case in some detail.
Use of dexmedetomidine in children after cardiac and thoracic surgery*

Objective: In this report, we describe our experience with the use of dexmedetomidine in spontaneously breathing as well as in mechanically ventilated patients, after congenital cardiac and thoracic surgery. Design: Retrospective case series. Setting: University hospital, pediatric cardiac intensive care unit. Patients: Thirty-three spontaneously breathing and five mechanically ventilated patients who received dexmedetomidine after cardiothoracic surgery. Interventions: None. Measurements and Main Results: Thirty-eight patients, age 8 ± 1.1 yrs old and weight 29 ± 3.8 kg, were included. Seven patients (18%) were <1 yr old. Dexmedetomidine was used as a primary sedative and analgesic agent, and when its effect was considered inadequate, despite incremental infusion doses, a rescue agent was administered. The initial dexmedetomidine infusion dose was 0.32 ± 0.15 &mgr;g/kg/hr followed by an average infusion of 0.3 ± 0.05 &mgr;g/kg/hr (range 0.1–0.75 &mgr;g/kg/hr). There was a trend toward higher dexmedetomidine infusion requirement in patients <1 yr old compared with older children, 0.4 ± 0.13 vs. 0.29 ± 0.17 &mgr;g/kg/hr (p = .06). Desired sedation and analgesia were achieved during 93% and 83% of the dexmedetomidine infusion, respectively. According to the intensive care unit sedation scale (score 0–3) and two pain scales (Numeric Visual Analog Scale and Face, Legs, Activity, Cry, and Consolability, score 0–10), the mean sedation score was 1.3 ± 0.6 (mild sedation) and the mean pain score was 1.5 ± 0.9 (mild pain). The most frequently rescue drugs administered were fentanyl, morphine, and midazolam. Overall, 49 rescue doses of sedatives/analgesics were given. Patients <1 yr old required more rescue boluses than older children, 22 boluses (3.19 ± 0.8) vs. 27 boluses (0.8 ± 0.2, p = .003). Throughout the dexmedetomidine infusion there was no significant change in the systolic and diastolic blood pressure trend. Six patients (15%) had documented hypotension. In three, hypotension resolved with decreasing the dexmedetomidine infusion dose whereas in the other three, hypotension resolved after discontinuing the infusion. Although there was a trend toward lower heart rates, this was not clinically significant. One patient had an episode of considerable bradycardia without hypotension, which resolved shortly after discontinuing the dexmedetomidine infusion. No significant changes in the arterial blood gases or respiratory rates were observed. There was no mortality, and the total intensive care unit length of stay was 19 ± 2 hrs. Conclusions: Our data suggest that dexmedetomidine is a well-tolerated and effective agent for both spontaneously breathing and mechanically ventilated patients following congenital cardiac and thoracic surgery.
The importance of trust in electronic commerce

In this paper a new concept “trust”, and how it influences the process of managing the security of an organization operating in an electronic commerce environment has been introduced. Pragmatically, the study suggests awareness for organizations entering into electronic commerce and theoretically the study aims to develop a framework of trust and security for electronic commerce thus providing a set of guidelines for secure electronic commerce.
Video summarization using line segments, angles and conic parts

Video summarization is a process to extract objects and their activities from a video and represent them in a condensed form. Existing methods for video summarization fail to detect moving (dynamic) objects in the low color contrast area of a video frame due to the pixel intensities of objects and non-objects are almost similar. However, edges of objects are prominent in the low contrast regions. Moreover, to represent objects, geometric primitives (such as lines, arcs) are distinguishable and high level shape descriptors than edges. In this paper, a novel method is proposed for video summarization using geometric primitives such as conic parts, line segments and angles. Using these features, objects are extracted from each video frame. A cost function is applied to measure the dissimilarity of locations of geometric primitives to detect the movement of objects between consecutive frames. The total distance of object movement is calculated and each video frame is assigned a probability score. Finally, a set of key frames is selected based on the probability scores as per user provided skimming ratio or system default skimming ratio. The proposed approach is evaluated using three benchmark datasets—BL-7F, Office, and Lobby. The experimental results show that our approach outperforms the state-of-the-art method in terms of accuracy.
Evaluation of Mast Cell Distribution in Oral Lichen Planus and Lichenoid Lesions by Immunohistochemical and Histochemical Analysis

