LLukas22/scidocs huggingface dataset:
Evaluation of novel formula of PSA, age, prostate volume, and race in predicting positive prostate biopsy findings.

OBJECTIVE
To develop a formula that incorporates age, prostate volume, race, and prostate-specific antigen (PSA) level into a single score for prostate cancer detection.


MATERIALS AND METHODS
We developed a PSA-age volume (AV) score by multiplying the patient age by the prostate volume and dividing it by the PSA level. The PSA-AV was developed using 1000 prostate biopsy specimens and was validated on 318 internal and 4406 external biopsy specimens.


RESULTS
We analyzed 1000 biopsy specimens (mean age 63 ± 8 years, 63% white and 35% black, mean PSA 6.8 ± 4 ng/mL, mean prostate volume 41 ± 18 cm(3), mean PSA-AV 485 ± 304). Of the 1000 biopsy specimens, 556 (55.6%) had positive findings. A lower PSA-AV score correlated with a greater cancer risk (R(2) = 0.91). A PSA-AV score of 700 had a sensitivity and specificity of 87% and 35%, respectively. These values matched or exceeded the sensitivity and specificity for age-adjusted PSA level and a PSA cutoff of 4 ng/mL. Compared with using the age-adjusted PSA level, using a score of 700 increased the number of biopsies by 64 and detected 62 more cancers. Using a PSA-AV cutoff of 700, rather than a PSA cutoff of 4 ng/mL, led to 16 fewer biopsies with 7 additional cancers detected. Our data were internally and externally validated.


CONCLUSION
According to our data, a PSA-AV score has shown to be a useful formula for predicting positive biopsy findings. A PSA-AV score of 700 is useful in ruling out cancer in younger patients and patients with small prostates, and in ruling in cancer in older patients and patients with a large prostate.
Early adolescent Internet game addiction in context: How parents, school, and peers impact youth

http://dx.doi.org/10.1016/j.chb.2015.03.079 0747-5632/ 2015 Elsevier Ltd. All rights reserved. Abbreviations: PAR, parent–adolescent relationship; IGA, internet game addiction; SC, school connectedness; DPA, deviant peer affiliation. ⇑ Corresponding author at: School of Psychology & Center for Studies of Psychological Application, South China Normal University, Guangzhou, Guangdong 510631, PR China. Tel.: +86 20 85216466. E-mail address: zhangwei@scnu.edu.cn (W. Zhang). Jianjun Zhu, Wei Zhang ⇑, Chengfu Yu, Zhenzhou Bao
Imperial Simla: The Political Culture of the Raj

A lively and well-documented picture of the social, historical and political development of Simla as hill-station-cum-capital. Drawing on contemporary reports, official documents and personal interviews with old residents of Simla, the book covers roughly the hundred years leading up to India's independence. This book is intended for historians and sociologists, and those with an interest in the history of colonial rule.
Activated alumina as an energy source for peptide bond formation: Consequences for mineral-mediated prebiotic processes

Summary. The catalytic properties of various forms of alumina were tested for alanine dimerization reaction. The catalytic efficiency of alumina depends on the structure, as well as on acid/base properties of the catalyst. The highest yields of Ala2 were achieved on activated alumina with surface of neutral pH (about 3% conversion after 2 weeks). Thermal analysis of Ala + alumina reaction systems shows that the thermal behavior of amino acid changes substantially in contact with the activated surface of the alumina catalyst. The reaction of Ala is detected as being strongly endothermic by differential thermal analysis of pure amino acid (above 250°C). The alanine endothermic reaction is shifted substantially to lower values (below 200°C) and hardly detectable if activated alumina is present. The reaction mechanism of amino acid activation on alumina surface and its significance for mineral-catalyzed prebiotic peptide bond formation are discussed.
Sea and air moving target measurements using a GSM based passive radar

A passive radar is essentially a receiver-only radar that does not transmit signals; it only receives and thus operates independently without the direct synchronization from the non-cooperative illuminator. GSM base station transmitter as the illuminator of opportunity in a passive radar offers a covert means of uninterrupted surveillance where the major advantage is that the emitters of such transmissions are abundant. This paper presents an overview description of a low-cost experimental GSM based passive radar developed and implemented in Nanyang Technological University, Singapore. It describes the hardware architecture design and integration as well as the associated signal processing scheme of this experimental passive radar. Numerous field experiments were conducted with interesting results on sea and air moving target Doppler frequency detection and tracking presented to demonstrate and ascertain the performances and operating capabilities of the GSM based passive radar.
Repositioning Dynamics and Pricing Strategy

