bluuebunny/crossref_metadata_2025 huggingface dataset:
Practical SMT-based type error localization
Authors: Pavlinovic Zvonimir , King Tim , Wies Thomas
Published: December 2015

Compilers for statically typed functional programming languages are notorious for generating confusing type error messages. When the compiler detects a type error, it typically reports the program location where the type checking failed as the source of the error. Since other error sources are not even considered, the actual root cause is often missed. A more adequate approach is to consider all possible error sources and report the most useful one subject to some usefulness criterion. In our previous work, we showed that this approach can be formulated as an optimization problem related to satisfiability modulo theories (SMT). This formulation cleanly separates the heuristic nature of usefulness criteria from the underlying search problem. Unfortunately, algorithms that search for an optimal error source cannot directly use principal types which are crucial for dealing with the exponential-time complexity of the decision problem of polymorphic type checking. In this paper, we present a new algorithm that efficiently finds an optimal error source in a given ill-typed program. Our algorithm uses an improved SMT encoding to cope with the high complexity of polymorphic typing by iteratively expanding the typing constraints from which principal types are derived. The algorithm preserves the clean separation between the heuristics and the actual search. We have implemented our algorithm for OCaml. In our experimental evaluation, we found that the algorithm reduces the running times for optimal type error localization from minutes to seconds and scales better than previous localization algorithms.
Interactively verifying absence of explicit information flows in Android apps
Authors: Bastani Osbert , Anand Saswat , Aiken Alex
Published: December 2015

App stores are increasingly the preferred mechanism for distributing software, including mobile apps (Google Play), desktop apps (Mac App Store and Ubuntu Software Center), computer games (the Steam Store), and browser extensions (Chrome Web Store). The centralized nature of these stores has important implications for security. While app stores have unprecedented ability to audit apps, users now trust hosted apps, making them more vulnerable to malware that evades detection and finds its way onto the app store. Sound static explicit information flow analysis has the potential to significantly aid human auditors, but it is handicapped by high false positive rates. Instead, auditors currently rely on a combination of dynamic analysis (which is unsound) and lightweight static analysis (which cannot identify information flows) to help detect malicious behaviors. We propose a process for producing apps certified to be free of malicious explicit information flows. In practice, imprecision in the reachability analysis is a major source of false positive information flows that are difficult to understand and discharge. In our approach, the developer provides tests that specify what code is reachable, allowing the static analysis to restrict its search to tested code. The app hosted on the store is instrumented to enforce the provided specification (i.e., executing untested code terminates the app). We use abductive inference to minimize the necessary instrumentation, and then interact with the developer to ensure that the instrumentation only cuts unreachable code. We demonstrate the effectiveness of our approach in verifying a corpus of 77 Android apps—our interactive verification process successfully discharges 11 out of the 12 false positives.
Selective control-flow abstraction via jumping
Authors: Blackshear Sam , Chang Bor-Yuh Evan , Sridharan Manu
Published: December 2015

We present jumping, a form of selective control-flow abstraction useful for improving the scalability of goal-directed static analyses. Jumping is useful for analyzing programs with complex control-flow such as event-driven systems. In such systems, accounting for orderings between certain events is important for precision, yet analyzing the product graph of all possible event orderings is intractable. Jumping solves this problem by allowing the analysis to selectively abstract away control-flow between events irrelevant to a goal query while preserving information about the ordering of relevant events. We present a framework for designing sound jumping analyses and create an instantiation of the framework for per- forming precise inter-event analysis of Android applications. Our experimental evaluation showed that using jumping to augment a precise goal-directed analysis with inter-event reasoning enabled our analysis to prove 90–97% of dereferences safe across our benchmarks.
Synthesizing Java expressions from free-form queries
Authors: Gvero Tihomir , Kuncak Viktor
Published: December 2015

We present a new code assistance tool for integrated development environments. Our system accepts as input free-form queries containing a mixture of English and Java, and produces Java code expressions that take the query into account and respect syntax, types, and scoping rules of Java, as well as statistical usage patterns. In contrast to solutions based on code search, the results returned by our tool need not directly correspond to any previously seen code fragment. As part of our system we have constructed a probabilistic context free grammar for Java constructs and library invocations, as well as an algorithm that uses a customized natural language processing tool chain to extract information from free-form text queries. We present the results on a number of examples showing that our technique (1) often produces the expected code fragments, (2) tolerates much of the flexibility of natural language, and (3) can repair incorrect Java expressions that use, for example, the wrong syntax or missing arguments.
Automating grammar comparison
Authors: Madhavan Ravichandhran , Mayer Mikaël , Gulwani Sumit , Kuncak Viktor
Published: December 2015

