LLukas22/scidocs huggingface dataset:
The ATM inhibitor KU55933 sensitizes radioresistant bladder cancer cells with DAB2IP gene defect.

PURPOSE
Our preliminary results showed that differentially expressed in ovarian cancer-2/disabled homolog 2 (DOC-2/DAB2) interactive protein (DAB2IP), a putative tumor suppressor gene, is down-regulated in bladder cancer (BCa) with aggressive phenotypes. In this study, we investigated how DAB2IP knockdown influenced BCa cell response to ionizing radiation (IR) and discussed possible ways to enhance cell radiosensitivity.


METHODS AND MATERIALS
The small interfering RNA (siRNA) system was implemented to inhibit endogenous DAB2IP expression in two human BCa cell lines, T24 and 5637. Cell sensitivity to IR alone or combined treatment was measured by a colony formation assay (CFA). Western blot was used to determine the phosphorylation levels of ataxia-telangiectasia mutated (ATM), catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs) and related DNA damage repair (DDR) proteins. Immunofluorescence as well as a flow cytometry assay were employed to detect DNA double-strand break (DSB) repair and cell cycle distribution, respectively.


RESULTS
DAB2IP-knockdown of BCa cells (i.e., siDAB2IP) exhibit increased clonogenic survival in response to IR compared with control cells (i.e., siCON) expressing an endogenous level of DAB2IP. The mechanism in siDAB2IP cells could be explained by elevated ATM expression and activation, increased S phase cell distribution as well as faster DSB repair kinetics. 2-morpholin-4-yl-6-thianthren-1-yl-pyran-4-one (KU55933) significantly sensitized siDAB2IP cells to IR due to inhibition of the phosphorylation of ATM and its downstream targets following IR and slower DSB repair kinetics.


CONCLUSIONS
Loss of DAB2IP expression in BCa cells signifies their radioresistance. KU55933, which suppresses ATM phosphorylation upon irradiation, could be applied in the radiotherapy of BCa patients with a DAB2IP gene defect.
Relationship between unit cell type and porosity and the fatigue behavior of selective laser melted meta-biomaterials.

Meta-materials are structures when their small-scale properties are considered, but behave as materials when their homogenized macroscopic properties are studied. There is an intimate relationship between the design of the small-scale structure and the homogenized properties of such materials. In this article, we studied that relationship for meta-biomaterials that are aimed for biomedical applications, otherwise known as meta-biomaterials. Selective laser melted porous titanium (Ti6Al4V ELI) structures were manufactured based on three different types of repeating unit cells, namely cube, diamond, and truncated cuboctahedron, and with different porosities. The morphological features, static mechanical properties, and fatigue behavior of the porous biomaterials were studied with a focus on their fatigue behavior. It was observed that, in addition to static mechanical properties, the fatigue properties of the porous biomaterials are highly dependent on the type of unit cell as well as on porosity. None of the porous structures based on the cube unit cell failed after 10(6) loading cycles even when the applied stress reached 80% of their yield strengths. For both other unit cells, higher porosities resulted in shorter fatigue lives for the same level of applied stress. When normalized with respect to their yield stresses, the S-N data points of structures with different porosities very well (R(2)>0.8) conformed to one single power law specific to the type of the unit cell. For the same level of normalized applied stress, the truncated cuboctahedron unit cell resulted in a longer fatigue life as compared to the diamond unit cell. In a similar comparison, the fatigue lives of the porous structures based on both truncated cuboctahedron and diamond unit cells were longer than that of the porous structures based on the rhombic dodecahedron unit cell (determined in a previous study). The data presented in this study could serve as a basis for design of porous biomaterials as well as for corroboration of relevant analytical and computational models.
Rethinking color cameras

Digital color cameras make sub-sampled measurements of color at alternating pixel locations, and then “demosaick” these measurements to create full color images by up-sampling. This allows traditional cameras with restricted processing hardware to produce color images from a single shot, but it requires blocking a majority of the incident light and is prone to aliasing artifacts. In this paper, we introduce a computational approach to color photography, where the sampling pattern and reconstruction process are co-designed to enhance sharpness and photographic speed. The pattern is made predominantly panchromatic, thus avoiding excessive loss of light and aliasing of high spatial-frequency intensity variations. Color is sampled at a very sparse set of locations and then propagated throughout the image with guidance from the un-aliased luminance channel. Experimental results show that this approach often leads to significant reductions in noise and aliasing artifacts, especially in low-light conditions.
Dejong Function Optimization by Means of a Parallel Approach to Fuzzified Genetic Algorithm

