Miracle-dz/UniFAR-FTUs huggingface dataset:
The Cafe ConstructionKit: a toolkit for sociality

Many user communities have a problem of delivering help and general assistance. Unfortunately, the user is often left to sift through reams of documentation, find his way through mail archives, or pursue answers through trial and error. Normally, one attempts to examine the documentation or other help sources, and then wanders out into a hallway in search of friendly colleagues.The problem becomes acute, however, in distributed communities. I take for my example the astrophysics community, although this problem exists in most scientific communities. In the astrophysics community, the users may be spread across the world, they may work in isolation, and they may have need of relatively specialized help. What I would like is to build is a surrogate for this hallway talk. Such a solution must avoid the broadcast problem of flooding everyone's electronic mail basket with thousands of questions. Instead, this research proposes building a system to narrow-cast a question to the appropriate others, whether those others are experts or colleagues.My thesis work consisted of building a Computer-Supported Cooperative Work system called Answer Garden [1] [4]. Answer Garden allows organizations to develop databases of commonly asked questions that grow "organically" as new questions arise and are answered. Answer Garden 2, the current project, attempts to solve the problems encountered in field studies of the original system [2]. A new architecture provides a customizable and adaptable set of software components that allow a variety of organizational and informational configurations.In order to construct Answer Garden 2, however, it has been necessary to develop an underlying communications infrastructure called the Cafe ConstructionKit. Cafe has turned out to be a generalized and quite useful system in its own right.
DNA compression using referential compression algorithm

With rapid technological development and growth of sequencing data, an umpteen gamut of biological data has been generated. As an alternative, Data Compression is employed to reduce the size of data. In this direction, this paper proposes a new reference-based compression approach, which is employed as a solution. Firstly, a reference has been constructed from the common sub strings of randomly selected input sequences. Reference set is a pair of key and value, where key is a fingerprint (or a unique id) and value is a sequence of characters. Next, these given sequences are compressed using referential compression algorithm. This is attained by matching the input with the reference and hence, replacing the match found in input by its fingerprints contained in the reference, thereby achieving better compression. The experimental results of this paper show that the approach proposed herein, outperforms the existing approaches and methodologies applied so far.
Een interdisciplinaire analyse van de klokkenluidersproblematiek in de openbare sector

Het fenomeen ‘klokkenluiden’ wordt steeds belangrijker, zowel in buitenals binnenland. Het toonaangevende Amerikaanse weekblad ‘Time’ omschreef het jaar 2002 als ‘het jaar van de klokkenluiders’ en duidde drie vrouwelijke klokkenluiders aan als ‘personen van het jaar. ’ Ook in eigen land stonden de afgelopen jaren enkele belangrijke casussen in de belangstelling, o.m. naar aanleiding van (vermeende) mistoestanden in ABOS, het Hoog Comite van Toezicht, de Vlaamse Huisvestingsmaatschappij enz. Hoewel klokkenluiden zowel in de publieke als in de particuliere sector voorkomt, en hoewel sommige klokkenluidersregelingen ook op beide sectoren van toepassing zijn, beperken we ons in deze bijdrage hoofdzakelijk tot de klokkenluidersproblematiek in de publieke sector. Voor deze bijdrage definieren we, naar Near en Miceli, klokkenluiden als ‘het bekendmaken door (vroegere of huidige) werknemers van illegale, immorele of niet-legitieme praktijken die onder de controle vallen
Verifying distributed systems: the operational approach

This work develops an integrated approach to the verification of behaviourally rich programs, founded directly on operational semantics. The power of the approach is demonstrated with a state-of-the-art verification of a core piece of distributed infrastructure, involving networking, a filesystem, and concurrent OCaml code. The formalization is in higher-order logic and proof support is provided by the HOL4 theorem prover. Difficult verification problems demand a wide range of techniques. Here these include ground and symbolic evaluation, local reasoning, separation, invariants, Hoare-style assertional reasoning, rely/guarantee, inductive reasoning about protocol correctness, multiple refinement, and linearizability. While each of these techniques is useful in isolation, they are even more so in combination. The first contribution of this paper is to present the operational approach and describe how existing techniques, including all those mentioned above, may be cleanly and precisely integrated in this setting. The second contribution is to show how to combine verifications of individual library functions with arbitrary and unknown user code in a compositional manner, focusing on the problems of private state and encapsulation. The third contribution is the example verification itself. The infrastructure must behave correctly under arbitrary patterns of host and network failure, whilst for performance reasons the code also includes data races on shared state. Both features make the verification particularly challenging.
Orthogonal Super Greedy Algorithm and Applications in Compressed Sensing ∗