We consider from a practical perspective the problem of checking equivalence of context-free grammars. We present techniques for proving equivalence, as well as techniques for finding counter-examples that establish non-equivalence. Among the key building blocks of our approach is a novel algorithm for efficiently enumerating and sampling words and parse trees from arbitrary context-free grammars; the algorithm supports polynomial time random access to words belonging to the grammar. Furthermore, we propose an algorithm for proving equivalence of context-free grammars that is complete for LL grammars, yet can be invoked on any context-free grammar, including ambiguous grammars. Our techniques successfully find discrepancies between different syntax specifications of several real-world languages, and are capable of detecting fine-grained incremental modifications performed on grammars. Our evaluation shows that our tool improves significantly on the existing available state of the art tools. In addition, we used these algorithms to develop an online tutoring system for grammars that we then used in an undergraduate course on computer language processing. On questions involving grammar constructions, our system was able to automatically evaluate the correctness of 95% of the solutions submitted by students: it disproved 74% of cases and proved 21% of them.
Giga-scale exhaustive points-to analysis for Java in under a minute
Authors: Dietrich Jens , Hollingum Nicholas , Scholz Bernhard
Published: December 2015

Computing a precise points-to analysis for very large Java programs remains challenging despite the large body of research on points-to analysis. Any approach must solve an underlying dynamic graph reachability problem, for which the best algorithms have near-cubic worst-case runtime complexity, and, hence, previous work does not scale to programs with millions of lines of code. In this work, we present a novel approach for solving the field-sensitive points-to problem for Java with the means of (1) a transitive-closure data-structure, and (2) a pre-computed set of potentially matching load/store pairs to accelerate the fix-point calculation. Experimentation on Java benchmarks validates the superior performance of our approach over the standard context-free language reachability implementations. Our approach computes a points-to index for the OpenJDK with over 1.5 billion tuples in under a minute.
Use at your own risk: the Java unsafe API in the wild
Authors: Mastrangelo Luis , Ponzanelli Luca , Mocci Andrea , Lanza Michele , Hauswirth Matthias , Nystrom Nathaniel
Published: December 2015

Java is a safe language. Its runtime environment provides strong safety guarantees that any Java application can rely on. Or so we think. We show that the runtime actually does not provide these guarantees---for a large fraction of today's Java code. Unbeknownst to many application developers, the Java runtime includes a "backdoor" that allows expert library and framework developers to circumvent Java's safety guarantees. This backdoor is there by design, and is well known to experts, as it enables them to write high-performance "systems-level" code in Java. For much the same reasons that safe languages are preferred over unsafe languages, these powerful---but unsafe---capabilities in Java should be restricted. They should be made safe by changing the language, the runtime system, or the libraries. At the very least, their use should be restricted. This paper is a step in that direction. We analyzed 74 GB of compiled Java code, spread over 86,479 Java archives, to determine how Java's unsafe capabilities are used in real-world libraries and applications. We found that 25% of Java bytecode archives depend on unsafe third-party Java code, and thus Java's safety guarantees cannot be trusted. We identify 14 different usage patterns of Java's unsafe capabilities, and we provide supporting evidence for why real-world code needs these capabilities. Our long-term goal is to provide a foundation for the design of new language features to regain safety in Java.
A sound and optimal incremental build system with dynamic dependencies
Authors: Erdweg Sebastian , Lichter Moritz , Weiel Manuel
Published: December 2015

Build systems are used in all but the smallest software projects to invoke the right build tools on the right files in the right order. A build system must be sound (after a build, generated files consistently reflect the latest source files) and efficient (recheck and rebuild as few build units as possible). Contemporary build systems provide limited efficiency because they lack support for expressing fine-grained file dependencies. We present a build system called pluto that supports the definition of reusable, parameterized, interconnected builders. When run, a builder notifies the build system about dynamically required and produced files as well as about other builders whose results are needed. To support fine-grained file dependencies, we generalize the traditional notion of time stamps to allow builders to declare their actual requirements on a file's content. pluto collects the requirements and products of a builder with their stamps in a build summary. This enables pluto to provides provably sound and optimal incremental rebuilding. To support dynamic dependencies, our rebuild algorithm interleaves dependency analysis and builder execution and enforces invariants on the dependency graph through a dynamic analysis. We have developed pluto as a Java API and used it to implement more than 25 builders. We describe our experience with migrating a larger Ant build script to pluto and compare the respective build times.
Declarative fence insertion
Authors: Bender John , Lesani Mohsen , Palsberg Jens
Published: December 2015

Previous work has shown how to insert fences that enforce sequential consistency. However, for many concurrent algorithms, sequential consistency is unnecessarily strong and can lead to high execution overhead. The reason is that, often, correctness relies on the execution order of a few specific pairs of instructions. Algorithm designers can declare those execution orders and thereby enable memory-model-independent reasoning about correctness and also ease implementation of algorithms on multiple platforms. The literature has examples of such reasoning, while tool support for enforcing the orders has been lacking until now. In this paper we present a declarative approach to specify and enforce execution orders. Our fence insertion algorithm first identifies the execution orders that a given memory model enforces automatically, and then inserts fences that enforce the rest. Our benchmarks include three off-the-shelf transactional memory algorithms written in C/C++ for which we specify suitable execution orders. For those benchmarks, our experiments with the x86 and ARMv7 memory models show that our tool inserts fences that are competitive with those inserted by the original authors. Our tool is the first to insert fences into transactional memory algorithms and it solves the long-standing problem of how to easily port such algorithms to a novel memory model.
Finding deep compiler bugs via guided stochastic program mutation
Authors: Le Vu , Sun Chengnian , Su Zhendong
Published: December 2015

