Miracle-dz/UniFAR-FTUs huggingface dataset:
An ensemble approach to handle out of vocabulary in multilabel document classification

In document classification, out of vocabulary occured when there are words that are not covered by the classifier. This condition can affect prediction performance. The classifier needs to be re-trained using new documents containing those words in order to handle out of vocabulary condition. In this paper, we proposed an ensemble method that able to re-train a classifier in incremental fashion. That is, it does not use any previous training documents, only the new ones. Our approach also handles multilabel classification where a document can be classified into more than one label, which is a the case to Indonesian news articles we use for this paper. Result from our experiment shows that the ensemble method can cover out of vocabulary words and correctly classify a document where other classifiers which do not cover the words can not. It some conditions, it can even outperform batch-trained classifier performance. And also, because our ensemble method is an incremental method, its training time and memory consumption depends to the training data it currently uses.
Assessment of the exhalation kinetics of volatile cancer biomarkers based on their physicochemical properties

The current review provides an assessment of the exhalation kinetics of volatile organic compounds (VOCs) that have been linked with cancer. Towards this end, we evaluate various physicochemical properties, such as ‘breath:air’ and ‘blood:fat’ partition coefficients, of 112 VOCs that have been suggested over the past decade as potential markers of cancer. With these data, we show that the cancer VOC concentrations in the blood and in the fat span over 12 and 8 orders of magnitude, respectively, in order to provide a specific counterpart concentration in the exhaled breath (e.g., 1 ppb). This finding suggests that these 112 different compounds have different storage compartments in the body and that their exhalation kinetics depends on one or a combination of the following factors: (i) the VOC concentrations in different parts of the body; (ii) the VOC synthesis and metabolism rates; (iii) the partition coefficients between tissue(s), blood and air; and (iv) the VOCs’ diffusion constants. Based on this analysis, we discuss how this knowledge allows modeling and simulating the behavior of a specific VOC under different sampling protocols (with and without exertion of effort). We end this review by a brief discussion on the potential role of these scenarios in screening and therapeutic monitoring of cancer.
On formation‐based sampling proxies and why they should not be used to correct the fossil record

The fossil record is a unique resource on the history of life, but it is well known to be incomplete. In a series of high‐profile papers, a residual modelling technique has been applied to correct the raw palaeodiversity signal for this bias and incompleteness, and the claim is made that the processed time series are more accurate than the raw data. We apply empirical and simulation approaches to test for correlation and directionality of any relationships between rock and fossil data. The empirical data comprise samples of the global fossil record through the Phanerozoic, and we use simulations to assess whether randomly sampled subsets of modelled data can be improved by application of the residual modelling technique. Our results show that using formation counts as a sampling proxy to correct the fossil record via residual modelling is ill founded. The supposedly independent model of sampling is information‐redundant with respect to the raw palaeodiversity data it seeks to correct, and so the outputs are generally likely to be further from the truth than the raw data. We recommend that students of palaeodiversity cease to use residual modelling estimates based on formation counts, and suggest that results from a substantial number of papers published in the past ten years require re‐evaluation.
Multiple phenotypes in phosphoglucomutase 1 deficiency.

