Miracle-dz/UniFAR-FTUs huggingface dataset:
Database-Guided Discovery of Potent Peptides to Combat HIV-1 or Superbugs

Antimicrobial peptides (AMPs), small host defense proteins, are indispensable for the protection of multicellular organisms such as plants and animals from infection. The number of AMPs discovered per year increased steadily since the 1980s. Over 2,000 natural AMPs from bacteria, protozoa, fungi, plants, and animals have been registered into the antimicrobial peptide database (APD). The majority of these AMPs (>86%) possess 11–50 amino acids with a net charge from 0 to +7 and hydrophobic percentages between 31–70%. This article summarizes peptide discovery on the basis of the APD. The major methods are the linguistic model, database screening, de novo design, and template-based design. Using these methods, we identified various potent peptides against human immunodeficiency virus type 1 (HIV-1) or methicillin-resistant Staphylococcus aureus (MRSA). While the stepwise designed anti-HIV peptide is disulfide-linked and rich in arginines, the ab initio designed anti-MRSA peptide is linear and rich in leucines. Thus, there are different requirements for antiviral and antibacterial peptides, which could kill pathogens via different molecular targets. The biased amino acid composition in the database-designed peptides, or natural peptides such as θ-defensins, requires the use of the improved two-dimensional NMR method for structural determination to avoid the publication of misleading structure and dynamics. In the case of human cathelicidin LL-37, structural determination requires 3D NMR techniques. The high-quality structure of LL-37 provides a solid basis for understanding its interactions with membranes of bacteria and other pathogens. In conclusion, the APD database is a comprehensive platform for storing, classifying, searching, predicting, and designing potent peptides against pathogenic bacteria, viruses, fungi, parasites, and cancer cells.
Computability Results Used in Differential Geometry

Abstract Topologists Nabutovsky and Weinberger discovered how to embed computably enumerable (c.e.) sets into the geometry of Riemannian metrics modulo diffeomorphisms. They used the complexity of the settling times of the c.e. sets to exhibit a much greater complexity of the depth and density of local minima for the diameter function than previously imagined. Their results depended on the existence of certain sequences of c.e. sets, constructed at their request by Csima and Soare, whose settling times had the necessary dominating properties. Although these computability results had been announced earlier, their proofs have been deferred until this paper. Computably enumerable sets have long been used to prove undecidability of mathematical problems such as the word problem for groups and Hilbert's Tenth Problem. However, this example by Nabutovsky and Weinberger is perhaps the first example of the use of c.e. sets to demonstrate specific mathematical or geometric complexity of a mathematical structure such as the depth and distribution of local minima.
Abundance, Diversity, and Activity of Ammonia-Oxidizing Prokaryotes in the Coastal Arctic Ocean in Summer and Winter

ABSTRACT Ammonia oxidation, the first step in nitrification, is performed by certain Beta- and Gammaproteobacteria and Crenarchaea to generate metabolic energy. Ammonia monooxygenase (amoA) genes from both Bacteria and Crenarchaea have been found in a variety of marine ecosystems, but the relative importance of Bacteria versus Crenarchaea in ammonia oxidation is unresolved, and seasonal comparisons are rare. In this study, we compared the abundance of betaproteobacterial and crenarchaeal amoA genes in the coastal Arctic Ocean during summer and winter over 2 years. Summer and winter betaproteobacterial amoA clone libraries were significantly different, although the gene sequences were similar to those found in temperate and polar environments. Betaproteobacterial and crenarchaeal amoA genes were 30- to 115-fold more abundant during the winter than during the summer in both years of the study. Archaeal amoA genes were more abundant than betaproteobacterial amoA genes in the first year, but betaproteobacterial amoA was more abundant than archaeal amoA the following year. The ratio of archaeal amoA gene copies to marine group I crenarchaeal 16S rRNA genes averaged 2.9 over both seasons and years, suggesting that ammonia oxidation was common in Crenarchaea at this location. Potential nitrification rates, as well as the total amoA gene abundance, were highest in the winter when competition with phytoplankton was minimal and ammonium concentrations were the highest. These results suggest that ammonium concentrations were important in determining the rates of ammonia oxidation and the abundance of ammonia-oxidizing Betaproteobacteria and Crenarchaea.
Neuroprotective effects of estradiol in the adult rat hippocampus: Interaction with insulin‐like growth factor‐I signalling