Compiler testing is important and challenging. Equivalence Modulo Inputs (EMI) is a recent promising approach for compiler validation. It is based on mutating the unexecuted statements of an existing program under some inputs to produce new equivalent test programs w.r.t. these inputs. Orion is a simple realization of EMI by only randomly deleting unexecuted statements. Despite its success in finding many bugs in production compilers, Orion’s effectiveness is still limited by its simple, blind mutation strategy. To more effectively realize EMI, this paper introduces a guided, advanced mutation strategy based on Bayesian optimization. Our goal is to generate diverse programs to more thoroughly exercise compilers. We achieve this with two techniques: (1) the support of both code deletions and insertions in the unexecuted regions, leading to a much larger test program space; and (2) the use of an objective function that promotes control-flow-diverse programs for guiding Markov Chain Monte Carlo (MCMC) optimization to explore the search space. Our technique helps discover deep bugs that require elaborate mutations. Our realization, Athena, targets C compilers. In 19 months, Athena has found 72 new bugs — many of which are deep and important bugs — in GCC and LLVM. Developers have confirmed all 72 bugs and fixed 68 of them.
Partial evaluation of machine code
Authors: Srinivasan Venkatesh , Reps Thomas
Published: December 2015

This paper presents an algorithm for off-line partial evaluation of machine code. The algorithm follows the classical two-phase approach of binding-time analysis (BTA) followed by specialization. However, machine-code partial evaluation presents a number of new challenges, and it was necessary to devise new techniques for use in each phase. - Our BTA algorithm makes use of an instruction-rewriting method that ``decouples'' multiple updates performed by a single instruction. This method counters the cascading imprecision that would otherwise occur with a more naive approach to BTA. - Our specializer specializes an explicit representation of the semantics of an instruction, and emits residual code via machine-code synthesis. Moreover, to create code that allows the stack and heap to be at different positions at run-time than at specialization-time, the specializer represents specialization-time addresses using symbolic constants, and uses a symbolic state for specialization. Our experiments show that our algorithm can be used to specialize binaries with respect to commonly used inputs to produce faster binaries, as well as to extract an executable component from a bloated binary.
Cross-layer memory management for managed language applications
Authors: Jantz Michael R. , Robinson Forrest J. , Kulkarni Prasad A. , Doshi Kshitij A.
Published: December 2015

Performance and energy efficiency in memory have become critically important for a wide range of computing domains. However, it is difficult to control and optimize memory power and performance because these effects depend upon activity across multiple layers of the vertical execution stack. To address this challenge, we construct a novel and collaborative framework that employs object placement, cross-layer communication, and page-level management to effectively distribute application objects in the DRAM hardware to achieve desired power/performance goals. In this work, we describe the design and implementation of our framework, which is the first to integrate automatic object profiling and analysis at the application layer with fine-grained management of memory hardware resources in the operating system. We demonstrate the utility of our framework by employing it to more effectively control memory power consumption. We design a custom memory-intensive workload to show the potential of our approach. Next, we develop sampling and profiling-based analyses and modify the code generator in the HotSpot VM to understand object usage patterns and automatically determine and control the placement of hot and cold objects in a partitioned VM heap. This information is communicated to the operating system, which uses it to map the logical application pages to the appropriate DRAM ranks according to user-defined provisioning goals. We evaluate our framework and find that it achieves our test goal of significant DRAM energy savings across a variety of workloads, without any source code modifications or recompilations.
Anticollocated Backstepping Observer Design for a Class of Coupled Reaction-Diffusion PDEs
Authors: Baccoli Antonello , Pisano Alessandro
Published: December 2015

The state observation problem is tackled for a system ofncoupled reaction-diffusion PDEs, possessing the same diffusivity parameter and equipped with boundary sensing devices. Particularly, a backstepping-based observer is designed and the exponential stability of the error system is proven with an arbitrarily fast convergence rate. The transformation kernel matrix is derived in the explicit form by using the method of successive approximations, thereby yielding the observer gains in the explicit form, too. Simulation results support the effectiveness of the suggested design.
Drought Occurrence in Central European Mountainous Region (Tatra National Park, Slovakia) within the Period 1961–2010
Authors: Vido Jaroslav , Tadesse Tsegaye , Šustek Zbyšek , Kandrík Radoslav , Hanzelová Miriam , Škvarenina Jaroslav , Škvareninová Jana , Hayes Michael
Published: December 2015

Drought has recently become a significant topic in the Central European region. It has been observed that the drought phenomenon has severe impacts on the agriculture, hydrology, social, and economic sectors of lowland areas. This study focuses on how drought, defined as a precipitation shortage, occurs in higher altitudes of the Tatra National Park (Tatra Mts., Slovakia), which is a significant biological reserve of the Central European fauna and flora. The main goals of this research include identifying drought variability and its characteristics over the Tatra National Park in the West Carpathians (Slovakia), especially to characterizing drought variability and its spatial pattern across the Tatra National Park from 1961 to 2010 using the Standardized Precipitation Index (SPI) and standard Geographic Information System (GIS) methods. The results showed that frequency of drought occurrence has cyclic pattern with approximately 30-year period. The spatial analyses showed that precipitation shadow of the mountains influences the risk of drought occurrence. The drought-prone areas over the mountains are also identified.
Multiclass Posterior Probability Twin SVM for Motor Imagery EEG Classification
Authors: She Qingshan , Ma Yuliang , Meng Ming , Luo Zhizeng
Published: December 2015

