Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying Insects with Incomplete DNA Barcode Libraries, African Fruit Flies (Diptera: Tephritidae) as a Test Case

We propose a general working strategy to deal with incomplete reference libraries in the DNA barcoding identification of species. Considering that (1) queries with a large genetic distance with their best DNA barcode match are more likely to be misidentified and (2) imposing a distance threshold profitably reduces identification errors, we modelled relationships between identification performances and distance thresholds in four DNA barcode libraries of Diptera (n = 4270), Lepidoptera (n = 7577), Hymenoptera (n = 2067) and Tephritidae (n = 602 DNA barcodes). In all cases, more restrictive distance thresholds produced a gradual increase in the proportion of true negatives, a gradual decrease of false positives and more abrupt variations in the proportions of true positives and false negatives. More restrictive distance thresholds improved precision, yet negatively affected accuracy due to the higher proportions of queries discarded (viz. having a distance query-best match above the threshold). Using a simple linear regression we calculated an ad hoc distance threshold for the tephritid library producing an estimated relative identification error <0.05. According to the expectations, when we used this threshold for the identification of 188 independently collected tephritids, less than 5% of queries with a distance query-best match below the threshold were misidentified. Ad hoc thresholds can be calculated for each particular reference library of DNA barcodes and should be used as cut-off mark defining whether we can proceed identifying the query with a known estimated error probability (e.g. 5%) or whether we should discard the query and consider alternative/complementary identification methods.
Revisiting the Processing of Internal and External Features of Unfamiliar Faces: The Headscarf Effect

Five experiments are reported in which the relative importance of internal and external features for unfamiliar face identification are examined by a matching task. In experiments 1–3, Egyptian adults showed a robust internal-feature advantage for matching photographs of Egyptian faces. In experiment 4, a cross-cultural comparison between the ability of Egyptian and British adults to match the internal and external features of unfamiliar Egyptian and British faces was made. Once again, Egyptians showed an internal-feature advantage, for all faces. In contrast, British observers—and also Egyptian children in experiment 5—showed external-feature advantages consistent with previous research. We attribute this contrast to the long-term experience of Egyptians in perceiving and recognising faces with headscarves, which might develop more expertise in processing the internal than the external features of unfamiliar faces.
Computational humor

In an effort to focus on tractable problems, computational natural language understanding systems have typically addressed language phenomena that are amenable to combinatorial approaches using static and stereotypical semantic representations. Although such approaches are adequate for much of language, they're not easily extended to capture humans' more creative language interpretation capacities. This paper proposes a model of humor comprehension based on frame-shifting within a simulation-based natural-language-understanding system.
Hybrid bayesian variational scheme to handle parameter selection in total variation signal denoising

Change-point detection problems can be solved either by variational approaches based on total variation or by Bayesian procedures. The former class leads to small computational time but requires the choice of a regularization parameter that significantly impacts the achieved solution and whose automated selection remains a challenging problem. Bayesian strategies avoid this regularization parameter selection, at the price of high computational costs. In this contribution, we propose a hybrid Bayesian variational procedure that relies on the use of a hierarchical Bayesian model while preserving the computational efficiency of total variation optimization procedures. Behavior and performance of the proposed method compare favorably against those of a fully Bayesian approach, both in terms of accuracy and of computational time. Additionally, estimation performance are compared to the Stein unbiased risk estimate, for which the knowledge of the noise variance is needed.
Integration and simplification of QoS guarantee and multicasting for a New-Generation network

In this paper, we clarify problems related to QoS guarantee and multicasting on the Internet, and suggest principles of solving the problems and implementing QoS guarantee and multicasting at the same time by means of integrating multicasting and QoS guarantee for a New-Generation Network (NwGN). These principles also simplify QoS/multicast routing protocols.
Backyard chicken keeping in the Greater London Urban Area: welfare status, biosecurity and disease control issues