We have previously shown that 17‐β‐estradiol protects neurons in the dentate gyrus from kainic acid‐induced death in vivo. To analyse whether this effect is mediated through estrogen receptors and through cross‐talk between steroid and insulin‐like growth factor (IGF) systems, we have concomitantly administered antagonists of estrogen receptor (ICI 182,780) or the IGF‐I receptor (JB1) with estradiol. In addition, we have also administered IGF‐I with or without the estrogen receptor antagonist. JB1 (20 μg/ml), ICI 182,780 (10‐7 M), and IGF‐I (100 μg/ml) were delivered into the left lateral ventricle of young ovariectomized rats via an Alzet osmotic minipump (0.5 μl/hr) for 2 weeks. All rats received kainic acid (7 mg/Kg b.w.) or vehicle i.p. injections at day 7 after minipump implant. Also on day 7, rats treated i.c. v.with only ICI 182,780 or JB1 received a single i.p. injection of 17‐β‐estradiol (150 μg/rat) or vehicle. On day 14 after minipump implant, the rats were killed, brains processed, and the number of surviving hilar neurons estimated by the optical disector technique. Both IGF‐I and estradiol treatments resulted in over 90% survival of hilar neurons. The neuroprotective action of estradiol was blocked by ICI 182,780 and by JB1. Furthermore, IGF‐I enhancement of neuronal survival was significantly reduced by ICI 182,780. These results indicate that in this model of hippocampal lesion, the neuroprotective effect of estradiol depends both on estrogen receptors and IGF‐I receptors, while the protection exerted by IGF‐I depends also on estrogen receptors. In conclusion, an interaction of estrogen receptor and IGF‐I receptor signalling may mediate neuroprotection in the adult rat hippocampus. J. Neurosci. Res. 58:815–822, 1999. © 1999 Wiley‐Liss, Inc.
Searching for Speciation Genes: Molecular Evidence for Selection Associated with Colour Morphotypes in the Caribbean Reef Fish Genus Hypoplectrus

Closely related species that show clear phenotypic divergence, but without obvious geographic barriers, can provide opportunities to study how diversification can occur when opportunities for allopatric speciation are limited. We examined genetic divergence in the coral reef fish genus Hypoplectrus (family: Serranidae), which comprises of 10–14 morphotypes that are distinguished solely by their distinct colour patterns, but which show little genetic differentiation. Our goal was to detect loci that show clear disequilibrium between morphotypes and across geographical locations. We conducted Amplified Fragment Length Polymorphism molecular analysis to quantify genetic differentiation among, and selection between, morphotypes. Three loci were consistently divergent beyond neutral expectations in repeated pair-wise morphotype comparisons using two different methods. These loci provide the first evidence for genes that may be associated with colour morphotype in the genus Hypoplectrus.
Investigation of Ground Level and Remote-Sensed Data for Habitat Classification and Prediction of Survival of Ixodes scapularis in Habitats of Southeastern Canada