Motor imagery electroencephalography is widely used in the brain-computer interface systems. Due to inherent characteristics of electroencephalography signals, accurate and real-time multiclass classification is always challenging. In order to solve this problem, a multiclass posterior probability solution for twin SVM is proposed by the ranking continuous output and pairwise coupling in this paper. First, two-class posterior probability model is constructed to approximate the posterior probability by the ranking continuous output techniques and Platt’s estimating method. Secondly, a solution of multiclass probabilistic outputs for twin SVM is provided by combining every pair of class probabilities according to the method of pairwise coupling. Finally, the proposed method is compared with multiclass SVM and twin SVM via voting, and multiclass posterior probability SVM using different coupling approaches. The efficacy on the classification accuracy and time complexity of the proposed method has been demonstrated by both the UCI benchmark datasets and real world EEG data from BCI Competition IV Dataset 2a, respectively.
A Facile Approach to Evaluate Thermal Insulation Performance of Paper Cups
Authors: Kuang Yudi , Chen Gang , Fang Zhiqiang
Published: December 2015

Paper cups are ubiquitous in daily life for serving water, soup, coffee, tea, and milk due to their convenience, biodegradability, recyclability, and sustainability. The thermal insulation performance of paper cups is of significance because they are used to supply hot food or drinks. Using an effective thermal conductivity to accurately evaluate the thermal insulation performance of paper cups is complex due to the inclusion of complicated components and a multilayer structure. Moreover, an effective thermal conductivity is unsuitable for evaluating thermal insulation performance of paper cups in the case of fluctuating temperature. In this work, we propose a facile approach to precisely analyze the thermal insulation performance of paper cups in a particular range of temperature by using an evaluation model based on the MISO (Multiple-Input Single-Output) technical theory, which includes a characterization parameter (temperature factor) and a measurement apparatus. A series of experiments was conducted according to this evaluation model, and the results show that this evaluation model enables accurate characterization of the thermal insulation performance of paper cups and provides an efficient theoretical basis for selecting paper materials for paper cups.
Protective Effects of Danhong Injection against Cerebral Damage during On-Pump Coronary Artery Bypass Graft Surgery
Authors: Xuejuan Zhang , Jietao Zhang , Di Han , Yu Zheng , Xiaozi Guo , Yunfa Li , Lihua Dong
Published: December 2015

To explore the protective effects of Danhong injection against cerebral damage during on-pump coronary artery bypass graft surgery and its mechanism.Methods. Fifty patients scheduled for on-pump CABG surgery were randomly divided into Danhong injection group (group D) and control group (group C). Group D was given Danhong injection while group C was given the same volume of normal saline when the artery was cut open. Jugular bulb blood right before the operation began (T1), when body temperature rewarming to 36°C (T2), 30 min after the termination of cardiopulmonary bypass (T3), and 6 hrs after the termination of CPB (T4) was collected. The superoxide dismutase activity by using xanthine oxidase method and concentration determination of malondialdehyde were examined.Results. In group C, SOD activity was less at T2–T4 than at T1. It was also less active comparatively in group D at T2–T4. The MDA concentration increased in both groups but was more obvious in group C. Levels of TNF-α, IL-6, IL-8, and IL-10 increased in both groups C and D at T3 and T4, compared to T1.Conclusions. Danhong injection shows significant protective effects against cerebral damage during on-pump coronary artery bypass graft surgery.
CT Appearance of Hepatocellular Carcinoma after Locoregional Treatments: A Comprehensive Review
Authors: Marin Daniel , Cappabianca Salvatore , Serra Nicola , Sica Assunta , Lassandro Francesco , D’Angelo Roberto , La Porta Michelearcangelo , Fiore Francesco , Somma Francesco
Published: December 2015

Hepatocellular carcinoma (HCC) is a major health problem worldwide, affecting more than 600,000 new patients per year. Curative treatments are available in a small percentage of patients, while most of them present in stages requiring locoregional treatments such as thermoablation, transarterial chemoembolization, and/or radioembolization. These therapies result in specific imaging features that the general radiologist has to be aware of in order to assess the response to treatment and to correctly manage the follow-up of treated patients. Multiphasic helical computed tomography has become a popular imaging modality for detecting hypervascular tumors and characterizing liver lesions. On this basis, many staging and diagnostic systems have been proposed for evaluating response to all different existing strategies. Radiofrequencies and microwaves generate thermoablation of tumors, and transarterial chemoembolization exploits the double effect of the locoregional administration of drugs and embolizing particles. Eventually radioembolization uses a beta-emitting isotope to induce necrosis. Therefore, the aim of this comprehensive review is to analyze and compare CT imaging appearance of HCC after various locoregional treatments, with regard to specific indications for all possible procedures.
An Unusual Case of Nonhealing Granulomatous Keratitis Caused byMycobacterium chelonaein a Healthy Middle Aged Adult
Authors: Bhandari Vipul , Sriganesh  , Relekar Kirti
Published: December 2015