1. The aim of the study was to collect baseline data on welfare, biosecurity and diseases of backyard chickens kept in the Greater London Urban Area (GLUA), United Kingdom (UK). 2. A total of 65 backyard chicken flock-keepers were recruited from May to July 2010 through adverts on websites, at City farms, veterinary practices and pet feed stores and surveyed by means of a questionnaire. A total of 30 responses were suitable for analysis. 3. Information on keepers’ and flocks’ characteristics, housing and husbandry practices and owners’ knowledge of health problems in chickens and zoonotic diseases was collected. A welfare assessment protocol was developed and the flocks assessed accordingly. 4. Results showed that chickens were generally provided with living conditions that allowed them to perform their natural behaviours. 5. Most of the flock owners did not comply with the regulations of the Department for Environment, Food and Rural Affairs (Defra) on the feeding of catering waste. 6. Disease prevention measures such as vaccination and biosecurity, including limiting the access of human visitors, wild birds and rodents to the flocks were rare. 7. A lack of avian and zoonotic disease knowledge and awareness among the owners has implications for disease control and highlights the need for improved communication between owners, authorities and veterinarians.
Comparison of different drying methods on the physical properties, bioactive compounds and antioxidant activity of raspberry powders.

BACKGROUND Dehydration has been considered as one of the traditional but most effective techniques for perishable fruits. Raspberry powders obtained after dehydration can be added as ingredients into food formulations such as bakery and dairy products. In this study, raspberry powders obtained by hot air drying (HAD), infrared radiation drying (IRD), hot air and explosion puffing drying (HA-EPD), infrared radiation and microwave vacuum drying (IR-MVD) and freeze drying (FD) were compared on physical properties, bioactive compounds and antioxidant activity. RESULTS Drying techniques affected the physical properties, bioactive compounds and antioxidant activity of raspberry powders greatly. FD led to significantly higher (P < 0.05) values of water solubility (45.26%), soluble solid (63.46%), hygroscopicity (18.06%), color parameters and anthocyanin retention (60.70%) of raspberry powder compared with other drying methods. However, thermal drying techniques, especially combined drying methods, were superior to FD in final total polyphenol content, total flavonoid content and antioxidant activity. The combined drying methods, especially IR-MVD, showed the highest total polyphenol content (123.22 g GAE kg(-1) dw) and total flavonoid content (0.30 g CAE kg(-1) dw). Additionally, IR-MVD performed better in antioxidant activity retention. CONCLUSION Overall, combined drying methods, especially IR-MVD, were found to result in better quality of raspberry powders among the thermal drying techniques. IR-MVD could be recommended for use in the drying industry because of its advantages in time saving and nutrient retention.
Repetitive Myocardial Ischemia Promotes Coronary Growth in the Adult Mammalian Heart

Background Coronary artery disease and ischemic cardiomyopathy represent the leading cause of heart failure and continue to grow at exponential rates. Despite widespread availability of coronary bypass surgery and percutaneous coronary intervention, subsequent ischemic events and progression to heart failure continue to be common occurrences. Previous studies have shown that a subgroup of patients develop collateral blood vessels that serve to connect patent and occluded arteries and restore perfusion to ischemic territories. The presence of coronary collaterals has been correlated with improved clinical outcomes; however, the molecular mechanisms governing this process remain largely unknown. Methods and Results To date, no mouse models of coronary arterial growth have been described. Using a closed‐chest model of myocardial ischemia, we have demonstrated that brief episodes of repetitive ischemia are sufficient to promote the growth of both large coronary arteries and the microvasculature. Induction of large coronary artery and microvascular growth resulted in improvements in myocardial perfusion after prolonged ischemia and protected from subsequent myocardial infarction. We further show that repetitive ischemia did not lead to increased expression of classic proangiogenic factors but instead resulted in activation of the innate immune system and recruitment of macrophages to growing blood vessels. Conclusions These studies describe a novel model of coronary angiogenesis and implicate the cardiac macrophage as a potential mediator of ischemia‐driven coronary growth.
Group-based hyperspectral image denoising using low rank representation

