Miracle-dz/UniFAR-FTUs huggingface dataset:
PASTA ADDED WITH CHICKPEA FLOUR: CHEMICAL COMPOSITION, IN VITRO STARCH DIGESTIBILITY AND PREDICTED GLYCEMIC INDEX PASTA ADICIONADA CON HARINA DE GARBANZO: COMPOSICIÓN QUÍMICA, DIGESTIBILIDAD IN VITRO DEL ALMIDÓNY PREDICCIÓN DEL ÍNDICE GLUCÉMICO

Abstract Pasta was prepared with of durum wheat flour mixed with chickpea flour at two different levels and its chemical composition, in vitro starch digestibility and predicted glycemic index were assessed. Protein, ash, lipid, and dietary fiber content increased while total starch decreased with the chickpea flour level in the composite pasta, all in accordance to the composition of the legume flour. Potentially available starch decreased and resistant starch (RS) increased by adding chickpea flour to the pasta. The main indigestible starch component in composite spaghetti was the fiber-associated RS, representing up to 50 % of total RS levels. The starch hydrolysis index (HI) decreased as chickpea flour in the pasta increased, reflecting the slow and low digestion of the starch in the leguminous ingredient. Predicted glycemic index was lower in spaghetti added with chickpea flour than in durum wheat-control pasta. Pasta added with chickpea flour might be a dietetic alternative for people with low-calorie requirements. Resumen Se elaboró pasta mezclando sémola de trigo con harina de garbanzo a dos niveles y se evaluó su composición química, digestibilidad del almidón in vitro y se predijo el índice glucémico. El contenido de proteína, ceniza, lípidos y fibra dietética incrementó mientras que el almidón total disminuyó con el contenido de harina de garbanzo en la pasta, esto debido a la composición de la harina de la leguminosa. El contenido de almidón disponible disminuyó y el almidón resistente (AR) incrementó con la adición de la harina de garbanzo a la pasta. El principal componente del almidón no digestible en el espagueti con harina de garbanzo fue el AR asociado a fibra, que representó más del 50 % del AR total. El índice de hidrólisis (IH) del almidón disminuyó con el incrementó del nivel de harina de garbanzo en la pasta, reflejando la baja y lenta digestión del almidón de la leguminosa. La predicción del índice glucémico fue menor en el espagueti adicionado con harina de garbanzo que la muestra control. La pasta adicionada con harina de garbanzo puede ser una alternativa dietética para personas con bajos requerimientos calóricos. Palabras clave: Índice glucémico, composición química, pasta, garbanzo, almidón resistente, fibra dietética
Replication of scientific research: addressing geoprivacy, confidentiality, and data sharing challenges in geospatial research

The ability to replicate, or reproduce, research is fundamental to the scientific process. Research combining a variety of georeferenced data is spreading rapidly across scientific domains and international borders. This suggests a growing potential for the use and integration of new and existing data sets to create new multi-disciplinary scientific collaborations. Yet, the unique characteristics of georeferenced data present special challenges to such collaborations. These data are highly identifiable when presented in maps and other visualizations or when combined with sensor data or other related geospatial data sets. The potential opportunities of collaboration may thus be constrained by the need to protect the locational privacy (geoprivacy) and confidentiality of subjects in research using georeferenced data. This paper reviews the obstacles to and potential methods for sharing georeferenced data in order to support a growing and dynamic geospatial research community and build capacity for data-intensive research across the social and environmental sciences. The development and implementation of a geospatial virtual data enclave methodology is proposed as an innovative and viable solution to share and archive georeferenced data among researchers while protecting the geoprivacy of research subjects and the confidentiality of these data. The ability to share confidential geospatial data among researchers is crucial to ensuring replicability of scientific research, and to enable researchers to verify and build upon the research of others.
Molecular and Functional Characterization of a Na+-K+ Transporter from the Trk Family in the Ectomycorrhizal Fungus Hebeloma cylindrosporum*