We measure the revenue and cost implications to supermarkets of changing their price positioning strategy in oligopolistic downstream retail markets. Our approach formally incorporates the dynamics induced by the repositioning in a model with strategic interaction. We exploit a unique dataset containing the price-format decisions of all U.S. supermarkets in the 1990s. The data contain the format-change decisions of supermarkets in response to a large shock to their local market positions: the entry of Wal-Mart. We exploit the responses of retailers to WalMart entry to infer the cost of changing pricing-formats using a “revealed-preference”argument similar in spirit to Bresnahan and Reiss (1991). The interaction between retailers and Wal-Mart in each market is modeled as a dynamic game. We find evidence that entry by Wal-Mart had a significant impact on the costs and incidence of switching pricing strategy. Our results add to the marketing literature on the organization of retail markets, and have implications for longrun market structure in the supermarket industry. Our approach, which incorporates long-run dynamic consequences, strategic interaction, and sunk investment costs, may be used to model empirically firms’positioning decisions in Marketing, more generally.
Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors (ProtVec) for proteins (amino-acid sequences) and gene-vectors (GeneVec) for gene sequences, this representation can be widely used in applications of deep learning in proteomics and genomics. In the present paper, we focus on protein-vectors that can be utilized in a wide array of bioinformatics investigations such as family classification, protein visualization, structure prediction, disordered protein identification, and protein-protein interaction prediction. In this method, we adopt artificial neural network approaches and represent a protein sequence with a single dense n-dimensional vector. To evaluate this method, we apply it in classification of 324,018 protein sequences obtained from Swiss-Prot belonging to 7,027 protein families, where an average family classification accuracy of 93%±0.06% is obtained, outperforming existing family classification methods. In addition, we use ProtVec representation to predict disordered proteins from structured proteins. Two databases of disordered sequences are used: the DisProt database as well as a database featuring the disordered regions of nucleoporins rich with phenylalanine-glycine repeats (FG-Nups). Using support vector machine classifiers, FG-Nup sequences are distinguished from structured protein sequences found in Protein Data Bank (PDB) with a 99.8% accuracy, and unstructured DisProt sequences are differentiated from structured DisProt sequences with 100.0% accuracy. These results indicate that by only providing sequence data for various proteins into this model, accurate information about protein structure can be determined. Importantly, this model needs to be trained only once and can then be applied to extract a comprehensive set of information regarding proteins of interest. Moreover, this representation can be considered as pre-training for various applications of deep learning in bioinformatics. The related data is available at Life Language Processing Website: http://llp.berkeley.edu and Harvard Dataverse: http://dx.doi.org/10.7910/DVN/JMFHTN.
Chelicerate neural ground pattern in a Cambrian great appendage arthropod

Preservation of neural tissue in early Cambrian arthropods has recently been demonstrated, to a degree that segmental structures of the head can be associated with individual brain neuromeres. This association provides novel data for addressing long-standing controversies about the segmental identities of specialized head appendages in fossil taxa. Here we document neuroanatomy in the head and trunk of a ‘great appendage’ arthropod, Alalcomenaeus sp., from the Chengjiang biota, southwest China, providing the most complete neuroanatomical profile known from a Cambrian animal. Micro-computed tomography reveals a configuration of one optic neuropil separate from a protocerebrum contiguous with four head ganglia, succeeded by eight contiguous ganglia in an eleven-segment trunk. Arrangements of optic neuropils, the brain and ganglia correspond most closely to the nervous system of Chelicerata of all extant arthropods, supporting the assignment of ‘great appendage’ arthropods to the chelicerate total group. The position of the deutocerebral neuromere aligns with the insertion of the great appendage, indicating its deutocerebral innervation and corroborating a homology between the ‘great appendage’ and chelicera indicated by morphological similarities. Alalcomenaeus and Fuxianhuia protensa demonstrate that the two main configurations of the brain observed in modern arthropods, those of Chelicerata and Mandibulata, respectively, had evolved by the early Cambrian.
Phase II trial of neoadjuvant weekly nanoparticle albumin-bound paclitaxel, carboplatin, and biweekly bevacizumab therapy in women with clinical stage II or III HER2-negative breast cancer.

BACKGROUND
We hypothesized that adding bevacizumab to neoadjuvant chemotherapy (NCT) with nab-P and carboplatin would increase the rates of pCR in BC patients and that early changes in tumor vascularity imaged by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) would predict pCR.


METHODS
Thirty-three women with clinical stage II or III HER2-negative BC received nab-P 100 mg/m2 and carboplatin area under the curve = 2 on days 1, 8, and 15 in combination with bevacizumab 10 mg/kg on days 1 and 15 administered every 28 days.


RESULTS
Six patients (18%) achieved pCR, all pCRs occurred in triple-negative BC (TNBC) (pCR = 50% for TNBC). At the end of cycle 2, the changes in relative angiogenic volume were significantly different between responders and nonresponders (P = .001). The major toxicity of this NCT was myelosuppression.