The histopathological assessment of Oral Lichen Planus (OLP) and oral lichenoid lesions is relatively subjective. The distinguishing criteria established by WHO effectively reproducible when all selection criteria were fulfilling but sometimes fail to provide a reliable diagnosis. The aim of the present study was to evaluate mast cell counts and their distribution among OLP and lichenoid lesions. The density and localization of mast cells was examined in 22 patients with a diagnosis of OLP (11 patients) or oral lichenoid reactions (11 patients) by c-kit/CD117 immunohistochemical and toluidine blue histochemical staining. Data were analyzed using either the Kruskal-Wallis or Mann-Whitney U tests. No significant difference in the total number of mast cells was observed between the two groups (P = 0.599); however, a significant difference was observed in mast cell counts between reticular and junctional zones (P<0.05). The findings of the present study suggest that mast cells play a key role in the pathogenesis of oral inflammation; however, the ability of mast cell measurements to reliably differentiate between lichen planus and other lichenoid mimickers was limited as the number of mast cells was found to be increased in both the conditions.
A Hybrid-Fuzzy Logic Guided Genetic Algorithm (H-FLGA) Approach for Resource Optimization in 5G VANETs

To support diversified quality of service demands and dynamic resource requirements of users in 5G driven VANETs, network resources need flexible and scalable resource allocation strategies. Current heterogeneous vehicular networks are designed and deployed with a connection-centric mindset with fixed resource allocation to a cell regardless of traffic conditions, static coverage, and capacity. In this paper, we propose a hybrid-fuzzy logic guided genetic algorithm (H-FLGA) approach for the software defined networking controller, to solve a multi-objective resource optimization problem for 5G driven VANETs. Realizing the service oriented view, the proposed approach formulates five different scenarios of network resource optimization in 5G VANETs. Furthermore, the proposed fuzzy inference system is used to optimize weights of multi-objectives, depending on the type of service requirements of customers. The proposed approach shows the minimized value of multi-objective cost function when compared with the GA. The simulation results show the minimized value of end-to-end delay as compared to other schemes. The proposed approach will help the network service providers to implement a customer-centric network infrastructure, depending on dynamic customer needs of users.
Between a rock and a hard place: TAVR and ESRD

Aortic stenosis in combination with end‐stage renal disease (ESRD) is a high‐risk combination for surgical valve replacement and little data exists on the role of transcatheter aortic valve replacement (TAVR) Pooled retrospective data from eight experienced TAVR sites suggests that TAVR can be accomplished in ESRD patients with first generation percutaneous valve at a risk similar to surgical approaches. Even with TAVR, valve replacement in the ESRD patient remain high risk and future improvements in technology and approaches to this poorly studied group are needed.
Polymorphisms of the Tryptophan Hydroxylase Gene and Serotonin 1 A Receptor Gene in Suicide Victims Among Japanese

Received November 10, 2003; revision accepted for publication December 26, 2003. Address for reprints: Maki Ohtani, Division of Forensic Sciences, Department of Social Medicine, Akita University School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan. e-mail: mohtani@arc.med.akita-u.ac. jp Polymorphisms of the Tryptophan Hydroxylase Gene and Serotonin 1A Receptor Gene in Suicide Victims Among Japanese
Fast and sensitive multiple sequence alignments on a microcomputer

A strategy is described for the rapid alignment of many long nucleic acid or protein sequences on a microcomputer. The program described can handle up to 100 sequences of 1200 residues each. The approach is based on progressively aligning sequences according to the branching order in an initial phylogenetic tree. The results obtained using the package appear to be as sensitive as those from any other available method.
Polypectomy of adenomas in the prevention of colorectal cancer: 10 years' follow-up of the Telemark Polyp Study I. A prospective, controlled population study.

