Miracle-dz/UniFAR-FTUs huggingface dataset:
Autophagy Primes Neutrophils for Neutrophil Extracellular Trap Formation during Sepsis

Rationale: Neutrophils are key effectors in the host's immune response to sepsis. Excessive stimulation or dysregulated neutrophil functions are believed to be responsible for sepsis pathogenesis. However, the mechanisms regulating functional plasticity of neutrophils during sepsis have not been fully determined. Objectives: We investigated the role of autophagy in neutrophil functions during sepsis in patients with community‐acquired pneumonia. Methods: Neutrophils were isolated from patients with sepsis and stimulated with phorbol 12‐myristate 13‐acetate (PMA). The levels of reactive oxygen species generation, neutrophil extracellular trap (NET) formation, and granule release, and the autophagic status were evaluated. The effect of neutrophil autophagy augmentation was further evaluated in a mouse model of sepsis. Measurements and Main Results: Neutrophils isolated from patients who survived sepsis showed an increase in autophagy induction, and were primed for NET formation in response to subsequent PMA stimulation. In contrast, neutrophils isolated from patients who did not survive sepsis showed dysregulated autophagy and a decreased response to PMA stimulation. The induction of autophagy primed healthy neutrophils for NET formation and vice versa. In a mouse model of sepsis, the augmentation of autophagy improved survival via a NET‐dependent mechanism. Conclusions: These results indicate that neutrophil autophagy primes neutrophils for increased NET formation, which is important for proper neutrophil effector functions during sepsis. Our study provides important insights into the role of autophagy in neutrophils during sepsis.
High-speed rail transport valuation

In this paper, the optimal timing for investing in high-speed rail projects under uncertainty in relation to the utility provided to railway users was investigated. To accomplish this, a continuous time real options analysis framework using a stochastic demand model was developed to determine the optimal time to invest. Uncertainty upon investment expenditures was also added in an extended framework. The value of the option to defer and the investment opportunity value were also assessed.
UvA-DARE (Digital Academic Distributed and Adaptive Darting Monte Carlo through Regenerations

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A patent search and classification system

We present a system for searching and classifying U.S. patent documents, based on Inquery. Patents are distributed through hundreds of collections, divided up by general area. The system selects the best collections for the query. Users can search for patents or classify patent text. The user interface helps users search in fields without requiring the knowledge of Inquery query operators. The system includes a unique “phrase help” facility, which helps users find and add phrases and terms related to those in their query.
Ultrastructural Characterization of Fresh and Vitrified In Vitro‐ and In Vivo‐Produced Sheep Embryos

The lower results in cryopreservation of in vitro‐produced (IVP) sheep embryos, when compared to the in vivo derived, limits its use. Four groups of blastocyst (BL) were evaluated: fresh IVP (n = 3), fresh in vivo derived (n = 3), warmed IVP cryopreserved in open pulled straws (OPS, n = 3) and warmed in vivo derived cryopreserved in OPS (n = 3). Ultrastructural observation of processed fresh embryos showed a reduced number of microvilli and mitochondria in the IVP ones, as well as a lower number of mature mitochondria, that can be associated with deficient metabolism in IVP embryos, possibly involved in the lower resistance to cryopreservation. Both in vivo‐derived and IVP embryos had a large number of vesicles, with light and dense content. In embryos vitrified by OPS, major changes were observed mainly in IVP embryos with small changes in grade 2 (fair) and high changes in grade 3 (bad) semithin scoring. The main changes associated with cryopreservation included disruption of cellular membranes and poor intracellular preservation, with loss of microvilli and the presence of cellular debris. In conclusion, ultrastructural evaluation of IVP blastocysts cryopreserved in OPS was herein described for the first time, reporting more severe cellular damage in these embryos when compared to those produced in vivo. This is probably associated with a lower cryotolerance that can be related to their lipid content and metabolism.
Choosing Your Pond: Location Choices and Relative Income

