Miracle-dz/UniFAR-FTUs huggingface dataset:
BCL2 Regulation according to Molecular Subtype of Breast Cancer by Analysis of The Cancer Genome Atlas Database

Purpose We investigated B-cell lymphoma 2 (BCL2) regulation across DNA, RNA, protein, and methylation status according to molecular subtype of breast cancer using The Cancer Genome Atlas (TCGA) database. Materials and Methods We analyzed clinical and biological data on 1,096 breast cancers from the TCGA database. Biological data included reverse phase protein array (RPPA), mRNA sequencing (mRNA-seq), mRNA microarray, methylation, copy number alteration linear, copy number alteration nonlinear, and mutation data. Results The luminal A and luminal B subtypes showed upregulated expression of RPPA and mRNAseq and hypomethylation compared to the human epidermal growth factor receptor 2 (HER2) and triple-negative subtypes (all p < 0.001). No mutations were found in any subjects. High mRNA-seq and high RPPA were strongly associated with positive estrogen receptor, positive progesterone receptor (all p < 0.001), and negative HER2 (p < 0.001 and p=0.002, respectively). Correlation analysis revealed a strong positive correlation between protein and mRNA levels and a strong negative correlation between methylation and protein and mRNA levels (all p < 0.001). The high BCL2 group showed superior overall survival compared to the low BCL2 group (p=0.006). Conclusion The regulation of BCL2 was mainly associated with methylation across the molecular subtypes of breast cancer, and luminal A and luminal B subtypes showed upregulated expression of BCL2 protein, mRNA, and hypomethylation. Although copy number alteration may have played a minor role, mutation status was not related to BCL2 regulation. Upregulation of BCL2 was associated with superior prognosis than downregulation of BCL2.
Lowering blood ammonia prevents hepatocyte injury and apoptosis.

UNLABELLED To study hepatocyte injure through establishing the rat model of acute hepatic failure (ALF). ALF rat model was established by administration with D-galactosamine and LPS, and then giving lowering blood ammonia (LBA) treatment. Besides, the intervention groups were injected with ornithine and aspartate. The control groups were injected saline. Blood ammonia, ALT, AST, TNF-α and IL-6 in blood samples were test at 12 hrs and 24 hrs after treatment with LBA. Hepatocyte apoptosis were tested by TUNEL and DNA Ladder. Expression of P53 and SPP1 were detected by RT-PCR. RESULTS showed that blood ammonia in hepatic failure group and intervention group compared with blank control group was significantly increased at 12 h, 24 h; intervention group compared with hepatic failure group was significantly reduced (P<0.05). Serum ALT, AST in 24 h group were higher than 12 h. 12 h intervention group was decreased compared with hepatic failure group, but there was no significant statistically difference (P>0.05). 24 h intervention group compared with hepatic failure group was significantly reduced (P<0.05). Except the control group, DNA ladder and the TUNEL results showed hepatocyte apoptosis rate increased in 24 h compared with 12 h. Intervention group compared with hepatic failure group was significantly reducing (P<0.05). IL-6, TNF-α, p53 expression levels were increased with time (24 h>12 h). The hepatic failure and intervention group compared with blank control group was significantly increased; Intervention group compared with hepatic failure group was significantly reducing (P<0.05). SPP1 gene was high expression in ALF rat model. SPP1 level in hepatic failure and intervention group compared with control group was significantly increased, and intervention group compared with hepatic failure group was significantly reducing (P<0.05). In conclusion, hepatocyte apoptosis is an important pathological change in ALF rat mode, and lowing ammonia can reduce liver injury and apoptosis. Blood TNF-α, IL-6 and SPP1 may be more sensitive injure indicators.
Redundant Vias Insertion for Performance Enhancement in 3D ICs

Three dimensional (3D) integrated circuits (ICs) have the potential to significantly enhance VLSI chip performance, functionality and device packing density. Interconnects delay and signal integrity issues are critical in chip design. In this paper, we extend the idea of redundant via insertion of conventional 2D ICs and propose an approach for vias insertion/placement in 3D ICs to minimize the propagation delay of interconnects with the consideration of signal integrity. The simulation results based on a 65nm CMOS technology demonstrate that our approach in general can result in a 9% improvement in average delay and a 26% decrease in reflection coefficient. It is also shown that the proposed approach can be more effective for interconnects delay improvement when it is integrated with the buffer insertion in 3D ICs.
Isolation of Non-Diptherial Coryne-bacterium (Diphteroids) and its Antibiogram from Various Clinical Samples.

