Miracle-dz/UniFAR-FTUs huggingface dataset:
The acquisition of word order in Dutch and German as L1 and L2

In a recent paper, Clahsen and Muysken (1986) argue that children acquiring German as their first language have access to the 'move alpha' matrix when constructing a grammar for German. This should explain why children have SOV base order and the rule of verb-fronting from the very beginning. In this paper, it is argued that children's OV utterances cannot be related trans formationally to VO utterances. Initially, children acquire OV and VO with different sets of verbs. Clahsen and Muysken (1986) also claim that interlanguage rules of adult L2 learners are not definable in linguistic theory. Du Plessis et al. (1987) reply to this in arguing that the interlanguage rules of adults acquiring L2 German word order fall within the range of systems permitted by the Headedness parameter, the Proper Government parameter, and the Adjunction parameter. Therefore, these adult learners should have access to Universal Grammar (UG). It is argued here that it is not necessary to make this assumption. The L2-acquisition data can be easily accounted for within a simple model of L1-structural transfer.
QDMR: a quantitative method for identification of differentially methylated regions by entropy

DNA methylation plays critical roles in transcriptional regulation and chromatin remodeling. Differentially methylated regions (DMRs) have important implications for development, aging and diseases. Therefore, genome-wide mapping of DMRs across various temporal and spatial methylomes is important in revealing the impact of epigenetic modifications on heritable phenotypic variation. We present a quantitative approach, quantitative differentially methylated regions (QDMRs), to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy. QDMR was applied to synthetic methylation patterns and methylation profiles detected by methylated DNA immunoprecipitation microarray (MeDIP-chip) in human tissues/cells. This approach can give a reasonable quantitative measure of methylation difference across multiple samples. Then DMR threshold was determined from methylation probability model. Using this threshold, QDMR identified 10 651 tissue DMRs which are related to the genes enriched for cell differentiation, including 4740 DMRs not identified by the method developed by Rakyan et al. QDMR can also measure the sample specificity of each DMR. Finally, the application to methylation profiles detected by reduced representation bisulphite sequencing (RRBS) in mouse showed the platform-free and species-free nature of QDMR. This approach provides an effective tool for the high-throughput identification of potential functional regions involved in epigenetic regulation.
Molecular Mechanisms and Therapeutic Effects of (−)-Epicatechin and Other Polyphenols in Cancer, Inflammation, Diabetes, and Neurodegeneration

With recent insight into the mechanisms involved in diseases, such as cardiovascular disease, cancer, stroke, neurodegenerative diseases, and diabetes, more efficient modes of treatment are now being assessed. Traditional medicine including the use of natural products is widely practiced around the world, assuming that certain natural products contain the healing properties that may in fact have a preventative role in many of the diseases plaguing the human population. This paper reviews the biological effects of a group of natural compounds called polyphenols, including apigenin, epigallocatechin gallate, genistein, and (−)-epicatechin, with a focus on the latter. (−)-Epicatechin has several unique features responsible for a variety of its effects. One of these is its ability to interact with and neutralize reactive oxygen species (ROS) in the cell. (−)-Epicatechin also modulates cell signaling including the MAP kinase pathway, which is involved in cell proliferation. Mutations in this pathway are often associated with malignancies, and the use of (−)-epicatechin holds promise as a preventative agent and as an adjunct for chemotherapy and radiation therapy to improve outcome. This paper discusses the potential of some phenolic compounds to maintain, protect, and possibly reinstate health.
TA Repeat Variation, Npr1 Expression, and Blood Pressure: Impact of the Ace Locus