BACKGROUND The efficacy of polypectomy in preventing colorectal cancer (CRC) has never been demonstrated in a controlled, prospective study. This must be done by randomization within a population with a high prevalence of colorectal polyps, and the feasibility and safety of endoscopic screening examination is a prerequisite for this type of study. METHODS The present study is a randomized, controlled study of the feasibility and safety of flexible sigmoidoscopic screening of a normal population sample of 799 men and women aged 50-59 years, findings at 2 and 6 years' colonoscopic follow-up, and the appearance of clinical colorectal cancer (CRC) after 10 years. RESULTS The attendance rate was high, and there were no complications. After 10 years 1 of 400 in the screening group had developed CRC (in the group of 76 (19%) not attending for screening examination). Four of 399 controls developed CRC. CONCLUSIONS Poor yield of polyps at follow-up, slow growth of in situ polyps, and no clinical CRC among screenees after 10 years provides support to infrequent or no colonoscopic follow-up after initial polypectomy in individuals with otherwise average risk of CRC.
Clinical role and biological function of CDK5 in hepatocellular carcinoma: A study based on immunohistochemistry, RNA-seq and in vitro investigation

To investigate the clinical role and biological function of cyclin-dependent kinase 5 (CDK5) in hepatocellular carcinoma (HCC), 412 surgically resected tissue samples (HCC, n=171; non-HCC=241) were obtained and analyzed with immunohistochemistry. The diagnostic and prognostic values of CDK5 expression levels in HCC were clarified. Moreover, RNA-seq data or microarray datasets from The Cancer Genome Atlas (TCGA) (HCC, n=374; normal, n=50) or other public databases (HCC, n=1864; non-tumor=1995) regarding CDK5 in HCC were extracted and examined. Several bioinformatic methods were performed to identify CDK5-regulated pathways. In vitro experiments were adopted to measure proliferation and apoptosis in HCC cells after CDK5 mRNA was inhibited in the HCC cell lines HepG2 and HepB3. Based on immunohistochemistry, CDK5 expression levels were notably increased in HCC tissues (n=171) compared with normal (n=33, P<0.001), cirrhosis (n=37, P<0.001), and adjacent non-cancerous liver (n=171, P<0.001) tissues. The up-regulation of CDK5 was associated with higher differentiation (P<0.001), metastasis (P<0.001), advanced clinical TNM stages (P<0.001), portal vein tumor embolus (P=0.003) and vascular invasion (P=0.004). Additionally, TCGA data analysis also revealed significantly increased CDK5 expression in HCC compared with non-cancerous hepatic tissues (P<0.001). The pooled standard mean deviation (SMD) based on 36 included datasets (HCC, n=2238; non-cancerous, n=2045) indicated that CDK5 was up-regulated in HCC (SMD=1.23, 95% CI: 1.00-1.45, P<0.001). The area under the curve (AUC) of the summary receiver operating characteristic (SROC) curve was 0.88. Furthermore, CDK5 knock-down inhibited proliferation and promoted apoptosis. In conclusion, CDK5 plays an essential role in the initiation and progression of HCC, most likely via accelerating proliferation and suppressing apoptosis in HCC cells by regulating the cell cycle and DNA replication pathways.
IN VITRO PRODUCTION OF BUFFALO (Bubalus bubalis) EMBRYOS