Purpose. To report a rare presentation of culture positiveMycobacterium chelonae(M. chelonae) corneal ulcer and its management.Case Report. We report a rare case with history of chronic pain and blurriness of vision. Examination revealed chronic nonhealing paracentral corneal ulcer inferiorly at 5 to 7 o’clock meridian with anterior chamber cells 1+ unresponsive to routine antibiotic and antifungal medications with Mantoux test (MT) positivity in a middle aged nondiabetic patient with no prior obvious history of trauma, ocular surgery, and contact lens usage.Discussion. Ziehl Neelsen (ZN) staining in nonhealing ulcer revealed acid fast bacilli typical ofM. chelonaewith subsequent culture positivity in Lowenstein Jensen (LJ) medium. Subsequent treatment with topical fortified amikacin and tobramycin resulted in rapid healing of corneal ulcer.Conclusion. M. chelonaepresenting as a chronic nonhealing corneal ulcer spontaneously occurring in a healthy young adult with no predisposing factor draws the need to have a good index of suspicion by performing ZN stain and culture and its subsequent successful management with topical fortified amikacin and tobramycin.
Salmon Muscle Adherence to Polymer Coatings and Determination of Antibiotic Residues by Reversed-Phase High-Performance Liquid Chromatography Coupled to Selected Reaction Monitoring Mass Spectrometry, Atomic Force Microscopy, and Fourier Transform Infrared Spectroscopy
Authors: Zumelzu E. , Wehrhahn M. J. , Muñoz O. , Rull F.
Published: December 2015

The persistent adhesion of salmon muscle to food container walls after treatment with urea solution was observed. This work evaluated the diffusion of antibiotics from the salmon muscle to the polyethylene terephthalate (PET) coating protecting the electrolytic chromium coated steel (ECCS) plates. New aquaculture production systems employ antibiotics such as florfenicol, florfenicol amine, oxytetracycline, and erythromycin to control diseases. The introduction of antibiotics is a matter of concern regarding the effects on human health and biodiversity. It is important to determine their impact on the adhesion of postmortem salmon muscle to can walls and the surface and structural changes affecting the functionality of multilayers. This work characterized the changes occurring in the multilayer PET polymer and steel of containers by electron microscopy, 3D atomic force microscopy (3D-AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared spectroscopy (FT-IR) analyses. A robust mass spectrometry methodology was employed to determine the presence of antibiotic residues. No evidence of antibiotics was observed on the protective coating in the range between 0.001 and 2.0 ng/mL; however, the presence of proteins, cholesterol, and alpha-carotene was detected. This in-depth profiling of the matrix-level elements is relevant for the use of adequate materials in the canning export industry.
P-FFT Accelerated EFIE with a Novel Diagonal Perturbed ILUT Preconditioner for Electromagnetic Scattering by Conducting Objects in Half Space
Authors: Guo Lan-Wei , Chen Yongpin , Hu Jun , Li Joshua Le-Wei
Published: December 2015

A highly efficient and robust scheme is proposed for analyzing electromagnetic scattering from electrically large arbitrary shaped conductors in a half space. This scheme is based on the electric field integral equation (EFIE) with a half-space Green’s function. The precorrected fast Fourier transform (p-FFT) is first extended to a half space for general three-dimensional scattering problems. A novel enhanced dual threshold incomplete LU factorization (ILUT) is then constructed as an effective preconditioner to improve the convergence of the half-space EFIE. Inspired by the idea of the improved electric field integral operator (IEFIO), the geometrical-optics current/principle value term of the magnetic field integral equation is used as a physical perturbation to stabilize the traditional ILUT perconditioning matrix. The high accuracy of EFIE is maintained, yet good calculating efficiency comparable to the combined field integral equation (CFIE) can be achieved. Furthermore, this approach can be applied to arbitrary geometrical structures including open surfaces and requires no extra types of Sommerfeld integrals needed in the half-space CFIE. Numerical examples are presented to demonstrate the high performance of the proposed solver among several other approaches in typical half-space problems.
Detailed Analysis of the Timing Measurements in Optical Position Sensing Devices Based on Laser Beam Deflection
Authors: Tortschanoff Andreas
Published: December 2015

I present a detailed analysis of the timing signals observed, when measuring the oscillation of a Lissajous scanner by sending a reflected laser beam onto carefully placed trigger diodes. This technique was used in a device which we have developed recently for the measurement of resonant MEMS scanner mirrors. For 2D scanner mirrors, cross talk between the two axes is observed. This cross talk can be well understood theoretically. In this paper, a quantitative analytical description is presented, which is confirmed by experimental results.
Spironolactone Effect in Hepatic Ischemia/Reperfusion Injury in Wistar Rats
Authors: Jiménez Pérez Julio César , Casillas Ramírez Araní , Torres González Liliana , Muñoz Espinosa Linda Elsa , Perales Quintana Marlene Marisol , Alarcón Galván Gabriela , Zapata Chavira Homero , Guzmán de la Garza Francisco Javier , Cámara Lemarroy Carlos Rodrigo , Fernández Garza Nancy Esthela , Pérez Rodríguez Edelmiro , Cordero Pérez Paula
Published: December 2015

