LLukas22/scidocs huggingface dataset:
Social-Aware Decentralization for Secure and Scalable Multi-party Computations

This work studies the problem of MPC decentralization - that is, identifying a set of computing nodes to securely and efficiently execute the multi-party computation protocol (MPC) over a sensitive dataset. To balance between underdecentralization with high risk and over-decentralization with high cost, our unique approach is to add social-awareness, that is, the MPC protocol, running over a social network, is properly decentralized among the computing nodes selected carefully based on their social relationship. The key technical challenge is in estimating the risk of collusion between nodes on whom the computation is run. We propose solutions to estimate the risk of collusion based on (incomplete) social relationship, as well as algorithms for finding the MPC nodes such that the risk of collusion is minimized. We evaluate our methods on several real-world network datasets, and show that they are effective in minimizing the risk levels. This work has potential in enabling efficient privacy-preserving data sharing and computation in emerging big-data federation platforms, in healthcare, financial marketplaces, and other application domains.
Phase I trial of three-weekly Docetaxel, Carboplatin and oral lenalidomide (Revlimid®) in patients with advanced solid tumors

Introduction: Lenalidomide is an immunomodulatory derivative of thalidomide with significantly greater in vitro activity and a different toxicity profile. In preclinical trials it has shown synergy with chemotherapy. Patients and methods: Primary objective of this study was to determine the maximum tolerated doses of docetaxel and carboplatin when combined with oral lenalidomide in a standard phase I study design. Between September 2004 and May 2005, 14 patients with pathologically proven solid tumors, ≤2 prior chemotherapy regimens, performance status ECOG 0/1, and adequate organ function were enrolled. Dose limiting toxicities (DLT) were defined as ≥ grade 3 non-hematological, or grade 4 hematological toxicity. No growth factors were used during cycle 1. Results: Three of four patients treated at dose level 1, docetaxel 60 mg/m2 and carboplatin AUC 6 on Day 1, and lenalidomide 10 mg orally daily on Days 1–14 of a 21 day cycle experienced DLT (grade 3 electrolyte changes in two patients, and grade 4 neutropenia in one patient). Ten patients were treated at dose level −1, docetaxel 60 mg/m2 and carboplatin AUC 6 on Day 1, and lenalidomide 5 mg orally daily on Days 1–14 of a 21 day cycle with one DLT (Grade 4 neutropenia). There were no treatment-related deaths or irreversible toxicities. Of the 14 response-evaluable patients, five achieved a partial response (5 out of 9 patients with non-small cell lung cancer. Conclusions: Docetaxel 60 mg/m2 and carboplatin AUC 6 on Day 1, with lenalidomide 5 mg orally daily on Days 1–14 days of a 21 day cycle is the maximum tolerated dose without the use of prophylactic growth factors. This combination is active and further evaluation in a phase II trial is warranted.
Cloud Computing – A Comprehensive Definition

Cloud computing is an evolving technology that is consistently generating impact in IT industry and academia. It performs all computational tasks over Internet by using virtualization techniques and remains isolated from intricate vast hardware and software infrastructures. The aim of this paper is to glance through the background and evolutions of cloud computing, its architecture and services to develop cumulative knowledge for future research extension and evaluation.
Idarubicin and intermediate-dose cytarabine for myeloid blast crisis of chronic myelogenous leukemia – results of a phase-II trial

