nils-herrmann/clean_scirepeval huggingface dataset:
Grid Long Short Term Memory
Venue: ICLR

This paper introduces Grid Long Short Term Memory, a network of LSTM cells arranged in a multidimensional grid that can be applied to vectors, sequences or higher dimensional data such as images. The network differs from existing deep LSTM architectures in that the cells are connected between network layers as well as along the spatiotemporal dimensions of the data. The network provides a unified way of using LSTM for both deep and sequential computation. We apply the model to algorithmic tasks such as 15 digit integer addition and sequence memorization, where it is able to significantly outperform the standard LSTM. We then give results for two empirical tasks. We find that 2D Grid LSTM achieves 1.47 bits per character on the Wikipedia character prediction benchmark, which is state of the art among neural approaches. In addition, we use the Grid LSTM to define a novel two dimensional translation model, the Reencoder, and show that it outperforms a phrase based reference system on a Chinese to English translation task.
Biomass production and removal of ammonium and phosphate by Chlorella sp. in sludge liquor at natural light and different levels of temperature control
Venue: SpringerPlus

Microalgae cultivation for biomass production and nutrient removal implies the use of natural light and minimal control of the temperature for obtaining a low cost production. The aim of this study was to quantify the effect of temperature control at natural light on biomass productivity and removal of NH4 N and PO4 P of a mesophilic strain of Chlorella. Chlorella sp. was grown in reject water of anaerobically digested municipal sludge, sludge liquor, inside a greenhouse compartment (As, Norway, 59degN) using batch cultures (300 mL) Five experiments were conducted from May to September, and effects of different levels of temperature control and diurnal variations were investigated. The highest biomass productivities (0.45 g L 1 day 1) in the linear growth phase were obtained at daily light integrals =12 mol day 1 m 2. Results showed that the average temperature was of more importance than the night or day temperature range. At average temperatures <22 degC for cultures with no temperature control, the productivity decreased by 23 and 39 compared to cultures with full temperature control (24 25 degC) In one experiment, the productivity was reduced at no temperature control due to prolonged high daytime temperatures >32 degC) and were followed by a lower NH4 N removal rate. Otherwise, temperature had little effect on NH4 N removal. The level of temperature control did not affect removal of PO4 P. Cellular starch content varied from ~15 38 in the evening and was generally lower at no temperature control. In the morning the starch content was reduced to ~4 12 with no difference between the different levels of temperature control.
Relationship between species diversity, biomass and light transmittance in temperate semi natural grasslands: is productivity enhanced by complementary light capture?

A positive plant diversity above ground productivity relationship is often demonstrated in synthetic grassland stands established for functional biodiversity research, but this relationship is rarely found along diversity gradients in natural and semi natural grasslands. One of the key mechanisms proposed to cause a positive species diversity above ground productivity relationship is increased complementarity in resource use. Using light transmittance to the ground as a measure of resource use intensity in semi natural grasslands, we tested the hypothesis that peak above ground biomass (as a proxy for productivity) increases and light transmittance decreases with increasing species richness, which would reflect higher complementarity in light capture. Location Semi natural temperate grasslands in Lower Saxony, Germany.  We investigated 31 grasslands with variable species richness on three different geological substrates (greywacke, limestone and sandstone) at two spatial scales (sub regional and regional) Results Structural equation modelling (SEM) and generalized linear models (GLM) revealed that species richness (5 22 species 0.09 m 2) was negatively related to above ground biomass (AGB; 200 1350 g*m 2) and sward cover. The most influential determinant of AGB at the regional scale was temperature. Light transmittance was determined by sward cover, the cover of competitive species and AGB at the regional, and in part also at the sub regional level. We found no evidence for increased light capture complementarity with higher species richness.  This suggests that competitive exclusion, but not complementarity in above ground resource use, mediates above ground productivity in species rich plant assemblages.
FairAccess: a new Blockchain based access control framework for the Internet of Things
Venue: Secur. Commun. Networks

Security and privacy are huge challenges in Internet of Things (IoT) environments, but unfortunately, the harmonization of the IoT related standards and protocols is hardly and slowly widespread. In this paper, we propose a new framework for access control in IoT based on the blockchain technology. Our first contribution consists in providing a reference model for our proposed framework within the Objectives, Models, Architecture and Mechanism specification in IoT. In addition, we introduce FairAccess as a fully decentralized pseudonymous and privacy preserving authorization management framework that enables users to own and control their data. To implement our model, we use and adapt the blockchain into a decentralized access control manager. Unlike financial bitcoin transactions, FairAccess introduces new types of transactions that are used to grant, get, delegate, and revoke access. As a proof of concept, we establish an initial implementation with a Raspberry PI device and local blockchain. Finally, we discuss some limitations and propose further opportunities.
What you Sculpt is What you Get: Modeling Physical Interactive Devices with Clay and 3D Printed Widgets
Venue: CHI