Abstract Do individuals care about their relative income? While this is a long-standing hypothesis, revealed-preference evidence remains elusive. We provide a unique test by studying residential choices: individuals often must choose between places with different income distributions, and as a result they “choose” their relative income. We conducted a field experiment with 1,080 senior medical students who participated in the National Resident Matching Program. We estimate their preferences by combining choice data, survey data on perceptions, and information-provision experiments. The evidence suggests that individuals care about their relative income and that these preferences differ across single and nonsingle individuals.
Sweet taste of aspartame and sucrose: effects on diet-induced thermogenesis

UNLABELLED Among factors that affect diet-induced thermogenesis (DIT) are the sensory characteristics of food. The aim of this study was to test whether the sweet flavour obtained with a low-energy sweetener (aspartame) or with sucrose have a different effect on DIT. Following a standardized breakfast, 24 healthy male subjects were served three test lunches in a randomized fashion. Lunch contained soft white cheese added with maltodextrins and aspartame, or sucrose, or maltodextrins only (non-sweetened control) (each 900 kcal). Energy expenditure (indirect calorimetry) was monitored during the five postprandial hours. For the first two periods of measurement (30-60 and 90-120 min after meal ingestion), postprandial energy expenditure was significantly increased with sucrose compared to maltodextrins and maltodextrins plus aspartame, whereas no significant difference was found between maltodextrins and maltodextrins plus aspartame. No significant difference between lunches was observed for DIT expressed as incremental area above premeal baseline energy expenditure. Plasma glucose area under the curve was significantly lower for sucrose compared to maltodextrins plus aspartame. Plasma insulin area under the curve was significantly lower for sucrose compared to the other tests foods. IN CONCLUSION (1) variation in sweet-taste induced by aspartame or by sucrose does not seem to have a major effect on DIT in healthy humans; (2) differences in energy expenditure observed in the early postprandial period suggest a substrate effect.
Role of Mammalian Chitinases in Asthma

Asthma is a chronic inflammatory disease characterized by airway inflammation, mucus hypersecretion and airway hyperresponsiveness. Mechanisms underlying the pathogenesis of asthma are not fully understood. In recent years, there are mounting evidences demonstrating that mammalian chitinases may play a key role in mediating the T-helper 2 cell-driven inflammatory response that is commonly associated with asthma. Chitinases (e.g., chitotriosidase and acidic mammalian chitinase) are enzymes that degrade chitin, the second most abundant biopolymer that can be found in the cell walls of fungi, microfilarial sheaths of helminths, and exoskeletons of insects and crustaceans. There are also chitinase-like proteins (e.g., YKL-40, Ym1 and Ym2) that lack chitinolytic activity but retain chitin-binding ability. Therefore, chitinases were originally believed to function in host defense against parasitic infections, but the first discovery of their role in inflammatory airway diseases came as a surprise. There is ample evidence to support an association of acidic mammalian chitinase and YKL-40 with allergic bronchial asthma in patients. Our recent studies in a mouse asthma model revealed that anti-inflammatory drugs like corticosteroid and cysteinyl leukotriene receptor antagonist were able to suppress elevated pulmonary levels of mammalian chitinases. Taken together, mammalian chitinases may be useful as biomarkers for asthma. Notwithstanding, large-scale multi-center association studies are required to confirm this hypothesis. Besides, substantially more works using knockout mice, recombinant chitinases and siRNA technology are required to investigate a potential role of chitinases in the pathogenesis of asthma.
Finding Representative Association Rules from Large Rule Collections

One of the most well-studied problems in data mining is computing association rules from large transactional databases. Often, the rule collections extracted from existing datamining methods can be far too large to be carefully examined and understood by the data analysts. In this paper, we address exactly this issue of overwhelmingly large rule collections by introducing and studying the following problem: Given a large collection R of association rules we want to pick a subset of them S ⊆ R that best represents the original collection R as well as the dataset from which R was extracted. We first quantify the notion of the goodness of a ruleset using two very simple and intuitive definitions. Based on these definitions we then formally define and study the corresponding optimization problems of picking the best ruleset S ⊆ R. We propose algorithms for solving these problems and present experiments to show that our algorithms work well for real datasets and lead to large reduction in the size of the original rule collec-
Diet in Relation to Endometrial Cancer Risk: A Case-Control Study in Greece