Abstract—The activity of the atrial natriuretic peptide receptor (Npr1) is altered in spontaneously hypertensive rats (SHR) in relation to its mRNA levels, suggesting abnormal transcriptional control in hypertension. A single-stranded conformational polymorphism caused by a repetitive dinucleotide segment of 10 TA in BN-Lx and of 40 TA in SHR was localized at position −943 relative to the transcription start site of the Npr1 gene, downstream of a putative cGMP-regulatory region, and was the only sequence difference noted between the two strains. Transient transfections of −1520 to −920 Npr1 promoter-SV40-luciferase fusion vector showed that the construct from BN-Lx stimulated the SV40 promoter, whereas that from SHR slightly inhibited it. In contrast to the BN-Lx construct, the activity of the SHR fragment was refractory to downregulation by atrial natriuretic peptide. Genotype-phenotype correlation studies in recombinant inbred strains (RIS) derived from BN-Lx and SHR crosses revealed significant correlations of the TA repeat with basal guanylyl cyclase activity and Npr1 mRNA levels. The correlations were heightened by a locus on chromosome 10 containing the Ace gene. The highest basal guanylyl cyclase activity and Npr1 mRNA values were found in RIS with both genes (Npr1/ Ace) of BN genotypes, whereas the lowest were recorded in RIS, with the SHR genotypes at both loci. This was inversely correlated with diastolic blood pressure in these strains. In conclusion, the longer TA repeat unit in the promoter of Npr1 of SHR, in tandem with a putative cGMP responsive element, regulates the transcription of the Npr1 gene with consequences on diastolic blood pressure.
Elastic windows: improved spatial layout and rapid multiple window operations

Most windowing systems follow the independent overlapping windows approach, which emerged as an answer to the needs of the 80s' application and technology. Advances in computers, display technology, and the applications demand more functionality from window management systems. Based on these changes and the problems of current windowing appraoches, we have updated the requirements for multiwindow systems to guide new methods of window management. We propose elastic windows with improved spatial layout and rapid multi-window operations. Multi-window operations are achieved by issuing operations on window groups hierachically organized in a space-filling tiled layout. Sophisticated multi-window operations and spatial layout dynamics helps users to handle fast task-switching and to structure thier work environment to their rapidly changing needs. We claim that these multi-window operations and the improved spatial layout decrease the cognitive load on users. Users found our prototype system to be comprehensible and enjoyable as they playfully explored the way multiple windows are reshaped.
An Evolutionary Approach to Software Modularity Analysis

Modularity determines software quality in terms of evolvability, changeability, maintainability, etc. and a module could be a vertical slicing through source code directory structure or class boundary. Given a modularized design, we need to determine whether its implementation realizes the designed modularity. Manually comparing source code modular structure with abstracted design modular structure is tedious and error-prone. In this paper, we present an automated approach to check the conformance of source code modularity to the designed modularity. Our approach uses design structure matrices (DSMs) as a uniform representation; it uses existing tools to automatically derive DSMs from the source code and design, and uses a genetic algorithm to automatically cluster DSMs and check the conformance. We applied our approach to a small canonical software system as a proof of concept experiment. The results supported our hypothesis that it is possible to check the conformance between source code structure and design structure automatically, and this approach has the potential to be scaled for use in large software systems.
Analysis of Exponential Backoff with Multipacket Reception in Wireless Networks

A collision resolution scheme is essential to the performance of a random-access wireless network. Most schemes employ exponential backoff (EB) to adjust the transmission attempt rate according to the changing traffic intensity. Previous work on exponential backoff was mostly based on the conventional single-packet-reception model where no more than one packet can be successfully received at any one time. In this paper, we analyze the performance of EB based on a multi-packet reception (MPR) model, in which multiple packets can be received successfully at once (i.e., collisions do not occur unless the number of packets transmitted exceeds a threshold that is more than 1). Using a Markov chain model, we derive the throughput expressions for both carrier-sensing and non-carrier-sensing networks with MPR capability under the saturated-traffic condition. We find that the two systems share a number of common performance results. In particular, the state of both systems can be characterized by the same Markov-chain model. The binary exponential backoff (BEB), in which the backoff factor r is set to 2, does not yield the optimum network throughput in both cases. In addition, in both cases, the asymptotic collision probability goes to 1/r and the maximum asymptotic throughput increases roughly linearly with M when the population size approaches infinity. We show how to adjust r to achieve the best throughput performance. Our results show that the optimal r that maximizes the asymptotic throughput increases with M for non-carrier-sensing systems and BEB is close to optimal for carrier-sensing systems. Simulation results validate the accuracy of our theoretical analysis
Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences

Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic) and Thaumarchaeota (mesophilic), were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about “methanogenic archaea composition” and “abundance” in the contrasting ecosystems like “landfill” and “marshland” may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process.
Role of caloric content on gastric emptying in humans.

