Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro and in vivo binding of human immunodeficiency virus type 1 Tat protein and Sp1 transcription factor

Recent genetic experiments have suggested that tat transactivation of the human immunodeficiency virus type 1 (HIV-1) long terminal repeat requires functional upstream enhancer sequences--Sp1 sites, in particular. In these experiments, HeLa cell nuclear extracts were passed over affinity matrices containing chemically synthesized or bacterially expressed HIV-1 Tat. Assay of material that bound to and eluted from the Tat matrices revealed the presence of the Sp1 transcription factor. Other transcription factors (Oct and NF-kappa B) also bound to Tat matrices but with less efficiency--in parallel with the lower capacities of these binding motifs to confer Tat responsiveness on a basal HIV-1 promoter compared with Sp1 sites. Passage of nuclear extracts over matrices containing other neutral proteins, including bovine serum albumin, ovalbumin, and lysozyme, revealed no or reduced binding. Cross-linking experiments indicated that the purified Sp1 and Tat proteins can form multimeric complexes in the absence of other proteins. The region of Tat responsible for Sp1 binding was localized to a region encompassing residues 30 to 62. Immunoprecipitation experiments with HIV-1-infected T lymphocytes indicated coimmunoprecipitation of Tat and Sp1. These experiments extend previous genetic experiments and suggest a direct interaction between Tat and Sp1 during transactivation.
Cytology‐based gene mutation tests to predict response to anti‐epidermal growth factor receptor therapy: A review

Recent therapeutic progresses in nonsmall cell lung cancer (NSCLC) and in colorectal cancer (CRC) are based on agents that specifically target the epidermal growth factor receptor (EGFR). To identify the patients most likely to benefit from such therapies, EGFR or KRAS gene mutation tests are mandatory, respectively, in NSCLC and in CRC. In patients with locally advanced or metastatic disease, exploiting cytological samples for these tests avoids not curative surgery. Here, we review the studies that have applied gene mutation assays on cytological samples of NSCLC and CRC to select patients for anti‐EGFR therapy. We argue that the standard of quality of gene mutation tests on cytological samples is closely dependent on the extent of the cytopathologist's involvement. Diagn. Cytopathol. 2010. © 2010 Wiley‐Liss, Inc.
Individual variability and predictors of driving simulator impairment in patients with obstructive sleep apnea.

STUDY OBJECTIVES Obstructive sleep apnea (OSA) is associated with driving impairment and road crashes. However, daytime function varies widely between patients presenting a clinical challenge when assessing crash risk. This study aimed to determine the proportion of patients showing "normal" versus "abnormal" driving simulator performance and examine whether anthropometric, clinical, and neurobehavioral measures predict abnormal driving. METHODS Thirty-eight OSA patients performed a 90-min simulated driving task under 3 conditions: normal sleep, restricted sleep (4 h in bed), and normal sleep + alcohol (BAC∼0.05 g/dL). Patients were classified as "resilient" drivers if, under all 3 experimental conditions their mean steering deviation fell within 2 standard deviations of the mean steering deviation of 20 controls driving under baseline normal sleep conditions, or a "vulnerable" driver if mean steering deviation was outside this range in at least one experimental condition. Potentially predictive baseline anthropometric, clinical, neurocognitive, and cortical activation measures were examined. RESULTS Of the 38 OSA patients examined, 23 (61%) and 15 (39%) were classified as resilient and vulnerable drivers, respectively. There were no differences in baseline measures between the groups, although the proportion of females was greater and self-reported weekly driving exposure was less among vulnerable drivers (p < 0.05). On univariate analysis gender, weekly driving hours, and auditory event related potential P2 amplitude were weakly associated with group status. Multivariate analysis showed weekly driving hours (OR 0.69, 95%CI, 0.51-0.94, p = 0.02) and P2 amplitude (OR 1.34, 95%CI 1.02-1.76, p = 0.035) independently predicted vulnerable drivers. CONCLUSIONS Most OSA patients demonstrated normal simulated driving performance despite exposure to further sleep loss or alcohol. Most baseline measures did not differentiate between resilient and vulnerable drivers, although prior driving experience and cortical function were predictive. Novel measures to assist identification of OSA patients at risk of driving impairment and possibly accidents are needed. TRIAL REGISTRATION Data presented in this manuscript was collected as part of a clinical trial "Experimental Investigations of Driving Impairment in Obstructive Sleep Apnea. " Trial ID: ACTRN12610000009011, URL: http://www.anzctr. org.au/trial_view. aspx? ID=334979.
Third metacarpal bone mineral density assessment in the standing horse by dual X-ray absorptiometry