Ectomycorrhizal symbiosis between fungi and woody plants strongly improves plant mineral nutrition and constitutes a major biological process in natural ecosystems. Molecular identification and functional characterization of fungal transport systems involved in nutrient uptake are crucial steps toward understanding the improvement of plant nutrition and the symbiotic relationship itself. In the present report a transporter belonging to the Trk family is identified in the model ectomycorrhizal fungus Hebeloma cylindrosporum and named HcTrk1. The Trk family is still poorly characterized, although it plays crucial roles in K+ transport in yeasts and filamentous fungi. In Saccharomyces cerevisiae K+ uptake is mainly dependent on the activity of Trk transporters thought to mediate H+:K+ symport. The ectomycorrhizal HcTrk1 transporter was functional when expressed in Xenopus oocytes, enabling the first electrophysiological characterization of a transporter from the Trk family. HcTrk1 mediates instantaneously activating inwardly rectifying currents, is permeable to both K+ and Na+, and displays channel-like functional properties. The whole set of data and particularly a phenomenon reminiscent of the anomalous mole fraction effect suggest that the transport does not occur according to the classical alternating access model. Permeation appears to occur through a single-file pore, where interactions between Na+ and K+ might result in Na+:K+ co-transport activity. HcTrk1 is expressed in external hyphae that explore the soil when the fungus grows in symbiotic condition. Thus, it could play a major role in both the K+ and Na+ nutrition of the fungus (and of the plant) in nutrient-poor soils.
MultiMLton : A Multicore-Aware Runtime for Standard

MULTIMLTON is an extension of the MLton compiler and runtime system that targets scalable, multicore architectures. It provides specific support for ACML, a derivative of Concurrent ML that allows for the construction of composable asynchronous events. To effectively manage asynchrony, we require the runtime to efficiently handle potentially large numbers of lightweight, short-lived threads, many of which are created specifically to deal with the implicit concurrency introduced by asynchronous events. Scalability demands also dictate that the runtime minimize global coordination. MULTIMLTON therefore implements a split-heap memory manager that allows mutators and collectors running on different cores to operate mostly independently. More significantly, MULTIMLTON exploits the premise that there is a surfeit of available concurrency in ACML programs to realize a new collector design that completely eliminates the need for read barriers, a source of significant overhead in other managed runtimes. These two symbiotic features a thread design specifically tailored to support asynchronous communication, and a memory manager that exploits lightweight concurrency to greatly reduce barrier overheads are MULTIMLTON’s key novelties. In this article, we describe the rationale, design, and implementation of these features, and provide experimental results over a range of parallel benchmarks and different multicore architectures including an 864 core Azul Vega 3, and a 48 core non-coherent Intel SCC (Single-Cloud Computer), that justify our design decisions.
interActors: A Model for Separating Complex Communication Concerns in Multiagent Computations

Multiagent computations increasingly require complex and diverse interactions. Existing approaches to separating these communication concerns offer static protocols, which cannot handle dynamically evolving numbers and sets of communicating agents, and leave complex initialization steps mixed in with functional concerns. We present interActors, a model for separating complex communication concerns of applications from their functional concerns. These first-class communications are self-driven and dynamically change in response to evolving communication needs; they can be easily created, reused and composed. A prototype implementation is presented. A case study illustrates improved programmability using interActors.
Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains

The degradation of the plant cell wall by glycoside hydrolases is central to environmentally sustainable industries. The major polysaccharides of the plant cell wall are cellulose and xylan, a highly decorated β-1,4-xylopyranose polymer. Glycoside hydrolases displaying multiple catalytic functions may simplify the enzymes required to degrade plant cell walls, increasing the industrial potential of these composite structures. Here we test the hypothesis that glycoside hydrolase family 43 (GH43) provides a suitable scaffold for introducing additional catalytic functions into enzymes that target complex structures in the plant cell wall. We report the crystal structure of Humicola insolens AXHd3 (HiAXHd3), a GH43 arabinofuranosidase that hydrolyses O3-linked arabinose of doubly substituted xylans, a feature of the polysaccharide that is recalcitrant to degradation. HiAXHd3 displays an N-terminal five-bladed β-propeller domain and a C-terminal β-sandwich domain. The interface between the domains comprises a xylan binding cleft that houses the active site pocket. Substrate specificity is conferred by a shallow arabinose binding pocket adjacent to the deep active site pocket, and through the orientation of the xylan backbone. Modification of the rim of the active site introduces endo-xylanase activity, whereas the resultant enzyme variant, Y166A, retains arabinofuranosidase activity. These data show that the active site of HiAXHd3 is tuned to hydrolyse arabinofuranosyl or xylosyl linkages, and it is the topology of the distal regions of the substrate binding surface that confers specificity. This report demonstrates that GH43 provides a platform for generating bespoke multifunctional enzymes that target industrially significant complex substrates, exemplified by the plant cell wall.
Kheper, a novel ZFH/deltaEF1 family member, regulates the development of the neuroectoderm of zebrafish (Danio rerio).