Genetic Algorithms are very powerful search methods that are used in different optimization problems. Parallel versions of genetic algorithms are easily implemented and usually increase algorithm performance [4]. Fuzzy control as another optimization solution along with genetic algorithms can significantly increase algorithm performance. Two variations for genetic algorithm and fuzzy system composition exist. In the first approach Genetic algorithms are used to optimize and model the structure of fuzzy systems through knowledge base or membership function design while the second approach exploits fuzzy to dynamically supervise genetic algorithm performance by speedily reaching an optimal solution. In this paper we propose a new method for fuzzy parallel genetic algorithms, in which a parallel client-server single population fuzzy genetic algorithm is configured to optimize the performance of the first three Dejong functions in order to reach a global solution in the least possible iterations. Simulations show much improvement in genetic algorithm performance evaluation.
Human Screams Occupy a Privileged Niche in the Communication Soundscape

Screaming is arguably one of the most relevant communication signals for survival in humans. Despite their practical relevance and their theoretical significance as innate [1] and virtually universal [2, 3] vocalizations, what makes screams a unique signal and how they are processed is not known. Here, we use acoustic analyses, psychophysical experiments, and neuroimaging to isolate those features that confer to screams their alarming nature, and we track their processing in the human brain. Using the modulation power spectrum (MPS [4, 5]), a recently developed, neurally informed characterization of sounds, we demonstrate that human screams cluster within restricted portion of the acoustic space (between ∼30 and 150 Hz modulation rates) that corresponds to a well-known perceptual attribute, roughness. In contrast to the received view that roughness is irrelevant for communication [6], our data reveal that the acoustic space occupied by the rough vocal regime is segregated from other signals, including speech, a pre-requisite to avoid false alarms in normal vocal communication. We show that roughness is present in natural alarm signals as well as in artificial alarms and that the presence of roughness in sounds boosts their detection in various tasks. Using fMRI, we show that acoustic roughness engages subcortical structures critical to rapidly appraise danger. Altogether, these data demonstrate that screams occupy a privileged acoustic niche that, being separated from other communication signals, ensures their biological and ultimately social efficiency.
Benefits and risks of raloxifene by vertebral fracture status.

OBJECTIVE
Women without versus those with vertebral fracture may have different benefits and risks during raloxifene treatment. Our objective was to compare the effects of raloxifene to decrease risk for vertebral fracture and invasive breast cancer with its effect to increase risk for venous thromboembolism in postmenopausal women without or with baseline vertebral fracture.


RESEARCH DESIGN AND METHODS
The Multiple Outcomes of Raloxifene Evaluation trial included postmenopausal women with osteoporosis randomized to placebo, raloxifene 60 mg/day, or raloxifene 120 mg/day for 4 years. The protocol specified subgroups based on whether or not patients had a vertebral fracture at baseline. Absolute differences between placebo and raloxifene 60 mg/day (the approved dose) for endpoints in these groups were defined as the incidence in the raloxifene group minus the incidence in the placebo group.


RESULTS
Raloxifene decreased the incidence of vertebral fracture and invasive breast cancer while increasing the incidence of venous thromboembolism. All treatment by vertebral fracture status interaction p-values were greater than 0.13, indicating that the effect of raloxifene on these outcomes was not significantly different between patients without versus those with vertebral fractures. In women without baseline vertebral fracture, absolute risk differences between the raloxifene and placebo group included vertebral fracture -2.83%, invasive breast cancer -1.21%, and venous thromboembolism +0.28%. In women with baseline vertebral fracture, absolute risk differences between raloxifene and placebo group included vertebral fracture -8.21%, invasive breast cancer -0.75% and venous thromboembolism +0.91%. The analysis had limited power to test whether raloxifene had a significantly different effect on venous thromboembolism in women without versus those with a vertebral fracture.


CONCLUSIONS
In women without and in those with vertebral fractures at baseline, the effects of raloxifene to decrease vertebral fracture and invasive breast cancer were greater than its effects to increase venous thromboembolism.
Counterfactual reasoning and learning systems: the example of computational advertising

This work shows how to leverage causal inference to understand the behavior of complex learning systems interacting with their environment and predict the consequences of changes to the system. Such predictions allow both humans and algorithms to select the changes that would have improved the system performance. This work is illustrated by experiments on the ad placement system associated with the Bing search engine.
Extended Resection: Is It Feasible for Pulmonary Metastases?