Two experiments (Exp) were carried out to test the effect of different media on in vitro maturation (IVM) (Exp 1; n = 1142 ovaries with 2666 oocytes) and to study in vitro fertilization (IVF) of buffalo oocytes (Exp 2; n = 110 ovaries with 330 oocytes). In exp 1 the collected cumulus oocyte complex (COCs) was allocated to three maturational media; TCM-199 supplemented with hormones (M1), TCM-199 supplemented with epidermal growth factor (M2) and m-SOF (M3) overlaid with paraffin oil before incubating under 5 % CO2 in air at 38.5 C. A part of COCs was fixed to determine the stages of nuclear maturation after 24 hr. In exp 2 the matured oocytes were allotted with sperm suspension before incubating under 5 % CO2 in air at 38.5 C, for 22-24 hr. Presumptive embryos were placed, individually in 96 wells petri dish to determine at 12 hr intervals the kinetics of cleavage up to blastocyst stage. Average of collected COCs per ovary was 2.4 with 86 % of excellent and good graded COC’s. M1 and M2 showed higher (P<0.05) maturation rate vs. M3. After culturing oocyte diameter and perivitalline space increased (P<0.05) relative to preculture diameters, while diameter of ooplasm and thickness of zona pellucida non significantly decreased . Fertilized ova and cleaved embryos (%) were 80.2 and 77.8 %, respectively. Early embryonic cleavage up to 32 cell stage lapsed took 84 hr, while corresponding periods to reach morula, and blastocyst stage were 101 and 134.5 hr, respectively. Out of the fertilized ova 31.5 % reached excellent and good graded blastocyst stage.
Posttraumatic Stress Disorder Following Preeclampsia and PPROM

Objective: A prospective longitudinal evaluation of the prevalence of and risk factors for posttraumatic stress disorder (PTSD) in women with preeclampsia (PE) or preterm premature rupture of membranes (PPROM) compared to uncomplicated pregnancies. Methods: Participating women completed PTSD and depression questionnaires during pregnancy, 6 weeks, and 15 months postpartum. Data regarding psychiatric history and indices of obstetric care were collected from patient charts. Results: We included 57 PE, 53 PPROM, and 65 healthy pregnant women, of whom 137 also participated in the 15-month follow-up (PE 70%, PPROM 48%, and controls 95%; P < .001). At 6 weeks postpartum, the prevalence of PTSD, but not depression, following childbirth was significantly higher in patients than in controls (14% vs 3%; P = .023). A history of depression, depressive symptoms during pregnancy, and infant death were significantly associated with symptoms of postpartum PTSD. The maternal condition seems to be of less decisive value, as there was no difference between the prevalence of PTSD after PE and PPROM (11% vs 17%; P = .324). At 15 months postpartum, 11% of women with PE had PTSD, some of which did not have PTSD 6 weeks postpartum. The low response rate in the PPROM group at 15 months postpartum does not allow for definite conclusions. Conclusion: Pregnancies complicated by PE or PPROM are associated with PTSD in a substantial number of women. Especially women with proven vulnerability for psychological problems are at risk of developing PTSD postpartum, as are women whose children died in the perinatal period.
How pupils on the autism spectrum make sense of themselves in the context of their experiences in a mainstream school setting: A qualitative metasynthesis

Evidence that interpersonal interactions and self-appraisal in social context are crucial in developing self-understanding raises concerns about how pupils with autism spectrum disorder make sense of themselves in school settings where many experience social marginalisation. Metasynthesis was used to systematically extract and integrate findings from qualitative studies examining the mainstream school experiences of these students. Synthesised findings identified three, intermeshing, aspects of experience which contribute to many pupils with autism spectrum disorder making sense of themselves as ‘different’ to typical peers in a negative way: difficulties linked to autism spectrum disorder; interpersonal relationships, particularly with peers; and accessibility of the school environment. Typical pupils’ attitudes and responses towards peers with autism spectrum disorder, unusual sensory reactions to the physical school environment and individual sense-making about the self are highlighted as key areas requiring further research and intervention to improve the experiences, self-esteem and well-being of pupils with autism spectrum disorder in inclusive settings and to inform educational policy and practice.