The risk of endometrial cancer is positively associated with obesity, but the role of specific nutrients remains unclear. Given the distinct characteristics of the Greek diet and the low incidence of this form of cancer among Greek women, we undertook a case-control study to investigate the association of endometrial cancer with food groups and micronutrients. Cases were 84 women with histologically confirmed endometrial cancer and controls were 84 women with intact uterus admitted to the same teaching hospital in Athens, Greece. Consumption of pulses, nuts, and seeds was significantly inversely related to the risk for endometrial cancer. No other significant association with food groups was detected, although a protective effect of added lipids, which in the Greek diet are primarily represented by olive oil, was highly suggestive. Retinol, nicotinic acid, vitamin B-6, and riboflavin were inversely associated with the disease. These findings need to be replicated, because this was a relatively small study with the statistical power to detect only strong associations between cases and controls; they appear, however, to support a role of diet in the etiology of endometrial cancer.
Double‐pulse facilitation of smooth muscle alpha 1‐subunit Ca2+ channels expressed in CHO cells.

Frequent strong depolarizations facilitate Ca2+ channels in various cell types by shifting their gating behavior towards mode 2, which is characterized by long openings and high probability of being open. In cardiac cells, the same type of gating behavior is potentiated by beta‐adrenoceptors presumably acting via phosphorylation of a protein identical to or associated with the channel. Voltage‐dependent phosphorylation has also been reported to underlie Ca2+ channel facilitation in chromaffin adrenal medulla and in skeletal muscle cells. We studied a possible voltage‐dependent facilitation of the principal channel forming alpha 1‐subunit of the dihydropyridine‐sensitive smooth muscle Ca2+ channel. Single channel and whole‐cell Ca2+ currents were recorded in Chinese hamster ovary cells stably expressing the class Cb Ca2+ channel alpha 1‐subunit. Strong depolarizing voltage‐clamp steps preceding the test pulse resulted in a 2‐ to 3‐fold increase of the single Ca2+ channel activity and induction of mode 2‐like gating behavior. Accordingly we observed a significant potentiation of the whole‐cell current by approximately 50%. In contrast to the previous suggestions we found no experimental evidence for involvement of channel phosphorylation by protein kinases (cAMP‐dependent protein kinase, protein kinase C and other protein kinases utilizing ATP gamma S) in the control and facilitated current. The data demonstrate that the L‐type Ca2+ channel alpha 1‐subunit solely expressed in Chinese hamster ovary cells is subject to a voltage‐dependent facilitation but not to phosphorylation. (ABSTRACT TRUNCATED AT 250 WORDS)
The Late Pleistocene microlithic at Putslaagte 8 rockshelter in the Western Cape, South Africa

This paper describes the late Pleistocene early microlithic at Putslaagte 8 (PL8) rockshelter in the eastern Cederberg of the Western Cape. Focus is placed on: 1) characterising the pre-Robberg Early Later Stone Age (ELSA) and Robberg at the site, and 2) determining if and how the ELSA anticipates the Robberg. Results suggest that the ELSA in the eastern Cederberg is associated with the production of hornfels blades with a shift in production emphasis towards smaller silcrete blades during the Robberg. Blade production systems and modes of delivery, however, are quite different in the two periods. Bipolar technology forms only a minor component of the ELSA technology and there is minimal use of quartz despite its presence in the landscape. This contrasts with the ELSA at sites on the opposite side of the Cape Fold Mountain Range and in the north of the subcontinent where bipolar technology and a preference for quartz appear to be defining features. The late Pleistocene sequence at PL8 is particularly significant for helping to characterise the pre-Robberg in the southwest of southern Africa - an area where the nature of the ELSA is currently underdefined.
IMPROVING THE ACCURACY OF MARINE GRAVITY ANOMALY DATA FROM COMBINATION OF SHIPBORNE GRAVITY AND GLOBAL MARINE GRAVITY DERIVED FROM SATELLITE ALTIMETRY