Extended resections may be necessary to achieve tumor-free borders for secondary pulmonary malignancies. This study was performed to analyze the outcomes that result from extended resections of pulmonary metastases. Between February 1991 and December 2008, a total of 25 extended pulmonary resections (resection of the chest wall and diaphragm, vascular procedures, sleeve resections, pneumonectomies, atrial resections, and completion pneumonectomies) were performed on 250 patients undergoing 319 metastasectomy procedures. The extended resection group was analyzed in terms of disease-free interval, type of resection, operative morbidity, mortality, and survival and was then compared with patients who underwent lobar or sublobar resections. The extended resection group consisted of 14 male and 11 female patients. The mean disease-free interval was 36.02 (minimum 6, maximum 132) months. The extended resection rate was 10%. After 30 days, all patients were alive. For all extended metastasectomy groups, actuarial 5-year survival rates from the time of the extended metastasectomy were 16.3%. Mean survival times of patients who underwent extended resection and lobar or sublobar resection were 40 months (SD = 11) (95% confidence interval, 19–61) and 20 months (SD = 3) (95% confidence interval, 14–26), respectively. This difference was not statistically significant (P = 0.09) (Fig. 2). In the subgroup analysis, survival in the extended resections and lobar or sublobar resections groups was not statistically significant (osteosarcoma, P = 0.758; epithelial tumor, P = 0.11). Extended resections, which can be performed during pulmonary metastasectomies of patients with tumor-free surgical borders, may establish curative benefits, with low rates of mortality and morbidity.
Measuring the Similarity between Automatically Generated Topics

Previous approaches to the problem of measuring similarity between automatically generated topics have been based on comparison of the topics’ word probability distributions. This paper presents alternative approaches, including ones based on distributional semantics and knowledgebased measures, evaluated by comparison with human judgements. The best performing methods provide reliable estimates of topic similarity comparable with human performance and should be used in preference to the word probability distribution measures used previously.
Gather customer concerns from online product reviews - A text summarization approach

Product reviews possess critical information regarding customers’ concerns and their experience with the product. Such information is considered essential to firms’ business intelligence which can be utilized for the purpose of conceptual design, personalization, product recommendation, better customer understanding, and finally attract more loyal customers. Previous studies of deriving useful information from customer reviews focused mainly on numerical and categorical data. Textual data have been somewhat ignored although they are deemed valuable. Existing methods of opinion mining in processing customer reviews concentrates on counting positive and negative comments of review writers, which is not enough to cover all important topics and concerns across different review articles. Instead, we propose an automatic summarization approach based on the analysis of review articles’ internal topic structure to assemble customer concerns. Different from the existing summarization approaches centered on sentence ranking and clustering, our approach discovers and extracts salient topics from a set of online reviews and further ranks these topics. The final summary is then generated based on the ranked topics. The experimental study and evaluation show that the proposed approach outperforms the peer approaches, i.e. opinion mining and clustering-summarization, in terms of users’ responsiveness and its ability to discover the most important topics. 2007 Elsevier Ltd. All rights reserved.
Saving womens lives: evidence-based recommendations for the prevention of postpartum haemorrhage.

Failure of the uterus to contract adequately after childbirth (atonicity) is the most common cause of postpartum haemorrhage (PPH), the leading cause of maternal death in Africa and Asia.1 Attempts to identify women at risk of atonic PPH have been unsuccessful. Numerically, more women without risk factors have atonic PPH compared to those with risk factors. To prevent atonic PPH, interventions should therefore be targeted at all women during childbirth. Active management of the third stage of labour has been described as a package comprising the following interlocking interventions: administration of a prophylactic uterotonic after birth of the baby, and usually also early cord clamping and cutting, and controlled cord traction.2 Other definitions in this package include uterine massage, but without reference to the timing of cord clamping.3 In contrast, expectant (also called physiological or conservative) management involves waiting for signs of separation and allowing the placenta to deliver spontaneously, or aided by gravity or nipple stimulation.2 While there is agreement on the beneficial effects of active management of the third stage of labour for prevention of PPH, there is less consensus on issues such as importance of the intervention’s individual components, the best methods and the requirements for safe administration of this intervention under conditions of limited resources. In particular, the choice of uterotonics has been the subject of discussion and debate. Injectable oxytocin has been recommended for routine use in the active management of the third stage of labour;3 however, a safe injection requires skills and sterile equipment. Oxytocin may be inactivated if exposed to high ambient temperatures.4 In contrast, misoprostol,
Gaussian Processes for Timeseries Modelling.

In this paper we offer a gentle introduction to Gaussian proc esses for timeseries data analysis. The conceptual framework of Bayesian modelling for timeseries data is discussed and the foundations of Bayesian non-parametric modelling presented for Gaussian processes . We discuss how domain knowledge influences design of the Gaussian process models and provide case examples to highlight the approaches.
Academic success across the transition from primary to secondary schooling among lower-income adolescents: understanding the effects of family resources and gender.