BACKGROUND Congenital disorders of glycosylation are genetic syndromes that result in impaired glycoprotein production. We evaluated patients who had a novel recessive disorder of glycosylation, with a range of clinical manifestations that included hepatopathy, bifid uvula, malignant hyperthermia, hypogonadotropic hypogonadism, growth retardation, hypoglycemia, myopathy, dilated cardiomyopathy, and cardiac arrest. METHODS Homozygosity mapping followed by whole-exome sequencing was used to identify a mutation in the gene for phosphoglucomutase 1 (PGM1) in two siblings. Sequencing identified additional mutations in 15 other families. Phosphoglucomutase 1 enzyme activity was assayed on cell extracts. Analyses of glycosylation efficiency and quantitative studies of sugar metabolites were performed. Galactose supplementation in fibroblast cultures and dietary supplementation in the patients were studied to determine the effect on glycosylation. RESULTS Phosphoglucomutase 1 enzyme activity was markedly diminished in all patients. Mass spectrometry of transferrin showed a loss of complete N-glycans and the presence of truncated glycans lacking galactose. Fibroblasts supplemented with galactose showed restoration of protein glycosylation and no evidence of glycogen accumulation. Dietary supplementation with galactose in six patients resulted in changes suggestive of clinical improvement. A new screening test showed good discrimination between patients and controls. CONCLUSIONS Phosphoglucomutase 1 deficiency, previously identified as a glycogenosis, is also a congenital disorder of glycosylation. Supplementation with galactose leads to biochemical improvement in indexes of glycosylation in cells and patients, and supplementation with complex carbohydrates stabilizes blood glucose. A new screening test has been developed but has not yet been validated. (Funded by the Netherlands Organization for Scientific Research and others.).
Channels: The first five years

In January 2007, Landes Bioscience launched Channels, a scientific journal focused on ion channels, transporters and ion exchangers. Although there had been a number of journals that regularly published ion channel related research, there was no publication venue dedicated specifically to the ion channel and transporter fields. Despite being a new journal with no track record or impact factor, there was considerable interest in the community to make this journal a success, leading not only to the recruitment of a top tier Editorial Board, but also to a steady stream of submissions in the various categories published in the journal. The first key milestone and measure of success was listing on PubMed (indeed, approximately 70% of all applications for PubMed listings are unsuccessful). Shortly thereafter, Channels was listed on ISI and received its first impact factor of 1.5 in 2008, followed by a steady increase to 1.9 and 2.1 in 2009 and 2010, respectively. The journal now has close to 900 to total citations and an h factor of 13. Channels is also indexed on Scopus. Annual PDF downloads of Channels articles have increased from ~5,200 in 2008 to ~12,000 in 2011. Altogether, this shows that the journal has gained a foothold in the channels community and is on an upward trajectory. Channels continues to be issued on a bimonthly basis. Categories for articles include Research Articles, Reviews, Technical Reports, Meeting Reports and Article Addenda. The latter category allows authors to expand on previous work published in other journals and has proven to be quite popular. Channels publishes occasional Journal Club articles, which are a forum for graduate students and postdoctoral fellows to comment on exciting publications in the field. Finally, due to the efforts of Special Features Editor Dr. Andrew Braun, Channels publishes commentaries on exciting developments in the ion channel and transporter fields. Over the past five years, there have been a number of special thematic review issues Channels The first five years
Functional coupling constrains craniofacial diversification in Lake Tanganyika cichlids

Functional coupling, where a single morphological trait performs multiple functions, is a universal feature of organismal design. Theory suggests that functional coupling may constrain the rate of phenotypic evolution, yet empirical tests of this hypothesis are rare. In fish, the evolutionary transition from guarding the eggs on a sandy/rocky substrate (i.e. substrate guarding) to mouthbrooding introduces a novel function to the craniofacial system and offers an ideal opportunity to test the functional coupling hypothesis. Using a combination of geometric morphometrics and a recently developed phylogenetic comparative method, we found that head morphology evolution was 43% faster in substrate guarding species than in mouthbrooding species. Furthermore, for species in which females were solely responsible for mouthbrooding the males had a higher rate of head morphology evolution than in those with bi-parental mouthbrooding. Our results support the hypothesis that adaptations resulting in functional coupling constrain phenotypic evolution.
CSNIPER - Annotation-by-query for Non-canonical Constructions in Large Corpora

We present CSniper (Corpus Sniper), a tool that implements (i) a web-based multi-user scenario for identifying and annotating non-canonical grammatical constructions in large corpora based on linguistic queries and (ii) evaluation of annotation quality by measuring inter-rater agreement. This annotation-by-query approach efficiently harnesses expert knowledge to identify instances of linguistic phenomena that are hard to identify by means of existing automatic annotation tools.
TRPV4 Forms a Novel Ca2+ Signaling Complex With Ryanodine Receptors and BKCa Channels