The general theory of greedy approximation is well developed. Much less is known about how specific features of a dictionary can be used for our advantage. In this paper we discuss incoherent dictionaries. We build a new greedy algorithm which is called the Orthogonal Super Greedy Algorithm (OSGA). OSGA is more efficient than a standard Orthogonal Greedy Algorithm (OGA). We show that the rates of convergence of OSGA and OGA with respect to incoherent dictionaries are the same. Greedy approximation is also a fundamental tool for sparse signal recovery. The performance of Orthogonal Multi Matching Pursuit (OMMP), a counterpart of OSGA in the compressed sensing setting, is also analyzed under RIP conditions.
Cannabinoids and Ghrelin Have Both Central and Peripheral Metabolic and Cardiac Effects via AMP-activated Protein Kinase*

Endocannabinoids and ghrelin are potent appetite stimulators and are known to interact at a hypothalamic level. However, both also have important peripheral actions, including beneficial effects on the ischemic heart and increasing adipose tissue deposition, while ghrelin has direct effects on carbohydrate metabolism. The AMP-activated protein kinase (AMPK) is a heterotrimeric enzyme that functions as a fuel sensor to regulate energy balance at both cellular and whole body levels, and it may mediate the action of anti-diabetic drugs such as metformin and peroxisome proliferator-activated receptor γ agonists. Here we show that both cannabinoids and ghrelin stimulate AMPK activity in the hypothalamus and the heart, while inhibiting AMPK in liver and adipose tissue. These novel effects of cannabinoids on AMPK provide a mechanism for a number of their known actions, such as the reduction in infarct size in the myocardium, an increase in adipose tissue, and stimulation of appetite. The beneficial effects of ghrelin on heart function, including reduction of myocyte apoptosis, and its effects on lipogenesis and carbohydrate metabolism, can also be explained by its ability to activate AMPK. Our data demonstrate that AMPK not only links the orexigenic effects of endocannabinoids and ghrelin in the hypothalamus but also their effects on the metabolism of peripheral tissues.
Data-driven customer behaviour model generation for agent based exploration

Customer retention is a critical concern for most mobile network operators because of the increasing competition in the mobile services sector. This concern has driven companies to exploit data as an avenue to better understand customer needs. Data mining techniques such as clustering and classification have been adopted to understand customer retention in the mobile services industry. However, the effectiveness of these techniques is debatable due to the increasing complexity of the mobile market itself. This study proposes an application of Agent-Based Modeling and Simulation (ABMS) as a novel approach to understanding customer retention. A dataset provided by a mobile network operator is utilized to automate decision trees and agent based models. The most popular churn modeling techniques were adopted in order to automate the development of models, from decision trees, and subsequently explore customer churn scenarios. ABMS is used to understand the behavior of customers and detect possible reasons why customers churned or stayed with their respective mobile network operators. Data analysis is able to identify that location and choice of mobile devices were determinants for the decision to churn or stay with their mobile network operator - with word of mouth as an important factor. Importantly, agent based simulation is able to explore further the determinants in the wider marketplace.
50,000 years of genetic uniformity in the critically endangered Iberian lynx

Low genetic diversity in the endangered Iberian lynx, including lack of mitochondrial control region variation, is thought to result from historical or Pleistocene/Holocene population bottlenecks, and to indicate poor long‐term viability. We find no variability in control region sequences from 19 Iberian lynx remains from across the Iberian Peninsula and spanning the last 50 000 years. This is best explained by continuously small female effective population size through time. We conclude that low genetic variability in the Iberian lynx is not in itself a threat to long‐term viability, and so should not preclude conservation efforts.
HCube: A Server-centric Data Center Structure for Similarity Search

The information society is facing a sharp increase in the amount of information driven by the plethora of new applications that sprouts all the time. The amount of data now circulating on the Internet is over zettabytes (ZB), resulting in a scenario defined in the literature as Big Data. In order to handle such challenging scenario, the deployed solutions rely not only on massive storage, memory and processing capacity installed in Data Centers (DC) maintained by big players all over the globe, but also on shrewd computational techniques, such as Big Table, MapReduce and Dynamo. In this context, this work presents a DC structure designed to support the similarity search. The proposed solution aims at concentrating similar data on servers physically close within a DC, accelerating the recovery of all data related to searches performed using a primitive get(k, sim), in which k represents the query identifier, i.e., the data used as reference, and sim a similarity level.
Automatic Assignment of Section Structure to Texts of Dutch Court Judgments