For the hyperspectral image (HSI) denoising problem, we propose a group-based low rank representation (GLRR) method. A corrupted HSI is divided into overlapping patches and the similar patches are combined into a group. The group is de-noised as a whole using low rank representation (LRR). Our method can employ both the local similarity within the patch and the nonlocal similarity across the patches within a group simultaneously, while nonlocal similar patches within the group can bring extra structure information for the corrupted patch, which makes the noise more significant to be detected as outliers. Since the uncorrupted patches have an intrinsic low-rank structure, LRR is employed for the denoising of the patch group. Both simulated and real data are used in the experiments. The effectiveness of our method is proved both qualitatively and quantitatively.
The effect of snoring and obstructive sleep apnea on the sleep quality of bed partners.

OBJECTIVE To measure the effect of snoring and obstructive sleep apnea (OSA) on the sleep of snorers' bed partners and to determine whether a bed partner's sleep improves when snoring and OSA are treated. MATERIALS AND METHODS We studied 10 married couples in which 1 member was undergoing polysomnography to evaluate suspected OSA. The patients and their spouses underwent simultaneous polysomnography. Midway through the 1-night study, the patients received nasal continuous positive airway pressure (CPAP) with the pressure adjusted to eliminate snoring and obstructive breathing events. Apnea-hypopnea index (episodes/hours of sleep time), arousal index (arousals/hours of sleep time), and sleep efficiency (percent time asleep) were calculated to measure sleep quality. RESULTS The patients (all male) demonstrated a median (range) apnea-hypopnea index of 26 (3-75) that decreased to 7 (0-34) during the trial of nasal CPAP therapy (P < .05). During the CPAP trial, the median (range) arousal index of the spouses decreased from 21 (14-34) to 12 (4-27) (P < .01), and the spouses' median (range) sleep efficiency increased from 74% (56%-80%) to 87% (64%-95%) (P < .01). CONCLUSION The elimination of snoring and OSA in these patients was associated with an improvement in the quality of their bed partners' sleep, as indicated by improved sleep efficiency and continuity, even when the spouses had been habitually exposed to snoring and OSA. Assuming that 480 minutes were spent in bed for sleep, a 13% improvement in sleep efficiency (i.e., from 74% to 87%) translates to an additional 62 minutes of sleep per night for the spouses of snorers with OSA.
Dissemination of contact activation in plasma by plasma kallikrein

The dissemination of contact activation of plasma was examined by measuring the cleavage of Hageman factor (HF) molecules on two separate sets of kaolin particles, one of which contained all of the components of the contact activation system, HF, prekallikrein (PK) and high molecular weight kininogen (HMWK) in whole normal plasma, and the second set of particles containing only HF and HMWK, being prepared with PK-deficient plasma. After mixing of the particles, cleavage of HF on the second set of particles occurred at a rate similar to that occurring on the first set of particles. This indicated that rapid dissemination and burst of activity of the contact reaction takes place in fluid phase. A supernatant factor, responsibel for the dissemination of the contact reaction, was identified as kallikrein. A rapid appearance of cleaved PK (kallikrein) and HMWK on both the kaolin surface and in the supernate was observed. Within 40 s, > 70-80% of the PK and HMWK in the supernate was cleaved. On the surface, approximately 70% of each radiolabeled protein was cleaved at the earliest measurement. Cleavage of PK by activated HF occurred at least 17 times faster on the surface than in the fluid phase, as virtually no cleavage of PK occurred in fluid phase. Each molecule of surface-bound, activated HF was calculated to cleave at a minimum, 20 molecules of PK per minute. It is concluded that the contact activaton of plasma may be divided into three phases: (a) the reciprocal activation of a few molecules of zymogen HF and PK on the surface, with HMWK acting as cofactor to bring these molecules into apposition; (b) the rapid release of kallikrein into the fluid phase and the continued conversion of PK to kallikrein by each surface-bound molecule of activated HF; and (c) the activation by fluid-phase kallikrein of multiple surface-bound HF molecules, and the cleavage of multiple molecules of MHWK both in fluid phase and on the surface by the soluble kallikrein. The evidence suggests that steps b and c account for a great majority of the generation of contact activation of plasma.
Genetic Differentiation among Mountain Island Populations of the Striped Plateau Lizard, Sceloporus virgatus (Squamata: Phrynosomatidae)