We present a method for fabricating prototypes of interactive computing devices from clay sculptures without requiring the designer to be skilled in CAD software. The method creates a "what you sculpt is what you get" process that mimics the "what you see is what you get" processes used in interface design for 2D screens. Our approach uses clay for modeling the basic shape of the device around 3D printed representations, which we call "blanks" of physical interaction widgets such as buttons, sliders, knobs and other electronics. Each blank includes 4 fiducial markers uniquely arranged on a visible surface. After scanning the sculpture, these fiducial marks allow our software to identify widget types and locations in the scanned model. The software then converts the scan into a printable prototype by positioning mounting surfaces, openings for the controls and a splitting plane for assembly. Because the blanks fit in the sculpted shape, they will reliably fit in the interactive prototype. Creating an interactive prototype requires about 30 minutes of human effort for sculpting, and after scanning, involves a single button click to use the process.
Invasion and Management of Agricultural Alien Insects in China.
Venue: Annual review of entomology

China is the world's fourth largest country in terms of landmass. Its highly diverse biogeography presents opportunities for many invasive alien insects. However, physical and climate barriers sometimes prevent locally occurring species from spreading. China has 560 confirmed invasive alien species; 125 are insect pests, and 92 of these damage the agricultural ecosystem. The estimated annual economic loss due to alien invasive species is more than $18.9 billion. The most harmful invasive insects exhibit some common characteristics, such as high reproduction, competitive dominance, and high tolerance, and benefit from mutualist facilitation interactions. Regional cropping system structure adjustments have resulted in mono agricultural ecosystems in cotton and other staple crops, providing opportunities for monophagous insect pests. Furthermore, human dietary shifts to fruits and vegetables and smallholder based farming systems result in highly diverse agricultural ecosystems, which provide resource opportunities for polyphagous insects. Multiple cropping and widespread use of greenhouses provide continuous food and winter habitats for insect pests, greatly extending their geographic range. The current management system consists of early warning, monitoring, eradication, and spread blocking technologies. This review provides valuable new synthetic information on integrated management practices based mainly on biological control for a number of invasive species. We encourage farmers and extension workers to be more involved in training and further research for novel protection methods that takes into consideration end users' needs.
Inspecting the supernova gamma ray burst connection with high energy neutrinos

Long duration gamma ray bursts (GRBs) have been often considered as the natural evolution of some core collapse supernovae (SNe) While GRBs with relativistic jets emit an electromagnetic signal, GRBs with mildly relativistic jets are opaque to photons and therefore could be detectable through neutrinos only. We discuss the possibility that successful GRBs and mildly relativistic jets belong to the same class of astrophysical transients with different Lorentz factor Gb and study the production of high energy neutrinos as a function of Gb, by including both proton photon and proton proton interactions. By assuming a SN GRB connection, we find that the diffuse neutrino emission from optically thick jets with Lorentz factors lower than the ones of successful GRBs can be one of the main components of the observed IceCube high energy neutrino flux. Moreover, under the assumption that all these jets belong to the same class of astrophysical transients, we show that the IceCube high energy neutrino data provide indirect constraints on the rate of nonsuccessful jets, favoring a local rate lower than tens of percent of the local SN rate. These limits are currently comparable to dedicated searches on choked sources and are expected to become tighter with the accumulation of more high energy neutrino data.
Diagnostic Accuracy of Antigen 5 Based ELISAs for Human Cystic Echinococcosis
Venue: PLoS neglected tropical diseases

Clinical diagnosis and follow up of cystic echinococcosis (CE) are based on imaging complemented by serology. Several immunodiagnostic tests are commercially available, but the development of new tools is still needed to overcome the lack of standardization of the target antigen, generally consisting of a crude extract of Echinococcus granulosus hydatid cyst fluid. In a previous work, we described a chromatographic method for the preparation of a highly enriched Antigen 5 fraction from hydatid cyst fluid. The high reactivity of patient sera against this preparation prompted us to evaluate further this antigen for the serodiagnosis of CE on a larger cohort of samples.  A total of 327 sera from CE patients with heterogeneous conditions for cyst stage, cyst number, organ localization, drug therapy, and surgical intervention, together with 253 sera from healthy controls, were first analyzed by an ELISA based on the Ag5 preparation in two different experimental setups and, in parallel, by a commercial ELISA routinely used in clinical laboratories for CE serodiagnosis. The Ag5 ELISAs revealed different sensitivity (88.3% vs 95.3% without significant differences in specificity (94.1% vs 92.5% for the two setups, respectively. Moreover, possible relationships between the Ag5 ELISA absorbance results and clinical variables were investigated. Chi squared test, bivariate logistic regression and multiple regression analyses highlighted differences in the serology reactivity according to pharmacological treatment, cyst activity, and cyst number.  The two Ag5 ELISAs revealed different performances depending on the setup. The good diagnostic sensitivity and the high reliability of the Ag5 preparation method make this antigen a promising candidate for the serodiagnosis of CE. Further studies will be needed to evaluate the ability of our test to provide useful information on specific CE clinical traits.
CSF generation by pineal gland results in a robust melatonin circadian rhythm in the third ventricle as an unique light/dark signal.
Venue: Medical hypotheses

