Miracle-dz/UniFAR-FTUs huggingface dataset:
KTU: K‐mer Taxonomic Units improve the biological relevance of amplicon sequence variant microbiota data

Amplicon sequencing is widely implemented in microbiome‐associated studies. In recent years, microbial ecologists have switched to new algorithms for taxonomic identification and quantification. The amplicon sequence variant (ASV) denoising algorithm of unbiased sequence picking has replaced the OTU clustering methods. ASV can be used to detect and distinguish biological variations to the species OTU level (≥97% similarity). However, the ASV quantification among samples is sparse and less prevalent within the same batch. Here, we present a k‐mer based, alignment‐free algorithm—‘KTU’ (K‐mer Taxonomic Unit)—to iteratively re‐cluster ASVs into optimal biological taxonomic units. The ‘KTU’ algorithm comprises four parts: (a) The k‐mer frequency calling is sliding window counted by tetranucleotide frequencies from both ends of the DNA sequence. (b) The similarities in k‐mer frequencies among the sequences are measured by cosine dissimilarity. (c) The KTUs are detected from the cosine dissimilarity matrix using the partition around medoids (PAM) clustering algorithm. The iterative PAM‐KTU detecting process searches for the numbers of KTU convergent clusters according to the maximum silhouette coefficient. (d) Finally, the ASVs are aggregated into the corresponding KTUs. KTU re‐clustered every 1.38–4.53 ASVs into a feature with >99% sequence similarity on average and 1% cosine divergence for each KTU. Additionally, the re‐clustering procedure improved biological explanations for correlations and significances of clinical and environmental factors.
Variability of Chlorophyll a Concentration and Halocline Depth in La Paz Bay (Gulf of California, Mexico) and the Relationship to Pacific Large-Scale Climatic Phenomena

ABSTRACT Guevara-Guillén, C. ; Shirasago-Germán, B. ; Pérez-Lezama, E.L. , and Obeso-Nieblas, M. , 2018. Variability of chlorophyll a concentration and Halocline depth in La Paz Bay (Gulf of California, Mexico) and the relationship to Pacific large-scale climatic phenomena. Variability of the chlorophyll a (Chl a) concentration and halocline depth in La Paz Bay were analyzed and compared against the variability of North Pacific (NP) large-scale phenomena and local winds during 1999–2009. Chl a data were obtained from satellite images, and halocline depth was obtained from in situ data. Eight large-scale phenomenon climate indices and satellite wind data were also used in this work. Chl a was processed on three timescales—interannual, mean annual cycle, and monthly time series. The halocline depth was processed as a time series. The Chl a interannual analysis revealed a high variability in the study period, with the highest concentration in 2001 and the lowest in 2005. The Pacific Decadal Oscillation (PDO) was the dominant phenomenon in this timescale. The Chl a mean annual cycle showed two concentration periods, a higher one during December to March and lower one during April to November. The El Niño Southern Oscillation (ENSO) and PDO were the most determinant phenomena in the mean annual cycle. The monthly time series also showed high variability with the highest anomalies during 2000–01 and the lowest anomalies in 2003 and 2005. The ENSO and PDO were the most influential phenomena on the monthly timescale. The halocline depth analysis revealed high and noncyclic variability, contrasting depths of 90 m during February 2002 and November 2005 with other sampling dates such as July 2001 and July 2002, when the halocline reached the surface. The NP and local winds were the main factors that influenced the halocline depth.
Remittances, Liquidity Constraints and Human Capital Investments in Ecuador

Over the last decade Ecuador has experienced a strong increase in financial transfers from migrated workers, amounting to 6.4 percent of GDP and 31.5 percent of total exports of goods and services in 2005. This paper investigates how remittances via trans-national networks affect human capital investments through relaxing resource constraints and facilitate households in consumption smoothing by reducing vulnerability to economic shocks. In particular, we explore the effects of remittances on school enrolment and child work in Ecuador. Identification relies on instrumental variables, exploiting information on source countries of remittances and regional variation in the availability of bank offices that function as formal channels for sending remittances. Our results show that remittances increase school enrolment and decrease incidence of child work, especially for girls and in rural areas. Furthermore, we find that aggregate shocks are associated with increased work activities, while remittances are used to finance education when households are faced with these shocks. This suggests that liquidity constraints and vulnerability to covariate risk are especially relevant in rural areas, as it affects household’s investments in human capital of school age children. In this context both child labour supply and transnational remittances serve as coping mechanisms.
Reverse Estuarine Circulation Due to Local and Remote Wind Forcing, Enhanced by the Presence of Along-Coast Estuaries: REVERSE ESTUARINE CIRCULATION DRIVERS