1. This study examined the effects of caloric content (caloric density and the nature of calories) on the rate of gastric emptying using the double‐sampling gastric aspiration technique. Four test meals of 600 ml (glucose, 0.1 kcal ml‐1; pea and whey peptide hydrolysates, both 0.2 kcal ml‐1; milk protein, 0.7 kcal ml‐1) were tested in six healthy subjects in random order on four separate occasions. 2. The glucose solution was emptied the fastest with a half‐time of 9.4 +/‐ 1.2 min (P < 0.05) and the milk protein the slowest with a half‐time of 26.4 +/‐ 10.0 min (P < 0.05); the pea peptide hydrolysate and whey peptide hydrolysate solutions had half‐times of emptying of 16.3 +/‐ 5.4 and 17.2 +/‐ 6.1 min, respectively. The rates of gastric emptying for the peptide hydrolysate solutions derived from different protein sources were not different. 3. Despite the lower rate of gastric emptying for the milk protein solution, the rate of caloric delivery to the duodenum during the early phase of the gastric emptying process was higher than that for the other three solutions (46.3 +/‐ 6, 63.5 +/‐ 22, 62.5 +/‐ 19 and 113.8 +/‐ 25 cal min‐1 kg‐1 for the glucose, pea peptide hydrolysate, whey peptide hydrolysate and milk protein meals, respectively; P < 0.05). The caloric density of the test solutions was linearly related to the half‐time of gastric emptying (r = 0.96, P < 0.05) as well as to the rate at which calories were delivered to the duodenum (r = 0.99, P < 0.001). 4. This study demonstrates that the rate of gastric emptying is a function of the caloric density of the ingested meal and that a linear relationship exists between these variables. Furthermore, the nature of the calories seems to play a minor role in determining the rate of gastric emptying in humans.
Structured Audio Player: Supporting Radio Archive Workflows with Automatically Generated Structure Metadata

Although techniques to automatically generate metadata have been steadily refined over the past decade, archive professionals at radio broadcasters continue to use conventional audio players in order to screen and annotate radio material. In order to facilitate technology transfer, the archives departments of two large German radio broadcasters, Deutsche Welle and WDR, commissioned Fraunhofer IAIS to develop a prototype audio archive and to investigate the practical aspects of integrating automatically generated metadata into their existing workflows. The project identified the structuring of radio programs as the area in which automatically generated metadata has the clearest potential to support the work of archive staff. This paper discusses the development and performance of the structured audio player, the component of the audio archive system that demonstrates this potential. The automatically generated structured metadata includes speaker boundaries, speaker IDs, speaker gender and identification of audio segments not containing speech. In contrast to similar systems, our prototype was designed, developed and optimized in a project group composed of both archive professionals and multimedia researchers. As a result, important insights were gained into how automatically generated metadata should (and should not) be deployed to support the work of archivists preparing radio content for archival.
A controlled pilot study of stress management training of elderly patients with congestive heart failure.