Background: Catalase-positive Aerobic Gram-positive non spore forming bacilli, morphologically resembling Corynebacterium diphthriae, commonly called “diphtheroids” or “coryneform” bacteria are placed under order Actinomycetales. Species of Cornybacterium other than diphtheriae were usually either considered as commensals or saprophytes that are present in human, animal and environment. Among more than eighty species of Corynebacerium identified so far, around 53 species have been associated with human or animal infections. The aim of study is to study the species isolation and antibiogram pattern of diphtheroids from various clinical specimens submitted to the department of microbiology, MRH. Methods: All specimens submitted for culture and sensitivity were observed by gram stain and inoculated on Blood agar, Mac conkey agar and Chocolate agar and incubated. Species of Corynebacteriae were identified by biochemical tests like nitrate, urease basic media, and catalase and pyrazinamide reactions. The antibiogram was determined by the disc diffusion method on 5% sheep blood agar. Results: Over a period of one year, a total of 2081 various clinical specimens were screened, among which 1206 were culture positive. 445(36.89%) were positive for diphtheroids and 761(63%) were positive for other organisms. Non diphtherial corynebacterial species like, C. amycolatum (40.6%), C. pseudo-diphtheriticum (12.1%), C. ulcerans (88%), C. urealyticum (64%), C. propinquum (36%), C. xerosis (4.9%) were isolated and identified. Most of the species were sensitive to antibiotics like Vancomycin(88.7%), Teicoplanin(91%), Linezolid(93%) and Clindamycin (82%). High resistant pattern was shown to antibiotics like Penicillin (83.1%), Amoxyclav (86.9%), Chloramphenicol (69.8%), Gentamicin (68.08%) and Tetracycline (64.04%). Conclusion: The present study is an attempt to identify non diphtherial Corynebacterium upto species level and report their antibiogram pattern. Determination of antibiogram of such pathogens is a must, as these species are highly resistant to many of the commonly used antibiotics including Beta-lactams, macrolides, and fluroquinolones. Emergence of multidrug resistance in various species has created the necessity for exact identification of non diphtherial coryneform organisms upto the species level, which helps the clinician to prescribe the antibiotic treatment based on the results of culture and antibiotic sensitivity report.
Temperature Modulation Reveals Three Distinct Stages of Wallerian Degeneration

After peripheral nerve transection, axons distal to the cut site rapidly degenerate, a process termed Wallerian degeneration. In wild-type mice the compound action potential (CAP) disappears by 3 d. Previous studies have demonstrated that cold temperatures and lower extracellular calcium ion (Ca2+) concentrations can slow the rate of Wallerian degeneration. We have incubated isolated sciatic nerve segments from wild-type and C57BL/Wld mice (which carry a gene slowing Wallerian degeneration) in vitro at 25 and 37°C. At 25°C we found that the degeneration rate of wild-type axons was slowed dramatically, with the CAP preserved up to 7 d post-transection. In contrast, at 37°C the CAPs were minimal at 2 d. When the temperature of wild-type nerves was raised to 37°C after 24–72 hr at 25°C, degeneration occurred within the subsequent 24 hr. Wld nerves, too, were preserved longer at 25°C but, on return to 37°C, degenerated promptly. Cooling the nerve within 12 hr after axotomy enhanced axonal preservation. Neither wild-type nor Wld nerves showed different degeneration rates when they were incubated with 250 μm or 5 or 10 mm extracellular Ca2+ for 1–2 d, suggesting that an abrupt increase in intracellular Ca2+ occurs at the time of axonal destruction. Wallerian degeneration, thus, appears to progress through three distinct stages. Initiation occurs at the time of injury with subsequent temperature-dependent and -independent phases. Nerves appear to remain intact and are able to exclude Ca2+ from entering until an as yet unknown process finally increases axolemmal permeability.
[Effect of squatting on sub-foveal blood flow defect in pseudophakic eyes operated by cerclage].