 Sixteen patients with Philadelphia chromosome-positive chronic myelogenous leukemia (CML) in myeloid blast crisis were treated with cytarabine (AraC) 600 mg/m2 two times daily for 5 days and idarubicin 12 mg/m2 for 3 days. Patients achieving a second chronic phase received interferon (IFN) alpha 2b 5 mio units/day daily and AraC 20 mg/day subcutaneously 14 days every month. Study end points were remission rate and survival. Four patients (25%) entered a second chronic phase and had a median survival of 31.1 weeks (range 16.1–111 weeks). Nine patients (56%) experienced blast crisis again and had a median survival of 12.9 weeks (range 5.1–59.3 weeks). Three patients (18.8%) died of septic complications during marrow aplasia. The median overall survival was 16.1 weeks (range 2.6–111 weeks) with no significant difference between responders and nonresponding patients. We conclude that AraC/idarubicin is as effective as other intensive regimens in inducing second chronic phase in patients with myeloid blast crisis of CML. Remission duration and survival are comparable to previous results. Further studies to improve survival are required.
Experiments with Open-Domain Textual Question Answering

This paper describes the integration of several knowledge-based natural language processing techniques into a Question Answering system, capable of mining textual answers from large collections of texts. Surprizing quality is achieved when several lightweight knowledge-based NLP techniques comI)lement mostly shallow, surface-based approaclms.
A novel tool for reliable and accurate prediction of renal complications in patients undergoing percutaneous coronary intervention.

OBJECTIVES
The aim of the study was to develop and validate a tool for predicting risk of contrast-induced nephropathy (CIN) in patients undergoing contemporary percutaneous coronary intervention (PCI).


BACKGROUND
CIN is a common complication of PCI and is associated with adverse short- and long-term outcomes. Previously described risk scores for predicting CIN either have modest discrimination or include procedural variables and thus cannot be applied for pre-procedural risk stratification.


METHODS
Random forest models were developed using 46 pre-procedural clinical and laboratory variables to estimate the risk of CIN in patients undergoing PCI. The 15 most influential variables were selected for inclusion in a reduced model. Model performance estimating risk of CIN and new requirement for dialysis (NRD) was evaluated in an independent validation data set using area under the receiver-operating characteristic curve (AUC), with net reclassification improvement used to compare full and reduced model CIN prediction after grouping in low-, intermediate-, and high-risk categories.


RESULTS
Our study cohort comprised 68,573 PCI procedures performed at 46 hospitals between January 2010 and June 2012 in Michigan, of which 48,001 (70%) were randomly selected for training the models and 20,572 (30%) for validation. The models demonstrated excellent calibration and discrimination for both endpoints (CIN AUC for full model 0.85 and for reduced model 0.84, p for difference <0.01; NRD AUC for both models 0.88, p for difference = 0.82; net reclassification improvement for CIN 2.92%, p = 0.06).


CONCLUSIONS
The risk of CIN and NRD among patients undergoing PCI can be reliably calculated using a novel easy-to-use computational tool (https://bmc2.org/calculators/cin). This risk prediction algorithm may prove useful for both bedside clinical decision making and risk adjustment for assessment of quality.
Vaginal birth after cesarean section: risk of uterine rupture with labor induction.

We assessed the rate of uterine rupture in patients undergoing labor induction for attempted vaginal birth after cesarean (VBAC). A retrospective study was performed of data from a computerized database. Deliveries from January 1, 1998, to June 30, 2001, in the Southern California Kaiser Permanente system were reviewed and various perinatal characteristics analyzed. A total of 16,218 patients had a prior low transverse cesarean section. Of these, 6832 (42.1%) had a trial of labor. Successful VBAC occurred in 86% of patients with spontaneous onset of labor and 66% of patients with labor induction ( p < 0.001). The uterine rupture rate was not different between patients with spontaneous or induced labor (1.0% versus 1.2%, p = 0.51). Similarly, there was no significant difference between oxytocin or prostaglandin E2 induction (1.4% versus 1.0%, p = 0.59). In our study, labor induction did not appear to increase the risk of uterine rupture in women attempting VBAC.
Relevance of expandable titanium cage for the treatment of cervical spondylotic myelopathy