The purpose of this study was to evaluate the effect of stress management training on quality of life, functional capacity, and heart rate variability in elderly patients with New York Heart Association class I-III congestive heart failure (CHF). While substantial research exists on stress management training for patients with coronary heart disease, there are few data on the value of psychosocial training on patients with CHF. Thirty-three multiethnic patients (mean age, 66+/-9 years) were assigned through incomplete randomization to one of two treatment groups or a wait-listed control group. The 14 participants who completed the treatment attended eight training sessions during a 10-week period. The training consisted of 75-minute sessions adapted from the Freeze-Frame stress management program developed by the Institute of HeartMath. Subjects were assessed at baseline and again at the completion of the training. Depression, stress management, optimism, anxiety, emotional distress, and functional capacity were evaluated, as well as heart rate variability. Significant improvements (p<0.05) were noted in perceived stress, emotional distress, 6-minute walk, and depression, and positive trends were noted in each of the other psychosocial measures. The 24-hour heart rate variability showed no significant changes in autonomic tone. The authors noted that CHF patients were willing study participants and their emotional coping and functional capacity were enhanced. This program offers a simple and cost-effective way to augment medical management of CHF. Given the incompleteness of CHF medical management and the exploding interest in complementary medical intervention, it seems imperative that further work in psychosocial treatment be undertaken.
Presence and regulation of cannabinoid receptors in human retinal pigment epithelial cells

Purpose Cannabinoid receptors have been detected in neuron cells and proposed as potential therapeutic agents in neurodegenerative disorders because of their involvement in controlling neural cell survival and death. However, their presence and role in human retinal pigment epithelial (RPE) cells, which play a key role in initiating and developing age related macular degeneration (ARMD), have never been investigated. Here we analyzed the expression of and changes in cannabinoid receptors (CB1 and CB2) and one enzyme responsible for endocannabinoid hydrolysis, fatty acid amide hydrolase (FAAH), in RPE cell oxidative damage process, a cellular model of ARMD. Methods Primary human RPE cells and cells from the ARPE-19 cell line were cultured and exposed to H2O2 for 24 h to induce oxidative damage. Real time RT–PCR, immunofluorescent staining, and western blot methods were performed to study the expression of and changes in CB1 and CB2 receptors, and FAAH. Cell viability and reactive oxygen species (ROS) production were measured by using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and a dichlorofluorescein (DCF) assay, respectively. PI3K/Akt and ERK1/2 protein expression and activation of signaling molecules were assessed by western blot analysis. Results By using real time RT–PCR, immunofluorescent staining and western blot methods, we showed that human RPE cells express CB1, CB2, and FAAH. Meanwhile, oxidative stress can upregulate CB1 and CB2 receptor expression, and downregulate FAAH expression. The CB1/CB2 receptor agonist, CP55,940, and the CB2 receptor agonist, JWH015 significantly protected RPE cells from oxidative damage. In addition, CP55,940 significantly reduced the levels of intracellular ROS, strengthened oxidative stress-induced activation of PI3K/Akt and reduced activation of the ERK1/2 signal pathway. Conclusions The results demonstrate the expression and regulation of CB1 and CB2 receptors and FAAH in human RPE cells. The modulation of cannabinoid receptor tone warrants consideration for future therapeutic strategies of ARMD.
Serotonin-gated inward currents are three times more frequent in rat hairy skin sensory afferents than in those innervating the skeletal muscle

Tight whole-cell patch clamp was performed in 191 DiI (1,1′-dioctadecyl-3,3,3′3′-tetramethylindocarbocyanine perchlorate) retrogradely labeled rat sensory afferents from skin shoulders (n = 93) and biceps femoris muscles (n = 98). 5-HT-gated inward currents were evoked with 50-µM serotonin (5-HT; 5-hydroxytryptamine), and their frequency and current densities were compared between skin and skeletal muscle sensory afferents. To evaluate if 5-HT-gated inward currents coexist with other ligand-gated currents, the skin and skeletal muscle sensory afferents were also sequentially exposed to external solution at pH 6.8, ATP (50 µM), and capsaicin (1 µM). 5-HT evoked inward currents in 72% (67 of 93) of hairy skin sensory afferents and in only 24% (24 of 98) of skeletal muscle sensory afferents, and this difference was statistically significant (p < 0.0000, chi-square test). The current densities obtained in hairy skin and skeletal muscle sensory afferents were not significantly different. They were −45.8 ± 7.7 and −32.4 ± 10.5 pA/pF, respectively (mean ± SEM, p < 0.30734). These results indicate that 5-HT-gated inward currents are three times more frequently evoked in small- to medium-sized sensory afferents (25–40 µm) innervating the hairy skin than on those innervating the skeletal muscle. When cells were gathered in two clusters, the difference was four times larger in the small-sized cluster (25–32 µm) and two times larger in the medium-sized cluster (33–40 µm). The results can be explained if the superficial somatic (cutaneous) nociceptive system is more exposed than the deep somatic nociceptive system (musculoskeletal) to physical and chemical stimuli inducing 5-HT-mediated inflammatory pain.
Cytokine‐Regulated Expression of Platelet‐Derived Growth Factor Gene and Protein in Cultured Human Astrocytes