: Currently, utilising satellite altimetry data to derive marine gravity anomalies is the preferred method due to its low cost and ability to cover large areas efficiently. However, accurately obtaining altimeter-derived gravity anomalies in coastal regions remains challenging. This paper aims to improve the accuracy of global marine gravity data in Peninsular Malaysia’s marine areas by incorporating both altimetry-derived and ship-track gravity data. After filtering 39,756 marine ship-borne gravity observations with a 95% confidence level and using cross-validation to identify errors, 24,142 gravity points were eliminated, resulting in a decrease in the standard deviation (STD) from 40.600 mGal to 15.663 mGal. Four (4) existing global marine gravity models were evaluated using the filtered ship-borne datasets, and the DTU model version 17 was deemed the optimal model with an RMSE of 10.762 mGal. The least-squares collocation method was used to integrate the gravity data from the ship-borne datasets with the DTU17 model. Validation of the new marine gravity model, which included 50 ship gravity data points, showed a significant improvement with an RMSE of 2.192 mGal.
CNTF, a key factor mediating the beneficial effects of inflammatory reactions in the eye

Sir, retinal ganglion cells (RGCs) are normally unable to regenerate axons. However, they can be transformed into a robust regenerative state by lens injury (LI) or by intravitreal injections of either lens-derived β-/γ-crystallins or zymosan (Fischer et al ., 2000, 2001, 2004, 2008; Leon et al ., 2000). Based on evidence provided in Muller et al . (2007) and the literature, we propose that astrocyte-derived CNTF and activation of its major downstream signalling pathway in RGCs, the JAK/STAT3 pathway, are both essentially involved in switching these neurons to an active regenerative state after LI. By arguing against a role of CNTF and JAK/STAT3 signalling in this context, Benowitz and colleagues have ignored important evidence in the literature and also presented data from our own and other groups inaccurately, as described later. The literature contains compelling evidence that CNTF directly stimulates axon regeneration of RGCs. For instance, using purified (immunopanned) RGCs, Lingor et al . (2008) have recently demonstrated that CNTF stimulates axon outgrowth of primary RGCs without requiring the elevation of cAMP. Benowitz and colleagues ignore this important piece of evidence, instead only mentioning the significant, but less-pronounced effects of CNTF on RGC-5 cells shown in the same paper (Lingor et al ., 2008). However, RGC-5 cells are not primary neurons but rather a transformed RGC cell line derived from animals at postnatal day 1 (Krishnamoorthy et al ., 2001). For this reason, the reported stronger effects on primary RGCs are much more relevant for assessing the neuritogenic potency of CNTF. Other papers provide further evidence that CNTF stimulates axon outgrowth of postnatal and adult RGCs in culture without requiring cAMP elevation (Lorber et al ., 2002, 2007). Consistent with these, we have also found that CNTF highly significantly stimulates axon regeneration of adult RGCs …
Nonlinear identification method corresponding to muscle property variation in FES - experiments in paraplegic patients

A model-based Functional Electrical Stimulation (FES) would be very helpful for the adaptive movement synthesis of spinal-cord-injured patients. The nonlinearity of the neuromuscular system can be captured through modeling and identification process. However, there are still critical limitations in FES: rapid muscle fatigue and time-varying property. In actual FES, in order to minimize the fatigue, the intermittent stimulation is adopted. In this case, fatigue and recovery occur in sequence. Thus, the time-varying muscle response is really difficult to be predicted for FES force control. In this paper, we propose an identification method to identify unknown internal states and the maximal force parameter which are inside the nonlinear differential equation. Among the internal parameters of muscle model, maximal force Fm should be mainly changed corresponding to the current muscle condition. Muscle fatigue or recovery itself is difficult to be modeled and predicted, however observing the input-output information from the muscle, the adaptive estimation will be achieved to correspond to the varying muscle response effected by a fatigue or unknown metabolic factor of human system. This identification method itself can be expected to be applied for general use in rehabilitation robotics.
Symptoms of posttraumatic stress, depression, and anxiety as predictors of suicidal ideation among South African university students