In patients with cervical spondylotic myelopathy, ventral disease and loss of physiological cervical lordosis are indications for anterior approach. As bone graft and titanium cage present many drawbacks, expandable titanium cage has been recently introduced for this indication. The authors present the clinical and radiological outcomes in patients undergoing the placement of an expandable cage in the treatment of spondylotic myelopathy with straight or kyphotic cervical spine alignment. This was a retrospective review of prospectively collected data. A total of 26 patients underwent cervical corpectomy and reconstruction using an expandable titanium cage and anterior plate between 2005 and 2008. Pain and functional disability were measured using VAS and mJOA preoperatively and at 3 months, 6 months, 1 year and 2 years. Kyphosis was measured using lateral radiographs at the same points of follow-up. Fusion was evaluated on flexion–extension radiographs at 2 years. The mean VAS improved from 4.2 to 1.7 and the mean mJOA increased from 12.85 to 16.04 at 2 years postoperatively (p < 0.05). The mean kyphosis angle decreased from 17° to 2° at the last follow-up (p < 0.05). The fusion rate was 100 % at 2 years. Three complications were reported including a transient dysphagia, an epidural hematoma and an early hardware migration. Expandable titanium cage is an effective device, which achieves good clinical and radiological outcomes at a minimum 2-year follow-up.
Interest Rate Pass-Through: Mortgage Rates, Household Consumption, and Voluntary Deleveraging

Exploiting variation in the timing of resets of adjustable-rate mortgages (ARMs), we find that a sizable decline in mortgage payments (up to 50 percent) induces a significant increase in car purchases (up to 35 percent). This effect is attenuated by voluntary deleveraging. Borrowers with lower incomes and housing wealth have significantly higher marginal propensity to consume. Areas with a larger share of ARMs were more responsive to lower interest rates and saw a relative decline in defaults and an increase in house prices, car purchases, and employment. Household balance sheets and mortgage contract rigidity are important for monetary policy pass-through. (JEL D12, D14, E43, E52, G21, R31)
Intercellular communication in the brain: Wiring versus volume transmission

During the past two decades several revisions of the concepts underlying interneuronal communication in the central nervous system have been advanced. We propose here to classify communicational phenomena between cells of the central neural tissue under two general frames: "wiring" and "volume" transmission. "Wiring" transmission is defined as intercellular communication occurring through a well-defined connecting structure. Thus, wiring transmission is characterized by the presence of physically identifiable communication channels within the neuronal and/or glial cell network. It includes synaptic transmission but also other types of intercellular communication through a connecting structure (e.g., gap junctions). "Volume" transmission is characterized by signal diffusion in a three-dimensional fashion within the brain extracellular fluid. Thus, multiple, structurally often not well characterized extracellular pathways connect intercommunicating cells. Volume transmission includes short- (but larger than synaptic cleft, i.e. about 20 nm) and long-distance diffusion of signals through the extracellular and cerebrospinal fluid. It must be underlined that the definitions of wiring and volume transmission focus on the modality of transmission and are neutral with respect to the source and target of the transmission, as well as type of informational substance transmitted. Therefore, any cell present in the neural tissue (neurons, astroglia, microglia, ependyma, tanycytes, etc.) can be a source or a target of wiring and volume transmission. In this paper we discuss the basic definitions and some distinctive characteristics of the two types of transmission. In addition, we review the evidence for different types of intercellular communication besides synaptic transmission in the central nervous system during phylogeny, and in vertebrates in physiological and pathological conditions.
A photosynthetic ancestry for all eukaryotes?