Vasodilatory factors produced by the endothelium are critical for the maintenance of normal blood pressure and flow. We hypothesized that endothelial signals are transduced to underlying vascular smooth muscle by vanilloid transient receptor potential (TRPV) channels. TRPV4 message was detected in RNA from cerebral artery smooth muscle cells. In patch-clamp experiments using freshly isolated cerebral myocytes, outwardly rectifying whole-cell currents with properties consistent with those of expressed TRPV4 channels were evoked by the TRPV4 agonist 4&agr;-phorbol 12,13-didecanoate (4&agr;-PDD) (5 &mgr;mol/L) and the endothelium-derived arachidonic acid metabolite 11,12 epoxyeicosatrienoic acid (11,12 EET) (300 nmol/L). Using high-speed laser-scanning confocal microscopy, we found that 11,12 EET increased the frequency of unitary Ca2+ release events (Ca2+ sparks) via ryanodine receptors located on the sarcoplasmic reticulum of cerebral artery smooth muscle cells. EET-induced Ca2+ sparks activated nearby sarcolemmal large-conductance Ca2+-activated K+ (BKCa) channels, measured as an increase in the frequency of transient K+ currents (referred to as “spontaneous transient outward currents” [STOCs]). 11,12 EET–induced increases in Ca2+ spark and STOC frequency were inhibited by lowering external Ca2+ from 2 mmol/L to 10 &mgr;mol/L but not by voltage-dependent Ca2+ channel inhibitors, suggesting that these responses require extracellular Ca2+ influx via channels other than voltage-dependent Ca2+ channels. Antisense-mediated suppression of TRPV4 expression in intact cerebral arteries prevented 11,12 EET–induced smooth muscle hyperpolarization and vasodilation. Thus, we conclude that TRPV4 forms a novel Ca2+ signaling complex with ryanodine receptors and BKCa channels that elicits smooth muscle hyperpolarization and arterial dilation via Ca2+-induced Ca2+ release in response to an endothelial-derived factor.
Pragma based parallelization — Trading hardware efficiency for ease of use?

One major obstacle for a wide spread FPGA usage in general-purpose computing is the development tool flow that requires much higher effort than for pure software solutions. Convey Computer promises a solution to this problem for their HC-1 platform, where the FPGAs are configured to run as a vector processor and the software source code can be annotated with pragmas that guide an automated vectorization process. We investigate this approach for a stereo matching algorithm that has abundant parallelism and a number of different computational patterns. We note that for this case study the automated vectorization in its current state doesn't hold its productivity promise. However, we also show that using the Vector Personality can yield a significant speedups compared to CPU implementations in two of three investigated phases of the algorithm. Those speedups don't match custom FPGA implementations, but can come with much reduced development effort.
Exploiting wireless channel State information for throughput maximization

We consider the problem of scheduling packets over channels with time-varying quality. This problem has received a lot of attention lately in the context of devising methods for providing quality of service in wireless communications. Earlier work dealing with this problem considered two cases. One case is that the arrival rate vector is in the throughput region and then policies that stabilize the system are pursued. The other case is that all packet queues are saturated and then policies that optimize an objective function of the channel throughputs are investigated. In this paper, we address the case where no assumption on the arrival rates is made. We obtain a scheduling policy that maximizes the weighted sum of channel throughputs. Under the optimal policy, in the general case, the system may operate in a regime where some queues are stable, while the other become saturated. If stability for the whole system is at all possible, it is always achieved. The optimal policy is a combination of a criterion that gives priorities based on queue lengths and a strict priority rule. The scheduling mechanism switches between the two criteria based on thresholds on the queue lengths and is modulated by the availability of the channels. The analysis of the operation of the system involves the study of a vector process which in steady state has some of its components stable while others are unstable. We adopt a novel model for time-varying channel availability that dispenses with the statistical assumptions and makes a rigorous description of system dynamics possible.
Time-resolved FUSE photometric and spectroscopic observations: PG 1219+534, PG 1605+072, and PG 1613+426