ABSTRACT Objective: To investigate the 2-week prevalence of suicidal ideations and their associations to symptoms of posttraumatic stress, depression, and anxiety among South African university students. Participants: Data were collected from 1,337 students between May and August 2013. Methods: Hierarchical regression analysis was used to investigate the relationship between suicidal ideation and symptoms of posttraumatic stress, depression, and anxiety. Results: Rates of suicidal ideation are higher among university students in South Africa than among the general population of the country and student populations in other parts of the world. Symptoms of depression and exposure to trauma predict suicidal ideation Conclusions: Findings bring into focus the high rates of suicidal ideation among a sample of university students in South African and the need for more research to investigate the psychosocial correlates of this phenomena within the cultural context of the country, especially given the correlation between suicidal ideation and other poor health outcomes.
A Modal Calculus for Exception Handling

The exception monad, while an adequate mechanism for providing the denotational semantics of exceptions, is somewhat awkward to program with. Just as any other monad, it forces a programming style in which exceptional computations are explicitly sequentialized in the program text. In addition, values of computation types must usually be tested before use, in order to determine if they correspond to a raised exception. In this paper we propose a type system that rearranges the monadic formulation, so that the above shortcomings are avoided. Instead of the exception monad, we propose the operator from the modal logic S4 to encode exceptional computation. The way tracking of exceptions is organized in the modal system is exactly dual to the monadic case, reecting the well-known property that is actually a comonad.
Green Extraction Strategy Using Bio-Based Aqueous Biphasic Systems for Polyphenol Valorization from Grape By-Product

Polyphenols are natural compounds with enhanced antioxidant properties. They are present in relatively high concentrations in fruit/vegetable by-products. Therefore, there is a need for the development of efficient and cost-effective methods for the separation and purification of these valuable compounds. Traditional extraction with organic solvents needs to be switched to novel methods that are more efficient, with reduced extraction times and low consumption of organic solvents. Aiming at developing sustainable processes for the separation and purification of phenolic compounds, we used three model compounds, namely resveratrol, quercetin, and gallic acid, to investigate ionic liquid-based aqueous biphasic systems (IL-ABSs) formed by cholinium-based IL in combination with polypropylene glycol with a molecular mass of 400 g/mol (PPG400). The ABS composition in the two-phase region was selected according to a previously determined phase diagram. Extraction studies indicated the preferential partition of resveratrol and quercetin toward the hydrophobic PPG-rich phase that is mainly dominated by its hydrophobic nature and the strong salting-out effect of ILs. On the other hand, due to its considerably hydrophilic nature, gallic acid preferentially migrates toward the IL phase. The achieved results from grape stem extract demonstrated high extraction efficiencies of cholinium dihydrogen phosphate (~99% for resveratrol for the PPG phase and 78% for gallic acid for the IL phase), with considerable selectivity, demonstrating promising outcomes for potential applications.
Repetition-based web page segmentation by detecting tag patterns for small-screen devices

Web page segmentation into logical blocks is an important preprocessing step for recognizing informative content blocks in a page that leads to efficient information extraction and convenient display on the devices with small-sized screens. Previous methods for Web page segmentation are not flexible in a dynamic Web environment because they largely relied on heuristic rules generated by exploiting structural tags and visual information inherent in a page. To resolve this problem, this paper proposes a new method of Web page segmentation by recognizing repetitive tag patterns called key patterns in the DOM tree structure of a page. We report on the Repetition-based Page Segmentation (REPS) algorithm, which detects key patterns in a page and generates virtual nodes to correctly segment nested blocks. A series of experiments performed for real Web sites showed that REPS greatly contributes to improving the correctness of Web page segmentation.