Introduction. Ischemia/reperfusion (IR) injury, often associated with liver surgery, is an unresolved problem in the clinical practice. Spironolactone is an antagonist of aldosterone that has shown benefits over IR injury in several tissues, but its effects in hepatic IR are unknown. Objective. To evaluate the effect of spironolactone on IR‐induced damage in liver. Materials and Methods. Total hepatic ischemia was induced in rats for 20 min followed by 60 min of reperfusion. Spironolactone was administered and hepatic injury, cytokine production, and oxidative stress were assessed. Results. After IR, increased transaminases levels and widespread acute inflammatory infiltrate, disorganization of hepatic hemorrhage trabeculae, and presence of apoptotic bodies were observed. Administration of SPI reduced biochemical and histological parameters of liver injury. SPI treatment increased IL‐6 levels when compared with IR group but did not modify either IL‐1β or TNF‐α with respect to IR group. Regarding oxidative stress, increased levels of catalase activity were recorded in IR + SPI group in comparison with group without treatment, whereas MDA levels were similar in IR + SPI and IR groups. Conclusions. Spironolactone reduced the liver damage induced by IR, and this was associated with an increase in IL‐6 production and catalase activity.
Investigation of Five Algorithms for Selection of the Optimal Region of Interest in Smartphone Photoplethysmography
Authors: Peng Rong-Chao , Yan Wen-Rong , Zhang Ning-Ling , Lin Wan-Hua , Zhou Xiao-Lin , Zhang Yuan-Ting
Published: December 2015

Smartphone photoplethysmography is a newly developed technique that can detect several physiological parameters from the photoplethysmographic signal obtained by the built-in camera of a smartphone. It is simple, low-cost, and easy-to-use, with a great potential to be used in remote medicine and home healthcare service. However, the determination of the optimal region of interest (ROI), which is an important issue for extracting photoplethysmographic signals from the camera video, has not been well studied. We herein proposed five algorithms for ROI selection: variance (VAR), spectral energy ratio (SER), template matching (TM), temporal difference (TD), and gradient (GRAD). Their performances were evaluated by a 50-subject experiment comparing the heart rates measured from the electrocardiogram and those from the smartphone using the five algorithms. The results revealed that the TM and the TD algorithms outperformed the other three as they had less standard error of estimate (<1.5 bpm) and smaller limits of agreement (<3 bpm). The TD algorithm was slightly better than the TM algorithm and more suitable for smartphone applications. These results may be helpful to improve the accuracy of the physiological parameters measurement and to make the smartphone photoplethysmography technique more practical.
Oxidative Stress‐Mediated Skeletal Muscle Degeneration: Molecules, Mechanisms, and Therapies
Authors: Choi Min Hee , Ow Jin Rong , Yang Nai-Di , Taneja Reshma
Published: December 2015

Oxidative stress is a loss of balance between the production of reactive oxygen species during cellular metabolism and the mechanisms that clear these species to maintain cellular redox homeostasis. Increased oxidative stress has been associated with muscular dystrophy, and many studies have proposed mechanisms that bridge these two pathological conditions at the molecular level. In this review, the evidence indicating a causal role of oxidative stress in the pathogenesis of various muscular dystrophies is revisited. In particular, the mediation of cellular redox status in dystrophic muscle by NF‐κB pathway, autophagy, telomere shortening, and epigenetic regulation are discussed. Lastly, the current stance of targeting these pathways using antioxidant therapies in preclinical and clinical trials is examined.
Atrial and Ventricular Arrhythmia-Associated Factors in Stable Patients with Chronic Obstructive Pulmonary Disease
Authors: Kusunoki Yuji , Nakamura Toshie , Hattori Kumiko , Motegi Takashi , Ishii Takeo , Gemma Akihiko , Kida Kozui
Published: December 2015

Background: Supraventricular and ventricular premature complexes (SVPC and VPC, respectively) are associated with chronic obstructive pulmonary disease (COPD) and with increased mortality in COPD patients. However, there are few reports on the causes of arrhythmia in COPD patients. Objectives: This study explores the associations between cardiopulmonary dysfunction and COPD by comparing patients with defined arrhythmias (>100 beats per 24 h) and those without, based on 24-hour electrocardiogram (ECG) recordings. Methods: Patients with arrhythmia underwent a 24-hour ECG and subsequent pulmonary function tests, computed tomography, ECG, 6-min walk test (6MWT), and BODE (body mass index, airflow obstruction, modified Medical Research Council Dyspnoea Scale, exercise capacity) index calculation. Results: Of 103 study patients (71 COPD patients and 32 at-risk patients), 36 had VPC, 45 had SVPC, 20 had both, and 42 had neither. The predicted post-bronchodilator forced expiratory volume in 1 s, the proportion of low-attenuation area on computed tomography, and BODE index values were significantly worse in the SVPC and VPC groups compared with the corresponding reference groups. Patients in the VPC group showed significantly increased right ventricular pressure and increased desaturation in the 6MWT compared with the reference group. In the multivariate analyses, bronchodilator use was a significant risk factor in the SVPC group, whereas in the VPC group, all parameters of the BODE index except for the dyspnoea score were identified as risk factors. Conclusions: Increased SVPC might be caused by bronchodilator use, whereas increased VPC is likely related to the peculiar pathophysiology of COPD.
Neural Network Spectral Robustness under Perturbations of the Underlying Graph
Authors: Rădulescu Anca
Published: December 2015