Summary Bone mineral density (BMD) is correlated to mechanical properties of bone. In the horse, dual energy X-ray absorptiometry (DXA) has yet only been performed ex-vivo, but a new portable DXA device would be ideal for in-vivo BMD measurement. We explored field suitability, precision and accuracy of this device for in-vivo third metacarpal density assessment. Precision was analysed by calculating measurement variation under repeated measurement tests with (reproducibility) and without (repeatability) limb repositioning. Repeatability and reproducibility were tested ex-vivo, at the same time that intra- and inter-operator reproducibility were assessed in-vivo. In order to test accuracy, bone mineral content (BMC) of several bone samples determined by DXA and ashing were compared. Repeatability was 1.47% and reproducibility 1.69% ex-vivo. In-vivo reproducibility varied between 2.91 and 4.06% for intraoperator test and between 3.13 and 5.53% for interoperator test. BMC measured by DXA and ash weight were highly correlated (R2>0.99). In conclusion, under described conditions this DXA device is usable, accurate and precise. Its sensitiveness reaches 8.23% in an individual longitudinal monitoring. Using the third metacarpal bone as an example, we have shown that this device is suitable for experimental or clinical monitoring.
Underarm cosmetics are a cause of breast cancer

Breast cancer is the major cancer of women in the Western world but shows a rising incidence all over Ž . the world Ursin et al., 1994 . Epidemiological evidence demonstrates that 90% of breast cancers are Ž . environmental in origin Lipworth, 1995 and linked to a Western lifestyle, but the specific environmental causes have never been identified. In recent years, Ž two tumour suppressor genes called BRCA1 Miki et . Ž . al., 1994 and BRCA2 Wooster et al., 1995 have been cloned. Although loss of function of these genes confers susceptibility to breast cancer, this effect accounts for only a maximum of 5 10% of Ž . cases of the disease Easton et al., 1993 . The main identified risk factors for breast cancer are hormonal and are linked, in particular, to lifetime exposure to oestrogen through variations in menarche, menopause, childbirth and personal choices such as use of the contraceptive pill or hormone replacement therŽ . apy Lipworth, 1995 . Diet, smoking and alcohol can Ž . also exert influences Lipworth, 1995 . However, these known risk factors confer only a small increased risk and the main causative agents of breast cancer remain unaccounted for. A novel, unexplored but plausible explanation for the cause of breast cancer is the use of underarm cosmetics. These chemicals are applied repetitively and frequently to an area directly adjacent to the breast area. They are not rinsed off but left always on the skin. They are used by women with ever increasing frequency and by ever-younger girls before puberty. They are now also being used by men in increasing amounts. The progressive increase in use of these cosmetics in the Western world over the past 100 years is illustrated by US sales figures Ž . Laden and Felger, 1988 . Sales in 1914 reached sufficient levels to support national advertising, and rose from there to represent US business worth $30 million in 1947, $300 million in 1970 and over $1 Ž . billion in 1983 Laden and Felger, 1988 . Although these cosmetics are sold as over-the-counter drugs Ž . Laden and Felger, 1988 , there are no indications on the containers of the safe level of usage or whether the constituent chemicals are safe for prolonged use by young children before puberty. Contrary to common belief, there is great diversity in use of these cosmetics across the population. My own unpublished survey within the University of Reading shows that women use a variety of different products, each containing different types and amounts of chemicals and that frequency of use varies from never to more than five times a day. Such diversity in usage provides ample possibility for cancer to arise through quantity used, through pattern of usage or through individual susceptibility to specific product formulations.
Defining a Freeway Mobility Index for Roadway Navigation