Kheper is a novel member of the ZFH (zinc-finger and homeodomain protein)/deltaEF1 family in zebrafish. kheper transcripts are first detected in the epiblast of the dorsal blastoderm margin at the early gastrula stage and kheper is expressed in nearly all the neuroectoderm at later stages. kheper expression was expanded in noggin RNA-injected embryos and also in swirl mutant embryos and was reduced in bmp4 RNA-injected embryos and chordino mutant embryos, suggesting that kheper acts downstream of the neural inducers Noggin and Chordino. Overexpression of Kheper elicited ectopic expansion of the neuroectoderm-specific genes fkd3, hoxa-1, and eng3, and the ectopic expression of hoxa-1 was not inhibited by BMP4 overexpression. Kheper interacted with the transcriptional corepressors CtBP1 and CtBP2. Overexpression of a Kheper mutant lacking the homeodomain or of a VP16-Kheper fusion protein disturbed the development of the neuroectoderm and head structures. These data underscore the role of Kheper in the development of the neuroectoderm and indicate that Kheper acts as a transcriptional repressor.
Selective electrochemical etching for the investigation of solder joint microstructures

Hereby we introduce a method called selective electrochemical etching for the investigation of solder joint microstructures. The aim of this technique is to remove the tin from the solder joint, which enables the examination of the remaining intermetallic microstructures in such a detail, which is unlike to any other previously established method. In our work we discuss the importance of intermetallic compound (IMC) investigation and compare the existing methods with our proposed technique. Pilot measurement results are also presented on selectively etched SAC (Sn-Ag-Cu) alloy solder joints. We present the found relationship between 1) the soldering methods and parameters, 2) the resulting microstructures, 3) the amount of the removed charge/Sn phase during the etching and 4) shear test results on the different solder joints. In our paper we will also investigate the effect of the etching conditions (e.g. etching time, electrolyte concentration, etc.) in order to reach the optimal etching depth, considering the detail and integrity of the intermetallic structures.
The Peutz-Jeghers kinase LKB 1 suppresses polyp growth from intestinal cells of a proglucagon-expressing lineage