UNLABELLED ZIEL: To investigate the relationship between velocity (Velch), blood volume (Volch) and blood flow (Fch), and the mean ocular perfusion pressure (PPm) in the foveal region, and to determine how the regulatory capacity of the choroidal circulation is affected after an encircling buckle procedure. METHODS We investigated both pseudophakic eyes of 6 patients (age range 56-79 years) in a masked study. Subjects presenting eye diseases (glaucoma, uveitis, diabetic retinopathy) as well as systemic diseases were excluded from the study. All subjects had in one eye a successful management of retinal detachment with an encircling buckling; the second eye was considered as control. Measurements of Velch, Volch and Fch were obtained by Laser Doppler Flowmetry (LDF) at baseline and during isometric exercise (squatting). RESULTS In the operated eyes, Velch and Fch increased significantly (ANOVA, p < 0.05) during the PPm raise, which was not the case for Volch (ANOVA, p > 0.05). In the control eyes, all hemodynamic parameters remained unaffected by the PPm increase (ANOVA, p > 0.05). The response of Velch and Fch was significantly different (ANCOVA, p < 0.002) between operated and control eyes. CONCLUSION These results suggest that encircling buckle does affect subfoveal choroidal blood flow regulation, which may explain a possible macular dysfunction in the operated eyes.
Homocysteine accumulates in supernatants of stimulated human peripheral blood mononuclear cells

Moderate hyperhomocysteinaemia is associated with atherosclerosis, thrombosis and also with stroke and dementia. Elevated homocysteine concentrations are related to deficiency of folate and also vitamin‐B12, as these two vitamins are essential co‐factors in the remethylation of homocysteine to methionine. A causal role of homocysteine in the pathogenesis of vascular disease has been discussed over years. Immune activation appears to be involved strongly in atherogenesis as well as in other diseases found to be associated with moderate hyperhomocysteinaemia. To study a possible influence of immune stimulation on homocysteine metabolism, in vitro experiments were performed using peripheral blood mononuclear cells upon stimulation with mitogens concanavalin A, phytohaemagglutinin and pokeweed mitogen. In stimulated cells a dose‐dependent increase of homocysteine concentrations was found. When cells were kept in medium supplemented with methionine, homocysteine concentrations increased further, while supplementation with folate had only a slight effect. We conclude that in supernatants of stimulated peripheral blood mononuclear cells homocysteine is accumulating. T cell activation could be involved in the development of moderate hyperhomocysteinaemia.
The geminivirus BL1 movement protein is associated with endoplasmic reticulum-derived tubules in developing phloem cells

Plant viruses encode movement proteins that are essential for systemic infection of their host but dispensable for replication and encapsidation. BL1, one of the two movement proteins encoded by the bipartite geminivirus squash leaf curl virus, was immunolocalized to unique approximately 40-nm tubules that extended up to and across the walls of procambial cells in systemically infected pumpkin leaves. These tubules were not found in procambial cells from pumpkin seedlings inoculated with BL1 mutants that are defective in movement. The tubules also specifically stained with antisera to binding protein (BiP), indicating that they were derived from the endoplasmic reticulum. Independent confirmation of this endoplasmic reticulum association was obtained by subcellular fractionation studies in which BL1 was localized to fractions that contained both endoplasmic reticulum membranes and BiP. Thus, squash leaf curl virus appears to recruit the endoplasmic reticulum as a conduit for cell-to-cell movement of the viral genome.
The effectiveness of different rat IgG subclasses as IgE‐blocking antibodies in the rat basophil leukaemia cell model