Roadway navigation systems have become increasingly popular, providing more efficient routing through a roadway network. In many cases, multiple routes are possible, and a specific route can be selected by minimizing some cost function. However, the number of possible routes varies by roadway network topology and location within the network. It is often useful to know how many possible routes exist; therefore, the authors developed a Navigational Mobility Index (NMI) with an initial focus on freeway networks that can be extended to other roadway facility types. NMI can be based on the number of possible routes weighted by shared segments among routes from a source to a destination (i.e., node-to-node pair NMI), as a single node to all other nodes (i.e., node-NMI), or on an average of nodes in a specific area (i.e., area-NMI). This article first reviews several of the existing accessibility or mobility measures that have been developed for other purposes and discusses how these are not well suited for navigational route selection. Then, NMI is defined in detail, highlighting its advantages for navigational purposes. Next, the authors present applications of NMI, including its ability to (a) measure the degree of freedom in which drivers can choose routes from a route choice perspective, (b) determine the potential effectiveness of navigation systems, (c) determine the overall connectivity level of an area, (d) guide the movement of people during evacuation in a disastrous event, and (e) determine a route on the basis of the least generalized cost that incorporates both distance and NMI. The author selected and evaluated two of California's freeway networks as case studies. Examples of node-NMI and area-NMI are calculated and plotted using data from the Census 2000 TIGER/LineShapefiles (2000). Last, the authors present experimental results to show the effectiveness of the proposed concept and algorithm.
A Modified Fascia Iliaca Compartment Block Has Significant Morphine-Sparing Effect after Total Hip Arthroplasty

We assessed whether a modified fascia iliaca compartment block in unilateral total hip arthroplasty provides a morphine-sparing effect in the first 24 hours. This involved a randomised, double blind study of 44 patients. Both groups received a modified fascia iliaca block with the trial group receiving 30 ml 0.5% bupivacaine with 1:200,000 adrenaline, 150 μg clonidine and 9 ml 0.9%> saline and the control group receiving 40 ml 0.9% saline. Otherwise both groups received identical care with a subarachnoid block for operative anaesthesia. Patient-controlled morphine analgesia was commenced postoperatively and data were collected at three, six, 12 and 24 hours post commencement of surgery. We found that the trial group used less morphine at 12 and 24 hours (P <0.001). The median morphine usage at 24 hours was 37.5 mg in the control patients and 22 mg in the trial patients. Pain scores were similar between groups. We conclude that a modified fascia iliaca compartment block has a significant morphine-sparing effect in unilateral total hip arthroplasty.
Cyclophosphamide‐induced ovarian failure and its therapeutic significance in patients with breast cancer

The effect of cyclophosphamide (CY) on ovarian function was studied in patients with breast cancer receiving prolonged daily administration of this agent (100 mg/day) after radical surgery. Out of 18 premenopausal patients that received 8.4–39.9 g CY, 15 developed permanent amenorrhea. The average dose given before the onset of amenorrhea was 5.2 g in patients in their 40s and 9.3 g in their 30s. Urinary estrogens and serum progesterone were measured weekly for approximately 6 months postoperatively in six patients receiving CY. After the onset of amenorrhea, the levels of both hormones ceased to show their normal cyclic changes and remained low persistently, meanwhile serum FSH and LH were markedly elevated. No ovarian follicle was histologically found in three amenorrheic patients who underwent therapeutic oopho‐rectomy after CY therapy. These findings indicate that CY induced primary ovarian failure.
Penguin Search Optimisation Algorithm for Finding Optimal Spaced Seeds