245 words Main text: 6141 words Abbreviations: EMT, epithelial-mesenchymal transition; GLP-1,-2, glucagon-like peptide-1, -2; LKB1, liver kinase B1; OXM, oxyntomodulin; PJS, Peutz-Jehgers syndrome; PYY, peptide tyrosine tyrosine © 2014. Published by The Company of Biologists Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. D ise as e M od el s & M ec ha ni sm s D M M Ac ce pt ed m an us cr ip t http://dmm.biologists. org/lookup/doi/10.1242/dmm.014720 Access the most recent version at DMM Advance Online Articles. Posted 4 September 2014 as doi: 10.1242/dmm.014720 2 ABSTRACT Liver kinase B1 (LKB1/STK11) is a serine/threonine kinase and tumour suppressor mutated in Peutz-Jeghers Syndrome (PJS), a premalignant syndrome associated with the development of gastrointestinal polyps. Proglucagon -expressing entero-endocrine cells are involved in the control of glucose homeostasis and the regulation of appetite through the secretion of gut hormones including glucagon-like peptide-1 (GLP-1) and peptide tyrosine tyrosine (PYY). To determine the role of LKB1 in these cells, we bred mice bearing flox’d alleles of Lkb1 against animals carrying Cre recombinase under proglucagon promoter control. These mice (GluLKB1KO) were viable and displayed near normal growth rates and glucose homeostasis. However, they developed large polyps at the gastro-duodenal junction, and displayed premature mortality, from 120 days of age. Histological analysis of the polyps demonstrated that they had a PJS-like appearance with an arborizing smooth muscle core. Circulating GLP1 levels were normal in GluLKB1KO mice and the polyps expressed low levels of the peptide, similar to those in the neighbouring duodenum. Lineage tracing using a Rosa26tdRFP transgene revealed, unexpectedly, that enterocytes within the polyps were derived from non-proglucagon expressing precursors whereas connective tissue was largely derived from proglucagon-expressing precursors. Developmental studies in wild type mice suggest that a subpopulation of proglucagon-expressing cells undergo epithelialmesenchymal transition (EMT) to become smooth muscle-like cells. Thus, it is likely that polyps in the GluLKB1KO mice developed from a unique population of smooth muscle-like cells derived from a proglucagon-expressing precursor. The loss of LKB1 within this subpopulation appears sufficient to drive tumorigenesis. D ise as e M od el s & M ec ha ni sm s D M M Ac ce pt ed m an us cr ip t
Assigning Belief Scores to Names in Queries

Assuming that the goal of a person name query is to find references to a particular person, we argue that one can derive better relevance scores using probabilities derived from a language model of personal names than one can using corpus based occurrence frequencies such as inverse document frequency (idf). We present here a method of calculating person name match probability using a language model derived from a directory of legal professionals. We compare how well name match probability and idf predict search precision of word proximity queries derived from names of legal professionals and major league baseball players. Our results show that name match probability is a better predictor of relevance than idf. We also indicate how rare names with high match probability can be used as virtual tags within a corpus to identify effective collocation features for person names within a professional class.
Human Cyclin-dependent Kinase 2-associated Protein 1 (CDK2AP1) Is Dimeric in Its Disulfide-reduced State, with Natively Disordered N-terminal Region*

Background: CDK2AP1 is a tumor suppressor important in cancer biology. Results: CDK2AP1 forms a four-helix dimeric structure. The disordered N-terminal region contains an IκB kinase ϵ phosphorylation site. Conclusion: The CDK2AP1 dimer does not require a disulfide bond, but the structure is poised for disulfide bond formation. Significance: The three-dimensional structure supports a potential role for disulfide bond formation in functional regulation of CDK2AP1. CDK2AP1 (cyclin-dependent kinase 2-associated protein 1), corresponding to the gene doc-1 (deleted in oral cancer 1), is a tumor suppressor protein. The doc-1 gene is absent or down-regulated in hamster oral cancer cells and in many other cancer cell types. The ubiquitously expressed CDK2AP1 protein is the only known specific inhibitor of CDK2, making it an important component of cell cycle regulation during G1-to-S phase transition. Here, we report the solution structure of CDK2AP1 by combined methods of solution state NMR and amide hydrogen/deuterium exchange measurements with mass spectrometry. The homodimeric structure of CDK2AP1 includes an intrinsically disordered 60-residue N-terminal region and a four-helix bundle dimeric structure with reduced Cys-105 in the C-terminal region. The Cys-105 residues are, however, poised for disulfide bond formation. CDK2AP1 is phosphorylated at a conserved Ser-46 site in the N-terminal “intrinsically disordered” region by IκB kinase ϵ.
Mcg in 2030: new techniques for atomic position determination of immune complexes