The degranulation of mast cells in an allergic response is initiated by the aggregation of high‐ affinity IgE receptors (FcεRI) by IgE and antigen. Recently it has been shown that such degranulation can be inhibited by cross‐linking FcεRI and low‐affinity IgG receptors (FcγRII) which are also expressed by mast cells. The ability of various monoclonal antibodies to block the degranulation of rat basophil leukaemia (RBL) cells sensitized with IgE antidinitrophenyl (DNP) antibodies has been investigated. Sensitized cells were challenged with immune complexes formed using varying concentrations of antigen, and of both high‐ and low‐valency antigen. It is reported here that rat IgG1 antibodies, which are associated in the rat with a Th1‐type response, act as highly effective blocking antibodies over a wide concentration range. Rat IgG2a antibodies, which are associated with a Th2‐type response, were able only to inhibit degranulation when immune complexes were formed with very low concentrations of high‐valency antigen (DNP32‐HSA). Under these conditions, some inhibitory activity was seen with high‐affinity murine IgA anti‐DNP but not with low‐affinity rat IgG2b anti‐DNP antibody‐containing immune complexes. In addition to this inhibitory activity, IgG2a antibodies were shown to be capable of inducing degranulation of cells via unoccupied FcεRI. These results demonstrate that blocking activity may arise via both inhibitory receptors and by masking of antigen.
Flagellar ultrastructure and flagella-associated antigens of Campylobacter fetus

Ultrastructural examinations of the flagellum of Compylobacter (Vibrio) fetus were performed throughout the growth cycle. Filament diameters, exceeding 17.6 nm during the exponential phase, were substantially greater than those reported for unsheathed flagella of other genera with the exception of Pseudomonas fluorescens. Filament diameters increased during growth, reaching a mean width of 21.2 nm in middle to late stationary phase. Internal flagellar structure, principally of the parallel lined variety, was observed during the later periods of growth but not during exponential or early stationary phase. Despite the unusually large filament sizes, no evidence of a flagellar sheath was observed after selected treatments (0.01 N HCl, 6 M urea, tris(hydroxymethyl) amino-methane-hydrochloride buffer, warm water) or examination of thin sections. To determine whether alterations in filament size and variable ability to demonstrate filament fine structure were correlated with progressive changes in serological activity, agglutination and immobilization tests were conducted with antisera directed against intact flagella, the principal flagellar antigen, the O antigen, and a superficial glycoprotein which has been found in association with the flagellum and the cell envelope. Significant differences in the serological activity of cells at different growth intervals were not noted with any of the sera employed.
Degeneration of substantia nigra in chronic Parkinson's disease visualized by transcranial color-coded real-time sonography

Article abstract-To detect morphologic abnormalities in Parkinson's disease (PD), we examined 30 patients with PD and 30 age- and sex-matched nonparkisonian controls by transcranial color-coded real-time sonography (TCCS). In 12 severely affected PD patients, the echogenicity of the substantia nigra was distinctly increased. In the remaining 18 PD patients and in all controls, the substantia nigra was poorly visualized or nondetectable by TCCS. The degree of hyperechogenicity of the substania nigra closely correlated with the severity and duration of PD (p < 0.001). The increased echogenicity of the substania nigra notably results from nigral gliosis and reflects the stage of degeneration. NEUROLOGY 1995;45: 182-184
Three‐dimensional MRI perfusion maps: a step beyond volumetric analysis in mental disorders

A new type of magnetic resonance imaging analysis, based on fusion of three‐dimensional reconstructions of time‐to‐peak parametric maps and high‐resolution T1‐weighted images, is proposed in order to evaluate the perfusion of selected volumes of interest. Because in recent years a wealth of data have suggested the crucial involvement of vascular alterations in mental diseases, we tested our new method on a restricted sample of schizophrenic patients and matched healthy controls. The perfusion of the whole brain was compared with that of the caudate nucleus by means of intrasubject analysis. As expected, owing to the encephalic vascular pattern, a significantly lower time‐to‐peak was observed in the caudate nucleus than in the whole brain in all healthy controls, indicating that the suggested method has enough sensitivity to detect subtle perfusion changes even in small volumes of interest. Interestingly, a less uniform pattern was observed in the schizophrenic patients. The latter finding needs to be replicated in an adequate number of subjects. In summary, the three‐dimensional analysis method we propose has been shown to be a feasible tool for revealing subtle vascular changes both in normal subjects and in pathological conditions.
als Role of MicroRNA in Endometrial Carcinoma