Abstract In southeastern Canada, most populations of Ixodes scapularis Say, the Lyme disease vector, occur in Carolinian forests. Climate change projections suggest a northward range expansion of I. scapularis this century, but it is unclear whether more northerly habitats are suitable for I. scapularis survival. In this study, we assessed the suitability of woodlands of the Lower Great Lakes/St. Lawrence Plain region for I. scapularis by comparing tick egg survival in four different woodlands. Woodlands where I. scapularis are established, and sand dune where I. scapularis do not survive, served as positive and negative control sites, respectively. At two woodland sites, egg survival was the same as at the positive control site, but at two of the sites survival was significantly less than either the positive control site, or one of the other test sites. Egg survival in all woodland sites was significantly higher than in the sand dune site. Ground level habitat classification discriminated among woodlands in which tick survival differed. The likelihood that I. scapularis populations could persist in the different habitats, as deduced using a population model of I. scapularis, was significantly associated with variations in Landsat 7 ETM+ data (normalized difference vegetation index [NDVI] and Tasselled Cap indices). The NDVI index predicted habitat suitability at Long Point, Ontario, with high sensitivity but moderate specificity. Our study suggests that I. scapularis populations could establish in more northerly woodland types than those in which they currently exist. Suitable habitats may be detected by ground-level habitat classification, and remote-sensed data may assist this process.
Water mass dynamics in Balikpapan Bay, Eastern Kalimantan Indonesia

Balikpapan Bay (BB) located 90 km southwest of Delta Mahakam is one of estuarine systems in eastern Kalimantan directly flows into Makassar Strait. Dimension of BB is about 36 km length and between 1-14 km width, with mouth is wider than head of the bay. Water depth is much deeper (18 m) at the middle part of the bay. More than 10 secondary rivers flow into the bay to contribute large amount of freshwater mass flux. To understand physical properties and water mass dynamics, field measurement during high and low tides were conducted. The results shows that the warmer and saltier water mass are dominant at the entrance of the bay at flood period. Warmer and less salty water mass remain in the inner bay. However, during ebb, salinity is slightly decreased near the entrance and freshwater are observed in the inner bay. During both high and low tides condition, vertical stratification of water mass is very weak. The model demonstrates that this is related to large seawater flux brought by flood current from coastal waters, as well as small freshwater influx from river runoffs. Hence, the tidal dynamics significantly controls stratification and dynamics of water mass in the bay.
Use of a reference material proposed by the International Federation of Clinical Chemistry and Laboratory Medicine to evaluate analytical methods for the determination of plasma lipoprotein(a).

BACKGROUND As part of the NIH/National Heart, Lung and Blood Institute Contract for the Standardization of Lipoprotein(a) [Lp(a)] Measurements, a study was performed in collaboration with the IFCC Working Group for the Standardization of Lp(a) Assays. The aims of the study, performed with the participation of 16 manufacturers and 6 research laboratories, were to evaluate the IFCC proposed reference material (PRM) for its ability to transfer an accuracy-based value to the immunoassay calibrators and to assess concordance in results among different methods. METHODS Two different purified Lp(a) preparations with protein mass concentrations determined by amino acid analysis were used to calibrate the reference method. A Lp(a) value of 107 nmol/L was assigned to PRM. After uniformity of calibration was demonstrated in the 22 evaluated systems, Lp(a) was measured on 30 fresh-frozen sera covering a wide range of Lp(a) values and apolipoprotein(a) [apo(a)] sizes. RESULTS The among-laboratory CVs for these samples (6-31%) were, in general, higher than those obtained for PRM (2.8%) and the quality-control samples (14%, 12%, and 9%, respectively), reflecting the broad range of apo(a) sizes in the 30 samples and the sensitivity of most methods to apo(a) size heterogeneity. Thus, although all of the assays were uniformly calibrated through the use of PRM, no uniformity in results was achieved for the isoform-sensitive methods. CONCLUSIONS Linear regression analyses indicated that to various degrees, apo(a) size heterogeneity affects the outcome of the immunochemical methods used to measure Lp(a). We have also shown that the inaccuracy of Lp(a) values determined by methods sensitive to apo(a) size significantly affects the assessment of individual risk status for coronary artery disease.
Advances in Radiotherapy in Operable Rectal Cancer