Abstract: To elucidate mechanisms regulating the production of platelet‐derived growth factor (PDGF) in the CNS, we analyzed the influence of a panel of cytokines on PDGF mRNA and protein levels in astrocyte‐enriched cultures from the human embryonic brain and spinal cord. Using a specific ELISA, PDGF AB protein was detected in serum‐free astrocyte supernatants and its levels were significantly increased after treatment of the cultures with transforming growth factor‐β1 (TGF‐β1) or tumor necrosis factor‐α (TNF‐α); the largest increase was detected after combined treatment with the two cytokines. Interleukin‐1β (IL‐1β) by itself had little or no effect but synergized with TGF‐β1 in enhancing PDGF AB production. Supernatants from human astrocyte cultures stimulated the proliferation of rat oligodendrocyte progenitors, and most of the mitogenic activity could be accounted for by PDGF. By northern blot analysis, both PDGF A‐ and PDGF B‐chain mRNAs were detected in untreated astrocytes. PDGF B‐chain mRNA levels were increased by TGF‐β1, TNF‐α, TNF‐α/TGF‐β1, or IL‐1β/TGF‐β1, whereas PDGF A‐chain mRNA levels were not consistently affected by cytokine treatments. These in vitro data indicate that TGF‐β1, TNF‐α, and IL‐1β are able to stimulate astrocyte PDGF production. This cytokine network could play a role in CNS development and repair after injury or inflammation.
Methyltransferase Set7/9 Maintains Transcription and Euchromatin Structure at Islet-Enriched Genes

OBJECTIVE—The activation of β-cell genes, particularly of those encoding preproinsulin, requires an appropriate euchromatin (or “open”) DNA template characterized by hypermethylation of Lys4 of histone H3. We hypothesized that this modification is maintained in islet β-cells by the action of the histone methyltransferase Set7/9. RESEARCH DESIGN AND METHODS—To identify the role of Set7/9, we characterized its expression pattern and gene regulation and studied its function using RNA interference in both cell lines and primary mouse islets. RESULTS—Within the pancreas, Set7/9 protein shows striking specificity for islet cells, including α- and β-cells, as well as occasional cells within ducts. Consistent with these findings, the Set7/9 gene promoter contained an islet-specific enhancer located between −5,768 and −6,030 base pairs (relative to the transcriptional start site) that exhibited Pdx1-responsive activation in β-cells. To study Set7/9 function, we depleted insulinoma cells and primary mouse islets of Set7/9 protein using siRNA. Following siRNA treatment, we observed striking repression of genes involved in glucose-stimulated insulin secretion, including Ins1/2, Glut2, and MafA. These changes in transcription were accompanied by loss of dimethylated H3 Lys4 and RNA polymerase II recruitment, particularly at the Ins1/2 and Glut2 genes. Consistent with these data, depletion of Set7/9 in islets led to defects in glucose-stimulated Ca2+ mobilization and insulin secretion. CONCLUSIONS—We conclude that Set7/9 is required for normal β-cell function, likely through the maintenance of euchromatin structure at genes necessary for glucose-stimulated insulin secretion.