flies (Cyrtodiopsis dalmanni) offers a new sort of test. Sensory exploitation is the idea that ‘selection favors male traits that exploit sensory biases in females’4. These sensory biases are ‘built into the sensory modality being used and may have no intrinsic adaptive value’s, Thus, ‘the female’s sensory system defined the possible evolutionary alternatives for more attractive male traits’6. Proponents of sensory exploitation argue that biases in females’ neural machinery are evolutionarily ancient, antedating the appearance of the male traits they promote. Phylogenetic reconstructions have been used to infer the history of such ‘preexisting’ biases in fish (Xiphophorus)7,8 and frogs (Physa/aemus)4,g, but conflicting phylogenies have resulted in tenuous concIusionsl,lo. Wilkinson and Reillo’s experiment2,3 suggests a different, potentially useful approach. They selected male flies for large (L) or small (S) eye span relative to body size, and examined females’ mate choices after 13 generations. Females from L-lines preferred L males (as did unselected controls), but S-line females preferred S males. These results implied ‘a genetic correlation between female preference and a sexually selected male trait’z, an interpretation that has been disputed11 and defendedI*. Biases in females’ neural machinery that are strong enough to steer male phenotypic evolution should be difficult to alter experimentally. Yet preferences of female C. dalmanni were rapidly reversed as a by-product of selecting for S males, implying that considerable genetic variability underlies their current expression. Sensory exploitation posits that fixed female preferences drive sexual selection. Plasticity in female preferences is not consistent with this hypothesis. Comparative studies using Wilkinson and Reillo’s approach (e.g. Ref. 13) will be useful for clarifying in other species whether or not female preferences represent fixed biases imbedded in their neural machinery.
China type 2 diabetes treatment status survey of treatment pattern of oral drugs users

BACKGROUND
The aim of the present study was to investigate the current status of oral anti-diabetic drug (OAD) therapy in patients with type 2 diabetes and influencing factors in a real-world setting in China.


METHODS
A total of 9872 outpatients with type 2 diabetes, who had received OADs (monotherapy or combination therapy) for at least 3 months were recruited in this study. Current antidiabetic treatment regimen and related clinical data were collected from medical records and analyzed.


RESULTS
The most common OADs in use were insulin secretagogues (70.2%) such as sulfonylureas (SUs; 42.7%) or glinides (27.5%), followed by metformin (53.7%), α-glucosidase inhibitors (35.9%), thiazolidinediones (17.2%), and dipeptidyl peptidase-4 (DPP-4) inhibitors (0.8%). Dual-drug combination therapy was more common (45.4%) than monotherapy (35.8%) and combination therapy with at least three drugs (17.0%). Patients on SU or glinide monotherapy were more likely to alter their treatment frequently (odds ratio [OR], 1.7; 95% CI, 1.38-2.08; P < 0.001).


CONCLUSIONS
The status of OAD use in China is varied with a majority of the patients altering their treatment regimen citing poor effectiveness. These observations from a real-world setting may serve as guidance for improving diabetes management in China.
On Identifying Strongly Connected Components in Parallel

The standard serial algorithm for strongly connected components is based on depth rst search, which is di cult to parallelize. We describe a divide-and-conquer algorithm for this problem which has signi cantly greater potential for parallelization. For a graph with n vertices in which degrees are bounded by a constant, we show the expected serial running time of our algorithm to be O(n log n).
Implants in the zygomatic bone for maxillary prosthetic rehabilitation: a systematic review.

The purpose of this systematic review was to evaluate clinical studies on the follow-up survival of implants inserted in the zygomatic bone for maxillary rehabilitation. A comprehensive search of studies published from 2000 to July 2012 and listed in the PubMed/MEDLINE, Embase, and Cochrane Library databases was performed in accordance with the PRISMA statement. Relevant studies were selected according to predetermined inclusion and exclusion criteria. The initial database search yielded 751 titles. After filtering, 313 abstracts were selected, culminating in 42 full text articles. Application of eligibility criteria led to the elimination of 17 articles. Hence 25 full-text articles were considered clinically relevant and were included. Calculations of the interval survival rates and cumulative survival rates of implants could be carried out on the data extracted from the final list of included studies for the different time intervals. These studies reported the insertion of a total of 1541 zygomatic implants and 33 implant failures. Failure generally occurred during the first year interval and was related to clinical complications, such as recurrent acute and chronic sinusitis. After a 36-month follow-up, the survival rate was 97.86%. Additional studies with longer follow-up periods, including the number of zygomatic implants inserted and details of the variations in the surgical techniques used and the impact of the maxillary morphology are still required.
A Novel Method for Constructing a WIFI Positioning System with Efficient Manpower