Aims: Radiotherapy (RT) reduces local recurrence in rectal cancer but the optimal treatment schedule is unknown. Relevant questions in designing optimal therapy are set out. This review identifies evidence that influences current practice and shapes future trials in treatment of operable rectal cancer. Methods: PubMed and MEDLINE search. Results: RT reduces local recurrence and pre-operative treatment is superior to post-operative treatment. Longer interval to surgery and concurrent chemotherapy are associated with greater downstaging, although influence on sphincter preservation and survival is minimal. Short-course RT (SCRT) demonstrates lower recurrence, but with long-term dysfunction and minimal survival benefit. The role of SCRT should be re-evaluated to encompass new criteria/areas. Conclusion: SCRT should be used selectively rather than as a blanket treatment policy. SCRT compounds functional morbidity caused by mesorectal excision which may be excessive in some patient groups, especially early-stage rectal cancer or frail elderly patients. RT and local excision may be a feasible surgical alternative in these groups. Alternatively, SCRT and delayed surgery may be a future alternative to current long-course chemoradiotherapy. As survival is only marginally affected despite low local recurrence, future trials should aim to address metastatic disease. End points which incorporate function and quality of life must be used.
Frequency and Predictors of Adverse Health Outcomes in Older Medicare Beneficiaries Discharged From the Emergency Department

Background:Older adults who are discharged from the emergency department (ED) may be at risk for subsequent adverse outcomes; however, this has not been fully investigated in national, population-based samples. The goal of this study was to determine the frequency and predictors of adverse outcomes among older adults discharged from the ED. Design:Secondary analysis of data from the Medicare Current Beneficiary Survey. Subjects:A total of 1851 community-dwelling, Medicare fee-for-service enrollees, ≥65 years old who were discharged from the ED between January 2000 and September 2002. Measures:The primary dependent variable was time to first adverse outcome defined as any repeat outpatient ED visit, hospital admission, nursing home admission or death within 90 days of the index ED visit. Results:Six hundred twenty-three of 1851 subjects (32.9%) discharged from the ED experienced an adverse outcome within 90 days of the index visit; 17.2% returned to the ED but were not admitted, 18.3% were hospitalized, 2.6% were admitted to a nursing home, and 4.1% died. Patients who were older [hazard ratios (HR), 1.01; confidence interval (CI), 1.00–1.02], with more chronic health conditions (HR, 1.12; CI, 1.07–1.19), Medicaid insurance (HR, 1.42; CI, 1.11–1.82), and recent ED (HR, 1.46; CI, 1.17–1.82) or hospital use (HR, 1.80; CI, 1.50–2.17) were at particularly high risk. Conclusions:A substantial proportion of older Medicare beneficiaries in this study experienced an adverse outcome after ED discharge. Further study is needed to determine whether simple prediction tools based on these identified risk factors may be useful in predicting adverse outcomes in this vulnerable population.
Discriminative recognition rate estimation for N-best list and its application to N-best rescoring

Techniques for estimating recognition rates without using reference transcriptions are essential if we are to judge whether or not speech recognition technology is applicable to a new task. We have proposed a discriminative recognition rate estimation (DRRE) method for 1-best recognition hypotheses and shown its good estimation performance experimentally. In this paper, we extend our DRRE to N-best lists of recognition hypotheses by modifying its feature extraction procedures and efficiently selecting N-best hypotheses for its discriminative model training. In addition, we apply our extended DRRE to N-best rescoring. In the experiments, the extended DRRE also showed good estimation performance for the N-best lists. And using the estimated recognition rates, the 1-best word accuracy was significantly improved by N-best rescoring from the baseline.
The implications of the values and behaviours of actors for ecotourism policy : a case study of Sebangau National Park, Central Kalimantan, Indonesia