Abstract We used DNA sequences from several mitochondrial regions (ND2, ND4, and adjacent tRNAs) to examine genetic structure and divergence among populations of the Striped Plateau Lizard, Sceloporus virgatus. In the northern portion of this species' range, populations occupy mesic habitats at higher elevations in the mountain ranges of the Madrean Archipelago, and are thus isolated by dry, inhospitable valleys. High genetic differentiation among four of these ranges, and low genetic variation within ranges, imply that gene flow among them has been limited and isolation is ancient, having occurred hundreds of thousands or even millions of years ago. These results conflict with expectations derived from geographical and paleontological data that indicate ecological conditions favoring gene flow occurred as recently as 11,000 years ago.
Endurance training alters the biophysical properties of hindlimb motoneurons in rats

The purpose of the study was to determine the effect of daily endurance treadmill training (2 h/day, 30 m/min) on motoneuron biophysical properties. Electrophysiological properties of tibial motoneurons were measured in situ in anesthetized (ketamine/xylazine) control and trained rats using sharp glass microelectrodes. Motoneurons from trained rats had significantly hyperpolarized resting membrane potentials and spike trigger levels, and faster antidromic spike rise‐times. “Fast” motoneurons (after‐hyperpolarization half‐decay time <20 ms) in trained rats also had a significantly larger mean cell capacitance than those in control rats, suggesting that they were larger, although this had no effect on indices of excitability (rheobase, cell input resistance). Motoneurons are thus targets for activity‐induced adaptations, which may have clinical significance for the role of physical activity as a therapeutic modality in cases of neurological deficit. The specific adaptations noted, which reflect alterations in ionic conductances, may serve to offset decreases in membrane excitability that occur during sustained excitation. © 2003 Wiley Periodicals, Inc. Muscle Nerve 27: 228–236, 2003
NEER: An Unsupervised Method for Named Entity Evolution Recognition

High impact events, political changes and new technologies are reflected in our language and lead to constant evolution of terms, expressions and names. Not knowing about names used in the past for referring to a named entity can severely decrease the performance of many computational linguistic algorithms. We propose NEER, an unsupervised method for named entity evolution recognition independent of external knowledge sources. We find time periods with high likelihood of evolution. By analyzing only these time periods using a sliding window co-occurrence method we capture evolving terms in the same context. We thus avoid comparing terms from widely different periods in time and overcome a severe limitation of existing methods for named entity evolution, as shown by the high recall of 90% on the New York Times corpus. We compare several relatedness measures for filtering to improve precision. Furthermore, using machine learning with minimal supervision improves precision to 94%.
Chemical Constituents of Muehlenbeckia tamnifolia (Kunth) Meisn (Polygonaceae) and Its In Vitro α-Amilase and α-Glucosidase Inhibitory Activities

The phytochemical investigation of Muehlenbeckia tamnifolia, collected in Loja-Ecuador, led to the isolation of nine known compounds identified as: lupeol acetate (1); cis-p-coumaric acid (2); lupeol (3); β-sitosterol (4) trans-p-coumaric acid (5); linoleic acid (6) (+)-catechin (7); afzelin (8) and quercitrin (9). The structures of the isolated compounds were determined based on analysis of NMR and MS data, as well as comparison with the literature. The hypoglycemic activity of crude extracts and isolated compounds was assessed by the ability to inhibit α-amylase and α-glucosidase enzymes. The hexane extract showed weak inhibitory activity on α-amylase, with an IC50 value of 625 µg·mL−1, while the other extracts and isolated compounds were inactive at the maximum dose tested. The results on α-glucosidase showed more favorable effects; the hexanic and methanolic extracts exhibited a strong inhibitory activity with IC50 values of 48.22 µg·mL−1 and 19.22 µg·mL−1, respectively. Four of the nine isolated compounds exhibited strong inhibitory activity with IC50 values below 8 µM, much higher than acarbose (377 uM). Linoleic acid was the most potent compound (IC50 = 0.42 µM) followed by afzelin, (+)-catechin and quercitrin.
Optimal proxy cache allocation for efficient streaming media distribution