This paper develops PeSeeD, a new metaheuristic algorithm for finding optimal spaced seed. Sequences matching is a hot topic in bio-informatics, which is used in many applications such as understanding the functional, structural, or evolutionary relationships between the sequences. The most relevant sequences matching methods are based on seeds designed to match two biological sequences. The first approach which introduced seeds was facilitated via Blastn tool, the approach builds seeds of 11 length size. However, it is clear that not all local alignments have to include an identical fragment of length 11. The spaced seeds approach is one of the methods which does not require a consecutive matching position. Dynamic programming is used to solve this kind of problem and it takes quadratic time. Several approaches have then been proposed to improve the sensitivity of searching in reasonable runtime. To reduce the complexity of such approaches, other heuristics based approaches can also be reviewed. The aim is to find spaced seeds subset which improves sensitivity without increasing the computation time. In this paper, the optimal subset spaced seeds are explored using the bio-inspired approach, penguins search optimisation algorithm ''PeSOA'' for short. The authors further propose an efficient heuristic for computing the overlap complexity between seeds. To evaluate the efficiency of the proposed approach, they compared the obtained results with the results of several seeds based software tools. The obtained results are very promising in terms of sensitivity and computation time for the overlap complexity.
Running Head: Water transport and xylem function of the pedicel

106 Xylem flow of water into fruits declines during fruit development, and literature indicates a 107 corresponding increase in hydraulic resistance in the pedicel. However, it is unknown how 108 pedicel hydraulics change developmentally in relation to xylem anatomy and function. In this 109 study on grape ( Vitis vinifera L.), we determined pedicel hydraulic conductivity ( k h ) from 110 pressure-flow relationships using hydrostatic and osmotic forces, and investigated xylem 111 anatomy and function using fluorescent light microscopy and x-ray computed 112 microtomography (microCT). Hydrostatic k h (xylem pathway) was consistently four orders of 113 magnitude greater than osmotic k h (intracellular pathway), but both declined before veraison 114 by ~40 % and substantially over fruit development. Hydrostatic k h declined most gradually for 115 low (< 0.08 MPa) pressures, and for water in- and out-flow conditions. Specific hydraulic 116 conductivity ( k h per xylem area) decreased in a similar fashion to k h despite substantial 117 increases in xylem area. MicroCT images provided direct evidence that losses in pedicel k h 118 were associated with blockages in vessel elements, whereas embolisms were negligible. 119 However, vessel elements were well inter-connected and some remained continuous post- 120 veraison suggesting that across the grape pedicel a xylem pathway of reduced k h remains 121 functional late into berry ripening. 122 124
Services for data integration

The fact that many decisions need a combination of information sources makes easy integration of geospatial data an important data usability issue. Our vision is to achieve automated just-in-time integration. As a foundation, we present a system architecture with distributed data and services. Existing and evolving standards and technologies fitting into this architecture are presented along with their scope and shortcomings. A major point is the appropriate definition of data and operation semantics. Further research is needed here to make the automatic formation of service chains for data integration possible.
Traumatic patellar dislocation in children and adolescents: treatment update and literature review.

PURPOSE OF REVIEW Traumatic patellar dislocation in children and adolescents is a complex problem resulting from a range of anatomic and mechanical conditions. A careful review of the literature demonstrates certain risk factors that predispose children to recurrent dislocation. With this understanding, these conditions can be managed more aggressively in the hope of an improved outcome. Additionally, a vast number of surgical procedures to correct patellar instability have been described, and recent cadaveric studies are now guiding surgical interventions. RECENT FINDINGS Risk factors for recurrent dislocation may include various skeletal abnormalities, increased quadriceps angle, generalized ligamentous laxity, and family history. Recent anatomic and biomechanical studies have demonstrated that the medial patellofemoral ligament and the vastus medialis obliquus are the primary restraints to lateral translation and ultimately dislocation of the patella. Management should therefore be directed both at correcting anatomic abnormalities when indicated and at reconstruction of medial restraints to patellar tracking. SUMMARY The recommendation for management of a traumatic patellar dislocation in a skeletally immature patient is initially conservative, emphasizing early motion and quadriceps strengthening. However, in patients for whom conservative management has failed or who are at particularly high risk for dislocation and require surgical intervention, repair or reconstruction of the medial patellofemoral ligament is the treatment of choice. Recent works have included investigation of less invasive techniques in children.
Frequency of Oral Glucose Tolerance Testing in the U.S.