CONCLUSION
NCT with weekly nab-P, carboplatin, and biweekly bevacizumab resulted in a pCR rate that was neither superior to the historical data with anthracycline- or taxane-containing NCT nor to carboplatin and taxane combinations in patients with HER2-negative BC. In patients with TNBC, the observed pCR rate was 50%. The early changes in the relative angiogenic volume imaged by DCE-MRI could predict pCR.
The religious factor in private education

This paper quantifies the religious factor in education demand by calibrating a political economy model of education finance and school choice in which parents who differ in the advantage they attribute to religious education choose from among public, privatenonsectarian and religious schools. The calibrated distribution of religious preferences indicates that the revealed advantage of religious education is strongly contingent on its high levels of subsidization. The results of the calibration are applied to compare the effect of publicly funded vouchers that do not exclude religious schools—to which the Supreme Court recently opened a door in Zelman v. Simmons-Harris—with vouchers restricted to nonsectarian schools. It supports the implicit conclusion of the Court, that participation of religious schools in the Cleveland voucher program was essential for achieving its goal of helping low-income parents in a failing school district. Larger vouchers would have reduced the share of religious schools in the program, though they would still have attracted a majority of students.
Management of Painful Chronic Pancreatitis With Single-Dose Radiotherapy

OBJECTIVES:Some patients with chronic pancreatitis present recurrent flare-ups of pancreatitis and/or unrelenting pain. Current management is mostly limited to analgesics and surgery. We reasoned that anti-inflammatory radiotherapy, which has proven useful to alleviate other painful inflammatory painful disorders, might prove valuable for severely symptomatic patients with chronic pancreatitis.METHODS:We prospectively studied the efficacy of single-dose anti-inflammatory radiotherapy in 15 consecutive patients with chronic pancreatitis who fulfilled the following criteria: either two flare-ups of pancreatitis in the previous 6 months and/or continuous pain for more than 3 months. Treatment consisted of a single radiation dose of 8 Gy to the pancreas. Exocrine function (fecal elastase), endocrine function (c peptide), quality of life (EuroQol questionnaire), and clinical outcome were assessed before and after radiation. Response was defined as no further pain or flare-ups of pancreatitis.RESULTS:During follow-up (median: 39 months; range: 4–72 months), 12 patients had no further pain or flare-ups. One patient required a second radiation dose 1 year after the initial treatment, but he has remained well ever since (50 months). Two other patients did not respond to radiotherapy. After radiotherapy either exocrine or endocrine pancreatic function, or both, deteriorated in three patients. Patients who responded to treatment (13/15) gained 4–20 kg in body weight during follow-up (median 4 kg) and EuroQol improved significantly from 0.58 to 0.86 (P<0.001).CONCLUSIONS:Radiotherapy for severe symptomatic chronic pancreatitis appears to be a useful and effective therapeutic choice that could potentially substitute for or delay surgery.
Graphene-based conducting inks for direct inkjet printing of flexible conductive patterns and their applications in electric circuits and chemical sensors

A series of inkjet printing processes have been studied using graphene-based inks. Under optimized conditions, using water-soluble single-layered graphene oxide (GO) and few-layered graphene oxide (FGO), various high image quality patterns could be printed on diverse flexible substrates, including paper, poly(ethylene terephthalate) (PET) and polyimide (PI), with a simple and low-cost inkjet printing technique. The graphene-based patterns printed on plastic substrates demonstrated a high electrical conductivity after thermal reduction, and more importantly, they retained the same conductivity over severe bending cycles. Accordingly, flexible electric circuits and a hydrogen peroxide chemical sensor were fabricated and showed excellent performances, demonstrating the applications of this simple and practical inkjet printing technique using graphene inks. The results show that graphene materials—which can be easily produced on a large scale and possess outstanding electronic properties—have great potential for the convenient fabrication of flexible and low-cost graphenebased electronic devices, by using a simple inkjet printing technique.
The 11-13-week scan: diagnosis and outcome of holoprosencephaly, exomphalos and megacystis.

OBJECTIVE
To determine the prevalence and outcome of fetuses with holoprosencephaly, exomphalos and megacystis diagnosed at 11-13 weeks of gestation.


METHODS
As part of a prospective screening study for trisomy 21 in singleton pregnancies at 11 + 0 to 13 + 6 weeks' gestation, transabdominal ultrasound examination was performed to diagnose holoprosencephaly, exomphalos and megacystis. Fetal karyotype and pregnancy outcome in fetuses with these defects were examined.


RESULTS
Screening was carried out in 57 119 pregnancies. The prevalence of holoprosencephaly, exomphalos and megacystis was 1 : 1298, 1 : 381 and 1 : 1632, respectively. Chromosomal abnormalities, mainly trisomies 18 and 13, were found in 65.9% of fetuses with holoprosencephaly, in 55.3% with exomphalos and in 31.4% with megacystis. There was spontaneous resolution of the defect by 20 weeks in 92.5% of euploid fetuses with exomphalos containing only bowel and in 90% of the euploid fetuses with megacystis and bladder length of < or = 15 mm.