In this paper, we address the problem of efficiently streaming a set of heterogeneous videos from a remote server through a proxy to multiple asynchronous clients so that they can experience playback with low startup delays. We develop a technique to analytically determine the optimal proxy prefix cache allocation to the videos that minimizes the aggregate network bandwidth cost. We integrate proxy caching with traditional server-based reactive transmission schemes such as batching, patching and stream merging to develop a set of proxy-assisted delivery schemes. We quantitatively explore the impact of the choice of transmission scheme, cache allocation policy, proxy cache size, and availability of unicast versus multicast capability, on the resultant transmission cost. Our evaluations show that even a relatively small prefix cache (10%-20% of the video repository) is sufficient to realize substantial savings in transmission cost. We find that carefully designed proxy-assisted reactive transmission schemes can produce significant cost savings even in predominantly unicast environments such as the Internet.
Improved error reporting for software that uses black-box components

An error occurs when software cannot complete a requested action as a result of some problem with its input, configuration, or environment. A high-quality error report allows a user to understand and correct the problem. Unfortunately, the quality of error reports has been decreasing as software becomes more complex and layered. End-users take the cryptic error messages given to them by programsand struggle to fix their problems using search engines and support websites. Developers cannot improve their error messages when they receive an ambiguous or otherwise insufficient error indicator from a black-box software component. We introduce Clarify, a system that improves error reporting by classifying application behavior. Clarify uses minimally invasive monitoring to generate a behavior profile, which is a summary of the program's execution history. A machine learning classifier uses the behavior profile to classify the application's behavior, thereby enabling a more precise error report than the output of the application itself. We evaluate a prototype Clarify system on ambiguous error messages generated by large, modern applications like gcc, La-TeX, and the Linux kernel. For a performance cost of less than 1% on user applications and 4.7% on the Linux kernel, the proto type correctly disambiguates at least 85% of application behaviors that result in ambiguous error reports. This accuracy does not degrade significantly with more behaviors: a Clarify classifier for 81 La-TeX error messages is at most 2.5% less accurate than a classifier for 27 LaTeX error messages. Finally, we show that without any human effort to build a classifier, Clarify can provide nearest-neighbor software support, where users who experience a problem are told about 5 other users who might have had the same problem. On average 2.3 of the 5 users that Clarify identifies have experienced the same problem.
Paratransgenic Control of Vector Borne Diseases

Conventional methodologies to control vector borne diseases with chemical pesticides are often associated with environmental toxicity, adverse effects on human health and the emergence of insect resistance. In the paratransgenic strategy, symbiotic or commensal microbes of host insects are transformed to express gene products that interfere with pathogen transmission. These genetically altered microbes are re-introduced back to the insect where expression of the engineered molecules decreases the host's ability to transmit the pathogen. We have successfully utilized this strategy to reduce carriage rates of Trypanosoma cruzi, the causative agent of Chagas disease, in the triatomine bug, Rhodnius prolixus, and are currently developing this methodology to control the transmission of Leishmania donovani by the sand fly Phlebotomus argentipes. Several effector molecules, including antimicrobial peptides and highly specific single chain antibodies, are currently being explored for their anti-parasite activities in these two systems. In preparation for eventual field use, we are actively engaged in risk assessment studies addressing the issue of horizontal gene transfer from the modified bacteria to environmental microbes.