Pineal gland is an important organ for the regulation of the bio clock in all vertebrate species. Its major secretory product is melatonin which is considered as the chemical expression of darkness due to its circadian peak exclusively at night. Pineal melatonin can be either released into the blood stream or directly enter into the CSF of the third ventricle via the pineal recess. We have hypothesized that rather than the peripheral circulatory melatonin circadian rhythm serving as the light/dark signal, it is the melatonin rhythm in CSF of the third ventricle that serves this purpose. This is due to the fact that melatonin circadian rhythm in the CSF is more robust in terms of its extremely high concentration and its precise on/off peaks. Thus, extrapineal generated melatonin or diet derived melatonin which enters blood would not interfere with the bio clock function of vertebrates. In addition, based on the relationship of the pineal gland to the CSF and the vascular structure of this gland, we also hypothesize that pineal gland is an essential player for CSF production. We feel it participates in both the formation and reabsorption of CSF. The mechanisms associated with these processes are reviewed and discussed in this brief review.
Melatonin Synthesis: Acetylserotonin O Methyltransferase (ASMT) Is Strongly Expressed in a Subpopulation of Pinealocytes in the Male Rat Pineal Gland.
Venue: Endocrinology

The rat pineal gland has been extensively used in studies of melatonin synthesis. However, the cellular localization of melatonin synthesis in this species has not been investigated. Here we focus on the localization of melatonin synthesis using immunohistochemical methods to detect the last enzyme in melatonin synthesis, acetylserotonin O methyltransferase (ASMT) and in situ hybridization techniques to study transcripts encoding ASMT and two other enzymes in melatonin synthesis, tryptophan hydroxylase (TPH) 1 and aralkylamine N acetyltransferase. In sections of the rat pineal gland, marked cell to cell differences were found in ASMT immunostaining intensity and in the abundance of Tph1, Aanat, and Asmt transcripts. ASMT immunoreactivity was localized to the cytoplasm in pinealocytes in the parenchyma of the superficial pineal gland, and immunopositive pinealocytes were also detected in the pineal stalk and in the deep pineal gland. ASMT was found to inconsistently colocalize with S antigen, a widely used pinealocyte marker; this colocalization was seen in cells throughout the pineal complex and also in displaced pinealocyte like cells of the medial habenular nucleus. Inconsistent colocalization between ASMT and TPH protein was also detected in the pineal gland. ASMT protein was not detected in extraepithalamic parts of the central nervous system or in peripheral tissues. The findings in this report are of special interest because they provide reason to suspect that melatonin synthesis varies significantly among individual pinealocytes.
Derandomizing Quantum Circuits with Measurement Based Unitary Designs.
Venue: Physical review letters

Entangled multipartite states are resources for universal quantum computation, but they can also give rise to ensembles of unitary transformations, a topic usually studied in the context of random quantum circuits. Using several graph state techniques, we show that these resources can "derandomize" circuit results by sampling the same kinds of ensembles quantum mechanically, analogously to a quantum random number generator. Furthermore, we find simple examples that give rise to new ensembles whose statistical moments exactly match those of the uniformly random distribution over all unitaries up to order t, while foregoing adaptive feedforward entirely. Such ensembles known as t designs often cannot be distinguished from the "truly" random ensemble, and so they find use in many applications that require this implied notion of pseudorandomness.
Mixing Properties of Stochastic Quantum Hamiltonians

Random quantum processes play a central role both in the study of fundamental mixing processes in quantum mechanics related to equilibration, thermalisation and fast scrambling by black holes, as well as in quantum process design and quantum information theory. In this work, we present a framework describing the mixing properties of continuous time unitary evolutions originating from local Hamiltonians having time fluctuating terms, reflecting a Brownian motion on the unitary group. The induced stochastic time evolution is shown to converge to a unitary design. As a first main result, we present bounds to the mixing time. By developing tools in representation theory, we analytically derive an expression for a local k th moment operator that is entirely independent of k, giving rise to approximate unitary k designs and quantum tensor product expanders. As a second main result, we introduce tools for proving bounds on the rate of decoupling from an environment with random quantum processes. By tying the mathematical description closely with the more established one of random quantum circuits, we present a unified picture for analysing local random quantum and classes of Markovian dissipative processes, for which we also discuss applications.
Association between tuberculosis, diabetes and 25 hydroxyvitamin D in Tanzania: a longitudinal case control study
Venue: BMC Infectious Diseases