are the symptomatic group to whom some authors have attributed a high mortality (2). Since symptomatic AN is not a very well defined condition and no individual symptom is clearly predictive for cardiovascular test results (3), it is possible to suggest that symptomatic AN must be considered present when the patient has four or five abnormal cardiovascular responses to the tests described by Ewing (2) and two or more of the following symptoms: dizziness on standing, diarrhea, fecal incontinence, gustatory sweating, dysphagia, vomiting, and urinary retention.
Association of CD38 Antigen Expression with Other Prognostic Parameters in Early Stages of Chronic Lymphocytic Leukemia

The expression of the surface molecule CD38 on B cell chronic lymphocytic leukemia (B-CLL) cells has recently been described as a prognostic marker for patient survival. We have analyzed CD19/CD38 expression in 81 patients with predominantly early stages of B-CLL (69 Binet A, seven Binet B, five Binet C). Sixty-two patients (77%) had less than 30% CD38+/CD19+ cells, while 19 (23%) had ≥30%. There was a significant association between Binet stages (A vs. B+C, p < 0.0001), Rai stages (0-II vs. III+IV, p < 0.001) and CD38 expression, confirming the published cut-off level of 30%. A particularly strong association between CD38 expression was found with soluble CD23 (sCD23) levels of ≥2000 U/ml (p < 0.0001) and β2-microglobulin (β2 MG) serum levels of ≥3 mg/l (p < 0.0001) indicating that CD38 is a marker of tumor mass as well as disease progression. A borderline association was found with lymphocyte doubling time (LDT) < 12 months (p = 0.05) due to low patient numbers, while there was no association with age, sex or immunoglobulin deficiency. Discordant results were obtained in a number of patients: 10 of 69 patients (14%) with Binet A had a CD38 ≥30% while three of seven patients with Binet B had a CD38 < 30%. In these two subgroups CD38 and other prognostic factors gave discrepant results. Due to the early stage and short median observation time (12 months, range 1–24 months), calculations concerning patient survival were not performed. However, our data show a strong association between CD38 and other known prognostic factors. The results also suggest that this factor is not always reliable in Binet A patients.
Microdomains in the membrane landscape shape antigen‐presenting cell function

The plasma membrane of immune cells is a highly organized cell structure that is key to the initiation and regulation of innate and adaptive immune responses. It is well‐established that immunoreceptors embedded in the plasma membrane have a nonrandom spatial distribution that is important for coupling to components of intracellular signaling cascades. In the last two decades, specialized membrane microdomains, including lipid rafts and TEMs, have been identified. These domains are preformed structures (“physical entities”) that compartmentalize proteins, lipids, and signaling molecules into multimolecular assemblies. In APCs, different microdomains containing immunoreceptors (MHC proteins, PRRs, integrins, among others) have been reported that are imperative for efficient pathogen recognition, the formation of the immunological synapse, and subsequent T cell activation. In addition, recent work has demonstrated that tetraspanin microdomains and lipid rafts are involved in BCR signaling and B cell activation. Research into the molecular mechanisms underlying membrane domain formation is fundamental to a comprehensive understanding of membrane‐proximal signaling and APC function. This review will also discuss the advances in the microscopy field for the visualization of the plasma membrane, as well as the recent progress in targeting microdomains as novel, therapeutic approach for infectious and malignant diseases.
Effect of Streptozotocin‐Induced Diabetes on Activities of Cholinesterases in the Rat Retina

The effect of streptozotocin‐induced diabetes on cholinesterases activities was studied in the retina and, for comparison, in other nervous and nonnervous tissues. Streptozotocin diabetes did not affect acetylcholinesterase activity in the retina but increased its activity in the cerebral cortex (100%) and in serum (55%), and decreased it by 30‐40% in erythrocytes. The butyrylcholinesterase activity was decreased by 30‐50% in retina and hippocampus and to a lesser extent in retinal pigment epithelium from rats treated with streptozotocin for one week. Changes observed in cholinesterase activities were not correlated with the fasting blood glucose concentration. The results suggest that diabetes might influence a specific subset of cells and isoforms of cholinesterases. This, in turn, could lead to alterations associated with diabetes complications.