Successful academic performance during adolescence is a key predictor of lifetime achievement, including occupational and social success. The present study investigated the important transition from primary to secondary schooling during early adolescence, when academic performance among youth often declines. The goal of the study was to understand how risk factors, specifically lower family resources and male gender, threaten academic success following this "critical transition" in schooling. The study involved a longitudinal examination of the predictors of academic performance in grades 7-8 among 127 (56 % girls) French-speaking Quebec (Canada) adolescents from lower-income backgrounds. As hypothesized based on transition theory, hierarchical regression analyses showed that supportive parenting and specific academic, social and behavioral competencies (including spelling ability, social skills, and lower levels of attention problems) predicted success across this transition among at-risk youth. Multiple-mediation procedures demonstrated that the set of compensatory factors fully mediated the negative impact of lower family resources on academic success in grades 7-8. Unique mediators (social skills, spelling ability, supportive parenting) also were identified. In addition, the "gender gap" in performance across the transition could be attributed statistically to differences between boys and girls in specific competencies observed prior to the transition, as well as differential parenting (i.e., support from mother) towards girls and boys. The present results contribute to our understanding of the processes by which established risk factors, such as low family income and gender impact development and academic performance during early adolescence. These "transitional" processes and subsequent academic performance may have consequences across adolescence and beyond, with an impact on lifetime patterns of achievement and occupational success.
Minimal Loss Hashing for Compact Binary Codes

We propose a method for learning similaritypreserving hash functions that map highdimensional data onto binary codes. The formulation is based on structured prediction with latent variables and a hinge-like loss function. It is efficient to train for large datasets, scales well to large code lengths, and outperforms state-of-the-art methods.
Validity of Antibodies in Lymphocyte Supernatant in Diagnosing Tuberculosis in Severely Malnourished Children Presenting with Pneumonia

BACKGROUND
The diagnosis of tuberculosis (TB) in young children can be challenging, especially in severely malnourished children. There is a critical need for improved diagnostics for children. Thus, we sought to evaluate the performance of a technique that measures antibodies in lymphocyte supernatant (ALS) for the diagnosis of TB in severely malnourished children presenting with suspected pneumonia.


METHODS
Children less than 5 years with severe acute malnutrition and radiological features of pneumonia admitted to the Dhaka Hospital of International Centre for Diarrhoeal Disease Research, Bangladesh, were enrolled consecutively following informed written consent. In addition to clinical and radiological assessment, samples taken for TB diagnosis included gastric lavage fluid and induced sputum for microbiological confirmation. ALS was measured from venous blood, and results were evaluated in children classified as "confirmed", "non-confirmed TB" or "not TB".


RESULTS
Among 224 children who had ALS analysis, 12 (5.4%) children had microbiologically "confirmed TB", a further 41 (18%) had clinically diagnosed "non-confirmed TB" and the remaining 168 (75%) were considered not to have TB. ALS was positive in 89 (40%) and negative in 85 (39%) of children, with a large number (47 or 21%) reported as "borderline". These proportions were similar between the three diagnostic groups. The sensitivity and specificity of ALS when comparing "Confirmed TB" to "Not TB" was only 67% (95% CI: 31-91%) and 51% (95% CI: 42-60%), respectively.


CONCLUSIONS AND SIGNIFICANCE
Our data suggest that ALS is not sufficiently accurate to improve the diagnosis of TB in children with severe malnutrition.
Nerve sparing ventral clitoroplasty: analysis of clitoral sensitivity and viability.

PURPOSE
Enlargement of the clitoris is often a prominent manifestation of virilizing congenital adrenal hyperplasia and other disorders of sexual development. Controversy persists regarding the viability and sensitivity of the clitoris following clitoroplasty. We present 51 consecutive cases of nerve sparing ventral clitoroplasty performed by a single surgeon.


MATERIALS AND METHODS
Nerve sparing ventral clitoroplasty was performed in all patients. Postoperative evaluation for clitoral viability included gross examination and capillary perfusion testing. Patients older than 5 years were evaluated for clitoral sensory testing and vibratory sensory testing.


RESULTS
A total of 51 patients 4 months to 24 years old (mean age +/- SD 4.6 +/- 6.8 years) with clitorimegaly underwent nerve sparing ventral clitoroplasty. Of the patients 41 had capillary perfusion testing of the clitoris, of whom all had a viable clitoris. Ten of the 41 patients underwent clitoral sensory testing. Patients reported an average degree of sensation of 3.6 +/- 0.9 at the labia minora and 4.8 +/- 0.4 at the clitoris. Nine of the 10 patients also underwent vibratory sensory testing. Average values for the introitus, clitoris, labia and thigh were 3.56, 1.61, 5.08, and 5.83, respectively. Mean time after surgery for the patients who underwent clitoral sensory testing/vibratory sensory testing was 2.0 +/- 0.8 years. No variations in the sensitivity results were reported at followup in 2 patients.


CONCLUSIONS
To our knowledge this is the largest report of followup testing of clitoral viability and sensation after clitoroplasty. Continued long-term followup is ongoing to document long-term sexual function using this nerve sparing ventral approach for clitoroplasty.