A growing number of Dutch court judgments is openly distributed on Rechtspraak.nl. Currently, many documents are not marked up or marked up only very sparsely, hampering our ability to process these documents automatically. In this paper, we explore the problem of automatic assignment of a section structure to these texts. We experiment with Linear-Chain Conditional Random Fields to label text elements with their roles in the document (text, title or numbering). In this subtask, we report F1 scores of around 0.91 for tagging section titles, and around 1.0 for the other types. Given a list of labels, we experiment with Probabilistic Context-Free Grammars to generate a parse tree which represents the section hierarchy of a document. In this task, we report an F1 score of 0.92.
Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data

UNLABELLED A critical step in any SAGE, MPSS and SBS data analysis is tag-to-gene assignment. Current available tools are limited by a tag-by-tag annotation process and/or do not provide the dataset that is used to produce a complete tag-to-gene mapping. We developed ACTG, a web-based application that allows a large-scale tag-to-gene mapping using several reference datasets. ACTG can annotate SAGE (14 or 21 bp), MPSS (17 or 20 bp) and SBS (16 bp) data for both human and mouse organisms. AVAILABILITY http://retina.med.harvard.edu/ACTG/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Characterization of antibodies against major fish CNS myelin protein: Immunoblot analysis and immunohistochemical localization of 36K and IP2 proteins in trout nerve tissue

Antisera against the trout CNS myelin proteins 36K and IP2 were prepared in rabbits and characterized by immunoblot analysis and immunohistochemistry. The anti‐36K antiserum exclusively stained its corresponding antigen from trout CNS myelin but failed to recognize any myelin polypeptide from either trout PNS or mammalian CNS and PNS. Antibodies against the IP2 glycoprotein specifically cross‐reacted with related intermediate proteins (IP) of both CNS and PNS myelin from trout but only faintly labeled the P0 protein of mouse peripheral nerve. Immunohistochemical localization of both antigens in the CNS of young trout was confined to the myelin sheath, except that anti‐36K antiserum also stained oligodendrocytes. Nodes of Ranvier, neuronal cell bodies, and dendrites, as well as other glial elements, were negative. Specificity of the immunofluorescent reaction was established by crossed immunoadsorption experiments. Whereas on adjacent sections through trout brain both antigens exhibited a nearly identical distribution pattern, immunostaining in peripheral nerves was seen only with anti‐IP2 antibodies.
A Statistical Framework for Joint eQTL Analysis in Multiple Tissues

Mapping expression Quantitative Trait Loci (eQTLs) represents a powerful and widely adopted approach to identifying putative regulatory variants and linking them to specific genes. Up to now eQTL studies have been conducted in a relatively narrow range of tissues or cell types. However, understanding the biology of organismal phenotypes will involve understanding regulation in multiple tissues, and ongoing studies are collecting eQTL data in dozens of cell types. Here we present a statistical framework for powerfully detecting eQTLs in multiple tissues or cell types (or, more generally, multiple subgroups). The framework explicitly models the potential for each eQTL to be active in some tissues and inactive in others. By modeling the sharing of active eQTLs among tissues, this framework increases power to detect eQTLs that are present in more than one tissue compared with “tissue-by-tissue” analyses that examine each tissue separately. Conversely, by modeling the inactivity of eQTLs in some tissues, the framework allows the proportion of eQTLs shared across different tissues to be formally estimated as parameters of a model, addressing the difficulties of accounting for incomplete power when comparing overlaps of eQTLs identified by tissue-by-tissue analyses. Applying our framework to re-analyze data from transformed B cells, T cells, and fibroblasts, we find that it substantially increases power compared with tissue-by-tissue analysis, identifying 63% more genes with eQTLs (at FDR = 0.05). Further, the results suggest that, in contrast to previous analyses of the same data, the majority of eQTLs detectable in these data are shared among all three tissues.
Incorporating uncertainty in predictive species distribution modelling

Motivated by the need to solve ecological problems (climate change, habitat fragmentation and biological invasions), there has been increasing interest in species distribution models (SDMs). Predictions from these models inform conservation policy, invasive species management and disease-control measures. However, predictions are subject to uncertainty, the degree and source of which is often unrecognized. Here, we review the SDM literature in the context of uncertainty, focusing on three main classes of SDM: niche-based models, demographic models and process-based models. We identify sources of uncertainty for each class and discuss how uncertainty can be minimized or included in the modelling process to give realistic measures of confidence around predictions. Because this has typically not been performed, we conclude that uncertainty in SDMs has often been underestimated and a false precision assigned to predictions of geographical distribution. We identify areas where development of new statistical tools will improve predictions from distribution models, notably the development of hierarchical models that link different types of distribution model and their attendant uncertainties across spatial scales. Finally, we discuss the need to develop more defensible methods for assessing predictive performance, quantifying model goodness-of-fit and for assessing the significance of model covariates.
Construction of a two-photon microscope for video-rate Ca(2+) imaging.