We report the detection of pulsations in the far ultraviolet (FUV) light curves of PG 1219+534, PG 1605+072 and PG 1613+426 obtained with the Far Ultraviolet Spectroscopic Explorer (FUSE) in time–tagged mode (TTAG). Exposures of the order of a few ksec were sufficient to observe the main frequencies of PG 1219+534 and PG 1605+072 and confirm the detection of a pulsation mode at the surface of PG 1613+426 as reported from ground. For the first time we derive time–resolved spectroscopic FUSE data of a sdB pulsator (PG 1605+072) and comment on its line profile variation diagram (lpv diagram). We observe the phase shift between the maximum luminosity and the maximum radius to be consistent with the model of an adiabatic pulsator. We also present evidence that the line broadening previously reported is not caused by rotation but is rather an observational bias due to the rapid Doppler shift of the lines with 17 km s −1 amplitude. Thus our observations do not support the previous claim that PG 1605+072 is (or will evolve into) an unusually fast rotating degenerate dwarf. These results demonstrate the asteroseismological potential of the FUSE satellite which should be viewed as another powerful means of investigating stellar pulsations, along with the MOST and COROT missions.
Prediction of disulfide connectivity in proteins

MOTIVATION A major problem in protein structure prediction is the correct location of disulfide bridges in cysteine-rich proteins. In protein-folding prediction, the location of disulfide bridges can strongly reduce the search in the conformational space. Therefore the correct prediction of the disulfide connectivity starting from the protein residue sequence may also help in predicting its 3D structure. RESULTS In this paper we equate the problem of predicting the disulfide connectivity in proteins to a problem of finding the graph matching with the maximum weight. The graph vertices are the residues of cysteine-forming disulfide bridges, and the weight edges are contact potentials. In order to solve this problem we develop and test different residue contact potentials. The best performing one, based on the Edmonds-Gabow algorithm and Monte-Carlo simulated annealing reaches an accuracy significantly higher than that obtained with a general mean force contact potential. Significantly, in the case of proteins with four disulfide bonds in the structure, the accuracy is 17 times higher than that of a random predictor. The method presented here can be used to locate putative disulfide bridges in protein-folding. AVAILABILITY The program is available upon request from the authors. CONTACT Casadio@alma.unibo. it; Piero@biocomp.unibo. it.
Asymmetries in the Sequential Learning of Brand Associations: Implications for the Early Entrant Advantage

The highlighting effect occurs when the order in which consumers learn about brands determines the strength of association between these brands and their attributes. In four experiments, we find that consumers more strongly associate common attributes with early learned brands and unique attributes with late-learned brands. These findings imply an advantage for late entrants when unique attributes offer a higher value than attributes that are common to late and early entrants. We extend an attention-based model of associative learning to accommodate sequential learning of brand associations and predict when late versus early entrants will be able to sustain an advantage.
The Mammal Fauna of the Nakanai Mountains, East New Britain Province, Papua New Guinea

We surveyed mammals around three sites in the Nakanai Mountains of East New Britain, including one at higher elevation than any previous work in this area. The survey produced records of ten species of terrestrial mammals (three marsupials and seven rodents), six pteropodid bats, and ten insectivorous bats. At least three (possibly four) of the rodents are undescribed species, two of them representing new genera, and at least one (possibly two) of these species is an entirely new discovery, with no previous record. One of the captured bats is probably an undescribed species related to Nyctimene albiventer. Further study of the bats may reveal additional species of special interest, especially in the genus Miniopterus. The results of the Nakanai RAP survey fundamentally alter our perception of the mammal fauna of New Britain. Rather than having a depauperate subset of the New Guinean mammal fauna, New Britain has its own deeply endemic mammal fauna that includes at least two endemic genera of murine rodents as well as endemic species of at least four other murine genera. In addition, it also supports numerous distinctive species or subspecies of bats, many of them shared with New Ireland and/or the northern Solomon Islands. The mammal fauna of New Britain thus contains many mammalian taxa of global significance. Effective protection of the large tracts of pristine forests that exist in the Nakanai Mountains is of fundamental importance to the long-term conservation of these taxa.
Study on the mobile robot reconfiguration control methods