ndometrial carcinoma (EC) is a hall mark of gynecological malignancies that usually affects women above the age 50. It is one of the major causes of mortality in females with ever increasing prevalence and the mortality rate is 1.7 to 2.4 per 100000 and each year 10000 death occur due to ECs. MiRNAs regulate the expression of different proto-oncogenes and signaling pathways that are directly or indirectly involved in the development of cancer. Different miRNAs i.e. (miRNA-449, miRNA 370, miRNA-424, and miRNA-152) which gets up or down regulated during endometrial cancer are the potential biomarkers for early diagnosis of EC. Targeting this relationship between the miRNA and signaling pathways may help in the development of new treatment in endometrial cancer. In current study, we reviewed literature from PubMed using miRNA and endometrial cancer as keywords and outlined the synthesis of potent miRNA and role of different miRNAs involved in ECs. The study revealed different sub types of miRNA played crucial role in the development of cancer by up and down regulation of different metabolic pathways. Many evidences have supported that miRNAs play role in control and regulation of different pathways leading to cancer and targeting these pathways may bring changes in the diagnosis as well as in treatment of EC. E Abstract www.als-journal.com/ ISSN 2310-5380/ November 2016
Synchronous rendezvous technique for multi-vehicle mine countermeasure operations

Advantages of multi-vehicle network over single autonomous underwater vehicle (AUV) platform include extended coverage area, potential cost and time efficiency, and more robust performance. A common issue that slows advancement in the field is the limited available communication between the platforms. The approach we propose is based on assigning a sequence of rendezvous points (RPs) where the vehicles can meet and exchange information. The work we present in this paper applies mainly to mine countermeasure (MCM) and suggests that despite the disadvantage of time to allow for the vehicles to reach the RPs, there are techniques that can minimise the losses and provide advantages such as easier coordination and access point for operator monitoring and system modifications.
Outcomes after Cognitive Perceptual Motor Retraining (CPM) of Patients with Acquired Brain Injury (ABI)

Background: Remediation of deficits is one approach used by occupational therapists in the treatment of clients with acquired brain injury (ABI). This retrospective study examined outcomes after participation in Cognitive Perceptual Motor Retraining (CPM) of clients with ABI and identified demographic and injury characteristics of clients that were associated with outcomes. CPM was delivered as part of the standard treatment and was not designed for research purposes. Method: A retrospective review of 59 client records was completed. CPM evaluation test scores, demographic information, and injury characteristics were extracted from the records. Results: There were moderate improvements in CPM test scores and good discharge outcomes for most clients. Discharge to home with independent status was associated with mild to moderate traumatic brain injury severity and being married. Longer time since injury and having a concurrent psychiatric diagnosis were associated with longer duration of CPM. Conclusion: This preliminary study demonstrates positive therapy outcomes after CPM. Recommendations were made for future research and considerations in the use of CPM. These include the need for addressing concurrent needs, such as psychological issues and repeated re-evaluations, to determine when clients have met maximum remediation and thereby minimizing cost. Comments Disclosures: Ms. Christy, Ms. Huffine, and Ms. Hannah are all employed by Origami Brain Injury Rehabilitation Center where CPM is administered.
Model-driven development using standard tools

The machine forms bales of circular cross section by continuously rolling the bale upon a supporting surface within a formation chamber while additional material is supplied to the chamber. The chamber is partially defined by two separate, cooperating sets of flexible belts, one set having an upwardly moving stretch at the rear of the chamber and the other having a forwardly moving stretch defining the top of the chamber such that material entering the chamber at the beginning of the baling cycle is lifted upwardly by the rear stretch and rolled forwardly by the top stretch. The top and rear stretches converge to an upper rear corner of the chamber spaced above the supporting surface for the rolling bale, and such corner may be adjustably shifted vertically and/or horizontally in a fore-and-aft direction as may be necessary or desirable to facilitate bale starting under differing crop conditions. Alternative belt arrangements are disclosed for obtaining the desired adjustability of the chamber corner. An improved belt-tensioning assembly is also disclosed wherein spring tension on the belts is rendered substantially constant throughout the full movement of swinging arms that control and take up slack in the belts.