Recent studies have been using graph-theoretical approaches to model complex networks (such as social, infrastructural, or biological networks) and how their hardwired circuitry relates to their dynamic evolution in time. Understanding how configuration reflects on the coupled behavior in a system of dynamic nodes can be of great importance, for example, in the context of how the brain connectome is affecting brain function. However, the effect of connectivity patterns on network dynamics is far from being fully understood. We study the connections between edge configuration and dynamics in a simple oriented network composed of two interconnected cliques (representative of brain feedback regulatory circuitry). In this article our main goal is to study the spectra of the graph adjacency and Laplacian matrices, with a focus on three aspects in particular: (1) the sensitivity and robustness of the spectrum in response to varying the intra- and intermodular edge density, (2) the effects on the spectrum of perturbing the edge configuration while keeping the densities fixed, and (3) the effects of increasing the network size. We study some tractable aspects analytically, then simulate more general results numerically, thus aiming to motivate and explain our further work on the effect of these patterns on the network temporal dynamics and phase transitions. We discuss the implications of such results to modeling brain connectomics. We suggest potential applications to understanding synaptic restructuring in learning networks and the effects of network configuration on function of regulatory neural circuits.
Winning the Battle and Losing the War: Child Rape in Post Conflict Liberia
Authors: Darkwa Linda
Published: December 2015

Ten years after the end of hostilities, post conflict Liberia is confronted with the daunting challenge of addressing child rape. Using mix methods of data collection and content analysis the paper interrogates the drivers of child rape in Liberia, and submits that there is a chasm between the legally constructed concept of childhood enshrined in statutory documents and reflected in official processes, and the traditional and cultural construction by the citizens and children themselves. The paper draws attention to the impossibility of assuring security in a context where the state has not been able to assert itself throughout the entire territory and is unable to provide basic services to its entire population. The paper postulates that current efforts at addressing sexual violence against children has not yielded many results because they are not sufficiently comprehensive, enforcement mechanisms are weak and the critical mass of support needed for attitudinal and behavioural change does not exist.
Species diversity within the Helvella crispa group (Ascomycota: Helvellaceae) in China
Authors: ZHAO QI , B TOLGOR , ZHAO YONGCHANG , YANG ZHULIANG , HYDE KEVIN D.
Published: December 2015

The white saddle-mushroom, a well-known European species, has long been named as Helvella crispa in China. In this study, phylogenetic analyses of combined ITS, nrLSU, tef1-α, rpb2 and mcm7 sequence data, showed that the Chinese H. crispa-like samples represent a species complex, which contains at least six phylogenetic species. Three of these species, H. involuta, H. orienticrispa and H. pseudoreflexa, are introduced as new species in this paper. The remaining two taxa are not described due to paucity of material. Among the six phylogenetic species, H. zhongtiaoensis is more closely related to European H. crispa than the remaining Chinese species. They are provided with descriptions, photographs and are compared with similar species. A key to the Chinese morphologically recognizable taxa of this complex is provided.
Re-evaluation of the Mandevilla subsessilis species complex and resurrection of M. platydactyla (Apocynaceae: Apocynoideae)
Authors: Pérez Lucio Lozada , Cárdenas Leonardo O. Alvarado
Published: December 2015

The present work re-evaluates the Mandevilla subsessilis complex (Apocynaceae: Apocynoideae). Based on morphological analysis, including UPGMA, we recognize two separate species, respectively distributed primarily west and east of the Isthmus of Tehuantepec: M. platydactyla (with M. mollis as a synonym) and M. subsessilis.  Mandevilla platydactyla is found from the Sierras de Chiapas to Nicaragua, whereas M. subsessilis is endemic to Mexico, particularly the Sierra Madre del Sur.
A review of the genus Nothris Hübner, 1825, with description of new species (Lepidoptera: Gelechiidae)
Authors: Karsholt Ole , Šumpich Jan
Published: December 2015

The West Palaearctic genus Nothris is reviewed. Eight species are distinguished, and adults and genitalia are described and figured. Two species are described as new for science: Nothris gregerseni sp. n. and N. skyvai sp. n. New synonymies are established: Nothris discretella Rebel, 1889 syn. n. and N. verbascella clarella Amsel, 1935 stat. n. are considered synonyms of N. verbascella ([Denis & Schiffermüller], 1775); and N. magna Nel & Peslier, 2007 syn. n. is synonymized with N. sulcella Staudinger, 1879. Most Nothris species occur in Turkey.
A new species-complex within the trapdoor spider genus Nemesia Audouin 1826 distributed in northern and central Italy, with descriptions of three new species (Araneae, Mygalomorphae, Nemesiidae)
Authors: DECAE ARTHUR , PANTINI PAOLO , ISAIA MARCO
Published: December 2015