With the rapid development of WIFI technology, WIFI-based indoor positioning technology has been widely studied for location-based services. To solve the problems related to the signal strength database adopted in the widely used fingerprint positioning technology, we first introduce a new system framework in this paper, which includes a modified AP firmware and some cheap self-made WIFI sensor anchors. The periodically scanned reports regarding the neighboring APs and sensor anchors are sent to the positioning server and serve as the calibration points. Besides the calculation of correlations between the target points and the neighboring calibration points, we take full advantage of the important but easily overlooked feature that the signal attenuation model varies in different regions in the regression algorithm to get more accurate results. Thus, a novel method called RSSI Geography Weighted Regression (RGWR) is proposed to solve the fingerprint database construction problem. The average error of all the calibration points' self-localization results will help to make the final decision of whether the database is the latest or has to be updated automatically. The effects of anchors on system performance are further researched to conclude that the anchors should be deployed at the locations that stand for the features of RSSI distributions. The proposed system is convenient for the establishment of practical positioning system and extensive experiments have been performed to validate that the proposed method is robust and manpower efficient.
Pathogenesis of allergic bronchopulmonary aspergillosis and an evidence-based review of azoles in treatment.

BACKGROUND
Allergic bronchopulmonary aspergillosis (ABPA) is a complex condition that affects people with asthma and cystic fibrosis (CF). It results from exposure to the fungus Aspergillus fumigatus, which leads to worsening airway inflammation and progressive damage to the lungs. The aim of this review is to outline the pathogenesis of the disorder, diagnostic criteria and to discuss the use of anti-fungal agents in its treatment.


METHODS
The Cochrane library of systematic reviews and the Cochrane database of controlled trials were searched for controlled trials on ABPA and its treatment in both asthma and CF. In addition, articles included within the reviews were examined separately, and a separate search carried out using Medline.


RESULTS
A systematic review for the use of azole anti-fungal agents in ABPA was identified for their use in both CF and non-CF-related disease. The review of ABPA alone identified two randomized-controlled trials of itraconazole in chronic disease. These trials demonstrated improvements in symptoms and immune activation, but were short-term trials and failed to show a significant change in lung function. No trials were identified in CF.


CONCLUSIONS
The use of anti-fungal agents in ABPA seems to be a rational one, with short-term efficacy demonstrated for the use of itraconazole. Further investigations are required to identify individuals who will benefit most from treatment and to establish the correct dose and means of delivering treatment in ABPA. Longer-term studies are required to demonstrate that treatment modifies the progressive decline in lung function seen with the disease.
Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment.

MOTIVATION
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes. We introduce Shouji, a highly-parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator that adopts modern FPGA (Field-Programmable Gate Array) architectures to further boost the performance of our algorithm.


RESULTS
Shouji significantly improves the accuracy of pre-alignment filtering by up to two orders of magnitude compared to the state-of-the-art pre-alignment filters, GateKeeper and SHD. Our FPGA-based accelerator is up to three orders of magnitude faster than the equivalent CPU implementation of Shouji. Using a single FPGA chip, we benchmark the benefits of integrating Shouji with five state-of-the-art sequence aligners, designed for different computing platforms. The addition of Shouji as a pre-alignment step reduces the execution time of the five state-of-the-art sequence aligners by up to 18.8x. Shouji can be adapted for any bioinformatics pipeline that performs sequence alignment for verification. Unlike most existing methods that aim to accelerate sequence alignment, Shouji does not sacrifice any of the aligner capabilities, as it does not modify or replace the alignment step.


AVAILABILITY
https://github.com/CMU-SAFARI/Shouji.


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.