The control strategies of reconfiguration and obstacles negotiation are the intensive topic in the filed of leg-wheel hybrid robot. Based on the analysis of structure characters of leg-wheel hybrid robot and the disadvantage of early control method, this paper proposes a new reconfiguration control method in rough terrain and an auto-control method to get over channels, ridges etc. These control strategies are experimented in a six-leg-wheel hybrid robot which is designed by Shenyang Institute of Automation, and the results show that these control strategies can be effective used in rough terrain.
Vitroid – the robot system with an interface between a living neuronal network and outer world

We have developed a neuro-robot-hybrid system using a living neuronal network and a miniature moving robot. The living network of rat hippocampal neurons can distinguish patterns of action potentials evoked by different inputs, suggesting that a cultured neuronal network can represent particular states as symbols. We used a Khepera II robot and a robot made using a LEGO mindstorm NXT kit to interface with a living neuronal network and the outer world. We call the system ‘vitroid’. Vitroid has living neurons, a robot body, and direct coupling controllers to interface the neurons with the robot. Vitroid was able to perform obstacle avoidance behaviour with premised control rule sets.
Identification of Fungicidal 2,6-Disubstituted Quinolines with Activity against Candida Biofilms

We have identified two subseries of 2,6-disubstituted quinolines, consisting of 6-amide and 6-urea derivatives, which are characterized by fungicidal activity against Candida albicans with minimal fungicidal concentration (MFC) values < 15 µM. The 6-amide derivatives displayed the highest fungicidal activity against C. albicans, in particular compounds 1, 5 and 6 characterized by MFC values of 6.25–12.5 µM. Compounds 1 and 5 of this series displayed fungicidal activity against the emerging pathogen Candida glabrata(MFC < 50 µM). The 6-amide derivatives 1, 2, 5, and 6 and the 6-urea derivatives 10, 12, 13 and 15 could also eradicate C. albicans biofilms. We found that the 6-urea derivatives 10, 13, and 15 induced accumulation of endogenous reactive oxygen species in Candida albicans biofilms.
Barriers in U . S . Benchmark Bond Yields

In this paper, we examine United States Treasury benchmark bond yields for the existence of barriers. We find evidence of yield barriers at integer multiples of 0.25% (e.g., 6.00%, 6.25%, 6.50%, 6.75%) in the widely followed 30-year and 10-year benchmark bonds. The robustness of these results are confirmed with Monte Carlo simulations and by the absence of barriers in several control series. However, using market prediction tests we find that barrier effects do not lead to significant predictable influences in the conditional mean or volatility of these yield series. Using Monte Carlo simulations of yield series with built-in barriers, we demonstrate that the absence of predictability in the conditional mean or volatility are not necessary conditions for the existence of barriers. We also employ the built-in barrier simulations to demonstrate the high sensitivity of barrier test results to the choice of alternative hypotheses.
Impact of a Process Variation on Nanowire and Nanotube Device Performance

In this paper, we present an in-depth analysis of the nanowire and nanotube device performance under process variability. Although every process parameter variation drastically affects the conventional MOSFET performance, we found that nanowire/nanotube FETs are significantly less sensitive to many process parameter variations due to their inherent device structures and geometric properties. It is observed that a two-input nand gate with nanowire or nanotube FETs shows a more than four times less performance variation than its bulk MOSFET counterpart and about two times less than FinFET devices at the 45 and 32 nm technologies, respectively. In other words, nanowire/nanotube FETs will have a larger margin for process parameter variations than bulk and FinFET devices for an allowable performance variation limit. While it is evident that process variations are going to be a major limiting factor for conventional MOSFET devices in future generations, this analysis is expected to further encourage nanowire and nanotube research for high-performance circuit applications.