Three new Nemesia Audouin 1826 species from northern and central Italy are named. They share a combination of sexual characters, not found in other described species. A new species-complex within Nemesia is here referred to as the apenninica group. Within the apenninica group, N. apenninica n. sp., N. hastensis n. sp., and N. pedemontana n. sp. differ in the morphology of the male palpal organ and the female spermathecae. The three species have different kinds of geographical distributions. While N. apenninica and N. hastensis have locally restricted and geographically separated distributions, the distribution of N. pedemontana overlaps with that of both of these species and extends widely in northern and central Italy. In its periphery, the distribution of N. pedemontana overlaps with that of species other than the apenninica group, e.g., N. meridionalis (Costa, 1835) in southern Italy and N. manderstjernae (L. Koch, 1871) and N. carminans (Latreille, 1818) in Liguria. Information on burrow structure, phenology and habitat are provided for all three new species. Some aspects of the behavior and feeding are discussed for N. pedemontana and N. hastensis.
Thinking Globally, Acting Locally
Authors: Fitzgerald Kathleen J.
Published: December 2015

In this address, I offer an explanation as to why I chose the theme “Locavore Sociology: Challenging Globalization, Embracing the Local” and the host city of Portland, Oregon, for the 2015 Association for Humanist Sociology meetings. I argue that locavorism is a distinctly humanist form of activism. I then explore the origins of locavorism, particularly in terms of its most obvious manifestation in the locavore food movement but also its extension to lesser known movements such as local living economies, local energy production and consumption, and local knowledges. The promise of locavorism and the limits of locavorism as a progressive movement are explored. Finally, I introduce the idea of locavore sociology as a challenge to dominant disciplinary narratives that interfere with understanding nuances associated with locality.
Tankyrase Inhibition Causes Reversible Intestinal Toxicity in Mice with a Therapeutic Index < 1
Authors: Zhong Yu , Katavolos Paula , Nguyen Trung , Lau Ted , Boggs Jason , Sambrone Amy , Kan David , Merchant Mark , Harstad Eric , Diaz Dolores , Costa Mike , Schutten Melissa
Published: December 2015

Activated Wnt/β-catenin signaling is frequently associated with colorectal cancer. Wnt inhibitors, including tankyrase inhibitors, are being explored as potential anticancer agents. Wnt signaling is also critical for intestinal tissue homeostasis, and Wnt inhibitors have been shown to cause intestinal toxicity in mice by affecting intestinal stem cells. This study sought to characterize the intestinal toxicity of tankyrase inhibitors, including reversibility, and to assess their therapeutic index. Novel tankyrase inhibitor G-631 caused dose-dependent intestinal toxicity with a therapeutic index < 1 after 14 days of dosing in mice. At a tolerated subtherapeutic dose level, the intestinal toxicity was composed of enteritis characterized by villus blunting, epithelial degeneration, and inflammation, which fully reversed after 14 days of recovery. Doubled exposure showed weak antitumor activity in a xenograft colorectal cancer model but also caused more severe intestinal toxicity characterized by multifocal-regionally extensive necrotizing and ulcerative enteritis leading to morbidity or moribundity in some animals. This toxicity was only partially reversed after 14 days of recovery, with evidence of crypt and villus regeneration, mildly blunted villi, and/or scarring in association with chronic inflammation of the submucosa. Therefore, the clinical utility of tankyrase inhibitors is likely limited by the on-target intestinal toxicity and a therapeutic index < 1 in mice.
Immunoexpression of Steroid Hormone Receptors and Proliferation Markers in Uterine Leiomyoma and Normal Myometrial Tissues from the Miniature Pig, Sus scrofa
Authors: Mozzachio Kristie , Moore Alicia B. , Kissling Grace E. , Dixon Darlene
Published: December 2015

Uterine leiomyomas in miniature pet pigs occur similarly to those in women with regard to frequency, age, parity, and cycling. Clinical signs, gross, and histologic features of the porcine tumors closely resemble uterine leiomyomas (fibroids) in women. Although fibroids are hormonally responsive in women, the roles of estrogen and progesterone have not been fully elucidated. In this study, immunohistochemistry was used to assess the expression of the steroid hormone receptors, estrogen receptor alpha (ER-α), estrogen receptor beta (ER-β) and progesterone receptor (PR), and cell proliferation markers, proliferating cell nuclear antigen (PCNA) and Ki-67 in tumor and matched myometrial tissues sampled from miniature pigs. A “quickscore” method was used to determine receptor expression and labeling indices were calculated for the markers. ER-α/β and PR were localized to the nuclei of smooth muscle cells in both tissues. PR expression was intense and diffuse throughout all tissues, with correlation between tumors and matched myometria. Conversely, ER-α expression was variable between the myometrial and tumor tissues, as well as between animals. ER-β expression was low. PCNA and Ki-67 were localized to the nucleus and expression varied among tumors; however, normal tissues were overall negative. These findings support further investigation into the use of the miniature pig as a model of fibroids in women.