We describe the construction of a video-rate two-photon laser scanning microscope, compare its performance to a similar confocal microscope, and illustrate its use for imaging local Ca(2+) transients from cortical neurons in brain slices. Key features include the use of a Ti-sapphire femtosecond laser allowing continuous tuning over a wide (700-1000 nm) wavelength range, a resonant scanning mirror to permit frame acquisition at 30 Hz, and efficient wide-field fluorescence detection. Two-photon imaging provides compelling advantages over confocal microscopy in terms of improved imaging depth and reduced phototoxicity and photobleaching, but the high cost of commercial instruments has limited their widespread adoption. By constructing one's own system the expense is greatly reduced without sacrifice of performance, and the microscope can be more readily tailored to specific applications.
Wilms’ Tumour 1 (WT1) peptide vaccination in patients with acute myeloid leukaemia induces short-lived WT1-specific immune responses

Wilms’ Tumour 1 (WT1) is a zinc finger transcription factor that is over‐expressed in acute myeloid leukaemia (AML). Its restricted expression in normal tissues makes it a promising target for novel immunotherapies aiming to accentuate the cytotoxic T lymphocyte (CTL) response against AML. Here we report a phase I/II clinical trial of subcutaneous peptide vaccination with two separate HLA‐A2‐binding peptide epitopes derived from WT1, together with a pan‐DR binding peptide epitope (PADRE), in Montanide adjuvant. Eight HLA‐A2‐positive patients with poor risk AML received five vaccination cycles at 3‐weekly intervals. The three cohorts received 0·3, 0·6 and 1 mg of each peptide, respectively. In six patients, WT1‐specific CTL responses were detected using enzyme‐linked immunosorbent spot assays and pWT126/HLA‐A*0201 tetramer staining, after ex vivo stimulation with the relevant WT1 peptides. However, re‐stimulation of these WT1‐specific T cells failed to elicit secondary expansion in all four patients tested, suggesting that the WT1‐specific CD8+ T cells generated following vaccination may be functionally impaired. No correlation was observed between peptide dose, cellular immune response, reduction in WT1 mRNA expression and clinical response. Larger studies are indicated to confirm these findings.
Dopamine Cells Respond to Predicted Events during Classical Conditioning: Evidence for Eligibility Traces in the Reward-Learning Network

Behavioral conditioning of cue-reward pairing results in a shift of midbrain dopamine (DA) cell activity from responding to the reward to responding to the predictive cue. However, the precise time course and mechanism underlying this shift remain unclear. Here, we report a combined single-unit recording and temporal difference (TD) modeling approach to this question. The data from recordings in conscious rats showed that DA cells retain responses to predicted reward after responses to conditioned cues have developed, at least early in training. This contrasts with previous TD models that predict a gradual stepwise shift in latency with responses to rewards lost before responses develop to the conditioned cue. By exploring the TD parameter space, we demonstrate that the persistent reward responses of DA cells during conditioning are only accurately replicated by a TD model with long-lasting eligibility traces (nonzero values for the parameter λ) and low learning rate (α). These physiological constraints for TD parameters suggest that eligibility traces and low per-trial rates of plastic modification may be essential features of neural circuits for reward learning in the brain. Such properties enable rapid but stable initiation of learning when the number of stimulus-reward pairings is limited, conferring significant adaptive advantages in real-world environments.
Construction and functional characterization of polyomavirus genomes that separately encode the three early proteins

Modified polyomavirus genomes that individually encode the large and small T proteins were constructed by exchanging restriction endonuclease fragments between cDNA copies of the respective mRNAs and cloned genomic DNA. The efficacies of the new constructs, and that of the middle T protein gene described previously (R. Treisman , U. Novak, J. Favaloro , and R. Kamen , Nature [London] 292:595-600, 1981), were demonstrated with simian virus 40 (SV40)-polyomavirus recombinants in which part or all of the SV40 late region was replaced with the modified polyomavirus early genes. Each of the three recombinant viruses induced the synthesis of only the expected polyomavirus early protein in infected CV-1 cells. The rates of synthesis of large, middle, and small T proteins were ca. 1.5, 4.0, and 9.0 times the rate of synthesis of SV40 large T protein, respectively. The deletion of introns had no detrimental effect on mRNA biogenesis. Indeed, a further polyomavirus-SV40 recombinant, containing wild-type polyomavirus early region DNA, expressed an aberrant 58,000-dalton form of the middle T protein which we believe to result from utilization of a cryptic splice site. Immunofluorescence studied with monkey cells infected by the recombinant viruses allowed us to determine the cellular locations of the polyomavirus early proteins. Overproduction of the middle T protein did not result in a corresponding overproduction of the middle T protein-associated tyrosine phosphokinase activity.