CONCLUSIONS
A high proportion of fetuses with holoprosencephaly, exomphalos and megacystis diagnosed at 11-13 weeks of gestation are aneuploid, but in the majority of cases exomphalos and megacystis represent temporary abnormalities that resolve spontaneously.
NORCCAP (Norwegian colorectal cancer prevention): a randomised trial to assess the safety and efficacy of carbon dioxide versus air insufflation in colonoscopy.

BACKGROUND
To eliminate the risk of combustion during electrosurgical procedures and to reduce patient discomfort, carbon dioxide (CO2) insufflation has been recommended during colonoscopy. However, air insufflation is still the standard method, perhaps due to the lack of suitable equipment and shortage of randomised studies.


AIMS
This randomised controlled trial was conducted to assess patient tolerance and safety when using CO2 insufflation during colonoscopy.


PATIENTS
Over an eight month period a successive series of patients referred for a baseline colonoscopy due to findings in a flexible sigmoidoscopy screening trial were randomly assigned to the use of either air or CO2 insufflation during colonoscopy.


METHODS
End tidal CO2 (ETCO2), a non-invasive parameter of arterial pCO2, was registered before and repeatedly during and after the examination. The patient's experience of pain during and after the examination was registered using a visual analogue scale (VAS). Sedation was not used routinely.


RESULTS
CO2 insufflation was used in 121 patients (51%) and air in 119 patients (49%). The groups were similar in age, sex, and caecal intubation rate. No rise in ETCO2 was registered. There were statistically significant differences in VAS scores between the groups with less pain reported when using CO2.


CONCLUSIONS
This randomised study of unsedated patients shows that CO2 insufflation is safe during colonoscopy with no rise in ETCO2 level. CO2 was found to be superior to air in terms of pain experienced after the examination.
Information Retrieval Data Structures & Algorithms, by William B. Frakes and Ricardo Baeza-Yates (Book Review)

This is an extremely welcome addition to the Information Retrieval (IR) literature. Because of its technical approach it is much different from most of the available books on IR. The book consists of five sections containing eighteen chapters. The chapters are written by different authors.
A single-layer tuneable microwave absorber using an active FSS

An experimental single-layer active microwave absorber in described. The absorber is a planar structure based upon the topology of a Salisbury screen, but in which the conventional resistive layer is replaced by an active frequency selective surface (FSS) controlled by pin diodes. The resulting structure has superior reflectivity-bandwidth characteristics compared to conventional passive absorbers of corresponding thickness. Measured data are presented and show that the reflectivity response of the absorber can be controlled over the frequency band from 9 to 13 GHz.
FLOSS: flexible ordered subset analysis for linkage mapping of complex traits

The FLOSS software package is a flexible framework for ordered subset analysis. FLOSS is specifically designed for use with the Merlin linkage analysis package, but FLOSS can be used with any linkage analysis software package that reports NPL Z-scores for each locus and family. When FLOSS is used with the Merlin linkage analysis package, one can use either non-parametric Z-scores or Kong and Cox linear allele sharing model LOD scores. Monte Carlo P-values are calculated using a permutation test with an efficient Besag-Clifford sequential stopping rule. FLOSS also has a flexible tool for assigning family covariate scores from Merlin input files. FLOSS includes user documentation and is written in Java for easy portability. The FLOSS source code is documented and designed to be extensible.
Adaptive Kalman filtering based navigation: An IMU/GPS integration approach

This paper investigates on the development and implementation of a high integrity navigation system based on the combined use of the Global Positioning System (GPS) and an inertial measurement unit (IMU) for land vehicle applications. The complementary properties of the GPS and the INS have motivated several works dealing with their fusion by using a Kalman Filter. The conventional kalman filter has a fix error covariance matrix in all times of processing. Multi-sensor based navigation system that is implemented in this paper is called data synchronization. Also, multi-rate operations that are compared with conventional Kalman filtering has fix error covariance matrix. Therefore, when GPS outage occurred we have improper treat by kalman filter. In this paper we present an Adaptive method instead of conventional methods. It is shown that proposed method has a better performance rather than conventional method. Experimental results show the effectiveness of the GPS/INS integrated system.
A practical theory for designing very deep convolutional neural networks

Going deep is essential for deep learning. However it is not easy, there are many ways of going deep but most of them are ineffective. In this work, we propose two novel constrains in the design of deep structure to guarantee the performance gain when going deep. Firstly, for each convolutional layer, its capacity of learning more complex patterns should be guaranteed; Secondly, the receptive field of the topmost layer should be no larger than the image region. Given these two constrains, we cast the task of designing deep convolutional neural network into a constrained optimization problem. We present an analytic optimal solution under certain conditions.