A number of studies have suggested that the management of national parks might be best served if undertaken according to the principles of ecotourism, a concept that potentially provides a ‘win-win’ solution to the conflicting aspects of conservation and recreation in protected areas. Therefore, the purpose of this study is to critically appraise the potential of ecotourism as a framework for implementing tourism in a national park. More specifically, it seeks to explore the implications of actors’ values for the effective implementation of ecotourism policy. Many studies overlook the importance of the understanding and response of different values as fundamental aspects in the process of policy-making. Based on a case study of Sebangau National Park, Kalimantan, Indonesia, and using Schwartz’s theory as the fundamental conceptual framework, this research progresses the argument that the development of ecotourism policy should be seen in terms of the values espoused by relevant actors by seeking to identify the values and behaviours of the actors involved in ecotourism development in the park and the subsequent management implications. This study adopts the philosophy of pragmatism and mixed methods as its methodological approach, and is carried out in three phases: interviews (qualitative), focus group discussions (qualitative) and a survey (quantitative), followed by appropriate methods of analysis, such as performing ANCOVA and performing grounded theory to analyse qualitative data, supported by NVivo software. The results show that the Indonesian people, from the tourists’ perspective, embrace the culture of embeddedness with a tendency towards the value of Conformity that implies they are willing to follow regulations because they are aware of the importance of the local community and of the natural resources in the park. Meanwhile, the value of Benevolence should be the value espoused by policy makers because it is exerts a more significant influence on the concept of ecotourism in comparison with the other nine Schwartz’s values. In addition, even though several studies show that the value of Power tends not to be pro-environment, the involvement of actors who embrace it cannot be ignored in the policy-making process because it is required to demonstrate leadership, participation, self-determination, competence and self-efficacy behaviour. Moreover, the importance of the Hedonism value based on tourists’ perspective implies that tourists have the potential to behave in an anti-conservation manner for the sake of personal satisfaction; thus, it will lead to consumptive behaviour at tourist locations, even for ecotourism destinations.
Love Thy Neighbour: Automatic Animal Behavioural Classification of Acceleration Data Using the K-Nearest Neighbour Algorithm

Researchers hoping to elucidate the behaviour of species that aren’t readily observed are able to do so using biotelemetry methods. Accelerometers in particular are proving particularly effective and have been used on terrestrial, aquatic and volant species with success. In the past, behavioural modes were detected in accelerometer data through manual inspection, but with developments in technology, modern accelerometers now record at frequencies that make this impractical. In light of this, some researchers have suggested the use of various machine learning approaches as a means to classify accelerometer data automatically. We feel uptake of this approach by the scientific community is inhibited for two reasons; 1) Most machine learning algorithms require selection of summary statistics which obscure the decision mechanisms by which classifications are arrived, and 2) they are difficult to implement without appreciable computational skill. We present a method which allows researchers to classify accelerometer data into behavioural classes automatically using a primitive machine learning algorithm, k-nearest neighbour (KNN). Raw acceleration data may be used in KNN without selection of summary statistics, and it is easily implemented using the freeware program R. The method is evaluated by detecting 5 behavioural modes in 8 species, with examples of quadrupedal, bipedal and volant species. Accuracy and Precision were found to be comparable with other, more complex methods. In order to assist in the application of this method, the script required to run KNN analysis in R is provided. We envisage that the KNN method may be coupled with methods for investigating animal position, such as GPS telemetry or dead-reckoning, in order to implement an integrated approach to movement ecology research.
QUICK RESPONSE CODES AROUND US: PERSONALITY TRAITS, ATTITUDES TOWARD INNOVATION, AND ACCEPTANCE

The Quick Response (QR) code service scanned by smartphones allows users to obtain information that would otherwise be difficult for them to access on their own. However, different personality traits and attitudes toward innovations might influence an individual’s acceptance of this technology. A parallel model, in which personality traits predict individuals’ attitudes toward innovation, which in turn predict acceptance of QR code services, is proposed. Participants (N = 689) completed an online questionnaire. The original findings did not confirm all of the hypotheses, especially in terms of the desire for uniqueness. Further analysis revealed that laggards and late majority consumers hold unfavorable attitudes toward innovation and are less willing to adopt QR code services. A comparison model suggests that the degree of mediation of the effects of personality traits on service acceptance by attitudes toward innovation varies across categories of consumers.