The λ‐type light chain dimer from a patient (Mcg) with multiple myeloma and amyloidosis was a pioneer protein for determining the three‐dimensional structures of immunoglobulins, understanding the effects of ligand binding, and exploring the use of combinatorial methods to identify novel peptides complementary to protein active sites. Despite 30 years of intense study, there are still unanswered questions about the structure of the Mcg dimer, especially with respect to positions of hydrogen atoms and solvent molecules. In the present report, we describe two techniques that will help define the roles of solvent in ligand interactions and complex formation with this immunoglobulin fragment: (1) introduction of helium as a cryogenic agent during X‐ray data collection; and (2) addition of neutron diffraction analyses. These techniques should provide improved resolution, and a more accurate structure of the Mcg dimer. Resolution enhancements of 0.5 Å have been achieved in preliminary experiments with cryogenic helium, as compared with the best X‐ray diffraction data obtained previously. In the near future, neutron diffraction studies should produce the first hydrogen structure for the Mcg dimer and help elucidate the ligand preferences and amyloidogenic properties of this eminently useful protein. Copyright © 2002 John Wiley & Sons, Ltd.
Progressive dopamine and hypocretin deficiencies in Parkinson’s disease: is there an impact on sleep and wakefulness?

Sleep–wake disturbances are frequent in patients with Parkinson’s disease, but prospective controlled electrophysiological studies of sleep in those patients are surprisingly sparse, and the pathophysiology of sleep–wake disturbances in Parkinson’s disease remains largely elusive. In particular, the impact of impaired dopaminergic and hypocretin (orexin) signalling on sleep and wakefulness in Parkinson’s disease is still unknown. We performed a prospective, controlled electrophysiological study in patients with early and advanced Parkinson’s disease, e.g. in subjects with presumably different levels of dopamine and hypocretin cell loss. We compared sleep laboratory tests and cerebrospinal fluid levels with hypocretin‐deficient patients with narcolepsy with cataplexy, and with matched controls. Nocturnal sleep efficiency was most decreased in advanced Parkinson patients, and still lower in early Parkinson patients than in narcolepsy subjects. Excessive daytime sleepiness was most severe in narcolepsy patients. In Parkinson patients, objective sleepiness correlated with decrease of cerebrospinal fluid hypocretin levels, and repeated hypocretin measurements in two Parkinson patients revealed a decrease of levels over years. This suggests that dopamine and hypocretin deficiency differentially affect sleep and wakefulness in Parkinson’s disease. Poorer sleep quality is linked to dopamine deficiency and other disease‐related factors. Despite hypocretin cell loss in Parkinson’s disease being only partial, disturbed hypocretin signalling is likely to contribute to excessive daytime sleepiness in Parkinson patients.
A simple electrophoretic procedure for fetal diagnosis of β‐thalassaemia due to short deletions

This study describes three couples a t risk for homozygous β‐thalassaemia in which one of the partners carried a short deletion β‐thalassaemia defect. Detection of short deletions in trophoblast DNA was accomplished by the very simple procedure of non‐denaturing polyacrylamide gel electrophoresis. This method may be applied to detect β‐thalassaemia mutations due to deletion or addition of more than two nucleotides.
A current re-use PA-VCO cell for low-power BLE transmitters

A current re-use PA-VCO cell for FSK transmitters is presented. High efficiency and low phase noise are obtained through the stacking of a PA and a class-C VCO. Without the use of any DC-DC converters, the voltage headroom of these two blocks can be set maximizing the efficiency of both the PA and the VCO. The structure is inserted in a 130nm CMOS BLE transmitter. A TX efficiency of 17.5% is achieved delivering an output power of -1dBm at 2.4GHz with a VCO phase noise of -129dBc/Hz @ 2.5MHz frequency offset.
Facial Keypoint Detection

This paper describes an approach to predicting keypoint positions on greyscale images of faces, as part of the Facial Detection (2016) Kaggle competition. Facial keypoints include centers and corners of the eyes, eyebrows, nose and mouth, among other facial features. Our methodology involves four steps to producing our output predictions. The first step involves a number of training time data augmentation techniques to expand the number of training examples, and generalizability of our model. For the second stage we will discuss a number of convolutional neural networks we trained, with the best architectures derived from former LeNet and VGG Net models. At test time, we will discuss our approach of again using data augmentation techniques to produce a composite of images from a single test image, allowing for averaged predictions. Lastly, we use a weighted ensemble of models to make our final keypoint predictions. We evaluate our di↵erent model architectures, with and without data augmentation techniques based on their Root Mean Squared Error scores they produce on the test set.