BackgroundVitamin D level is inversely associated with tuberculosis (TB) and diabetes (DM) Vitamin D could be a mediator in the association between TB and DM. We examined the associations between vitamin D, TB and DM.MethodsConsecutive adults with TB and sex and age matched volunteers were included in a case control study in Dar es Salaam, Tanzania. Glycemia and total vitamin D (25(OH)D) were measured at enrolment and after TB treatment in cases. The association between low 25(OH)D <75 nmol/l) and TB was evaluated by logistic regression adjusted for age, sex, body mass index, socioeconomic status, sunshine hours, HIV and an interaction between low 25(OH)D and hyperglycemia.ResultsThe prevalence of low 25(OH)D was similar in TB patients and controls (25.8 versus 31.0 p 0.22) In the subgroup of patients with persistent hyperglycemia (i.e. likely true diabetic patients) the proportion of patients with low 25(OH)D tended to be greater in TB patients (50 versus 29.7 p 0.20) The effect modification by persistent hyperglycemia persisted in the multivariate analysis (pinteraction 0.01).ConclusionsLow 25(OH)D may increase TB risk in patients with underlying DM. Trials should examine if this association is causal and whether adjunct vitamin D therapy is beneficial in this population.
Glycated hemoglobin screening identifies patients admitted for retreatment of tuberculosis at risk for diabetes in Tanzania.
Venue: Journal of infection in developing countries

World Health Organization recommendations of bidirectional screening for tuberculosis (TB) and diabetes have been met with varying levels of uptake by national TB programs in resource limited settings.  Infectious Diseases Hospital (KIDH) is a referral hospital for TB from northern Tanzania, and the national referral hospital for multidrug resistant (MDR) TB. Glycated hemoglobin (HgbA1c) testing was done on patients admitted to KIDH for newly diagnosed TB, retreatment TB, and MDR TB, to determine the point prevalence of diabetes (HgbA1c 6.5% and prediabetes (HgbA1c 5.7% 6.4% RESULTS Of 148 patients hospitalized at KIDH over a single week, 59 (38% had no prior TB treatment, 22 (15% were retreatment cases, and 69 (47% had MDR TB. Only 3 (2% had a known history of diabetes. A total of 144 (97% had successful screening, of which 110 (77% had an HgbA1c 5.6% 28 (19% had 5.7 6.5, and 6 (4% had 6.5. Comparing subjects with prediabetes or diabetes to those with normal A1c levels, retreatment patients were significantly more likely to have a A1c 5.7% (odds ratio: 3.2, 95% CI: 1.2 9.0; p 0.02) compared to those without prior TB treatment. No retreatment case was a known diabetic, thus the number needed to screen to diagnose one new case of diabetes among retreatment cases was 11.  Diabetes prevalence by HgbA1c was less common than expected, but higher HgA1c values were significantly more frequent among retreatment cases, allowing for a rational, resource conscious screening approach.
Geomorphology and Morphometric Analysis Used as A Significant Indicator for Groundwater Prospects: A Case Study of the Kousika Manadi Sub Basin Vaigai River Tamil Nadu

A morphometric analysis was done to evaluate the drainage characteristics of Kousika Manadi sub basin using topographical maps with digital elevation data. This analysis can be achieved through measurement of basic, derived, and shape aspects of the sub basin. In the present study, quantitative morphometric analysis is carried out for 28 micro watersheds of Kousika Manadi, which is located in Madurai and Virudhunagardistricts, Tamil Nadu. Geological setting of the study area with all complexities leads to unique hydrogeological features. The study has strengthened in understanding the hydrological, geological and geomorphological characteristics of the Kousika Manadi sub basin.
Sensitivity analysis of environmental models: A systematic review with practical workflow
Venue: Environ. Model. Softw.

Sensitivity Analysis (SA) investigates how the variation in the output of a numerical model can be attributed to variations of its input factors. SA is increasingly being used in environmental modelling for a variety of purposes, including uncertainty assessment, model calibration and diagnostic evaluation, dominant control analysis and robust decision making. In this paper we review the SA literature with the goal of providing: (i) a comprehensive view of SA approaches also in relation to other methodologies for model identification and application; (ii) a systematic classification of the most commonly used SA methods; (iii) practical guidelines for the application of SA. The paper aims at delivering an introduction to SA for non specialist readers, as well as practical advice with best practice examples from the literature; and at stimulating the discussion within the community of SA developers and users regarding the setting of good practices and on defining priorities for future research. We present an overview of SA and its link to uncertainty analysis, model calibration and evaluation, robust decision making.We provide a systematic review of existing approaches, which can support users in the choice of an SA method.We provide practical guidelines by developing a workflow for the application of SA and discuss critical choices.We give best practice examples from the literature and highlight trends and gaps for future research.