Estuarine exchange ﬂow governs the interaction between oceans and estuaries and thus plays a large role in their biogeochemical processes. This study investigates the variability in estuarine exchange ﬂow due to offshore oceanic conditions including upwelling/downwelling, and the presence of a river plume offshore (from a neighboring estuary). We address these processes via numerical simulations at the mouth of the Salish Sea, a large estuarine system in the Northeast Paciﬁc. An analysis of the Total Exchange Flow indicates that during the upwelling season, the exchange ﬂow is fairly consistent in magnitude and oriented in a positive (into the estuary at depth and out at the surface) direction. However, during periods of downwelling favorable winds, the exchange ﬂow shows signiﬁcantly more variability including multiple reversals, consistent with observations, and surface intrusions of the Columbia River plume which originates 250 km to the south. Numerical along-strait momentum budgets show that the exchange ﬂow is forced dominantly by the pressure gradients, particularly the baroclinic. The pressure gradient is modiﬁed by Coriolis and sometimes advection, highlighting the importance of geostrophy and local adjustments. In experiments conducted without the offshore river plume, reversals still occur but are weaker, and the baroclinic pressure gradient plays a reduced role. These results suggest that estuaries along strong upwelling coastlines should experience signiﬁcant modulation in the exchange ﬂow during upwelling versus downwelling conditions. Additionally, they highlight the importance of nearby estuaries impacting one-another, not only in terms of connectivity, but also altering the exchange ﬂow. impacted, threatening their important functionality. Understanding estuarine dynamics is critical to understanding estuarine ecosystems. Hydrodynamic connectivity between estuaries and the coastal ocean is a key dynamical driver impacting critical biological and biogeochemical processes such as ocean/estuarine nutrient and phytoplankton exchange and regulation of estuarine residence time, dissolved oxygen, and acidiﬁcation levels. Typically estuarine-ocean exchange brings oceanic water into the estuary at depth, mixes it upwards within the estuary, and returns an outﬂowing mixture of oceanic and riverine water at the surface to the ocean. This manuscript documents seasonal reversals to this typical circulation pattern and the hydrodynamic drivers of the reversals. It highlights the importance of offshore winds and connectivity with neighboring estuaries. Improved understanding of these mechanisms can help us predict how estuaries will respond to a changing climate.
Irrational System Behavior in a System of Systems

System of systems (SoS) failures can sometimes be traced to a system within the SoS behaving in unexpected ways. Due to their emergent complexity, these types of failures are notoriously challenging to foresee. This paper presents a method to aid in predicting unknown unknowns in a SoS. Irrationality initiators – failure flows emanating from one system that serve as unexpected initiating events in another system – are introduced into quantitative risk analysis methods such as the Failure Flow Identification and Propagation framework and Probabilistic Risk Assessment. Analysis of models built using this approach yield a probability distribution of failure paths through a system within the SoS that are initiated by unexpected behaviors of other systems within the SoS. The method is demonstrated using an example of an autonomous vehicle network operating in a partially denied environment with hostile forces present. Using the concept of irrationality initiators, it is possible to identify and prioritize vulnerabilities in the system of interest in the SoS.
Qualitative Spatio-Temporal Representation and Reasoning: Trends and Future Directions

This chapter discusses the use of transition graphs for reasoning about continuous spatial change over time. The chapter first presents a general definition of a transition graph for a partition of a topological space. Then it defines the path-connected and the homogeneous refinements of such a partition. The qualitative behavior of paths through the space corresponds to the structure of paths through the associated transition graphs, and of associated interval label sequences, and the authors prove a number of metalogical theorems that characterize these correspondences in terms of the expressivity of associated first-order languages. They then turn to specific real-world problems and show how this theory can be applied to domains such as rigid objects, strings, and liquids. DOI: 10.4018/978-1-61692-868-1.ch003
Socio-economic factors determining the commitment to participate in an agricultural development project in rural Ethiopia

Ethiopia is suffering a massive exodus of rural people towards the capital. Thus, the Government is trying to support projects carried out to stimulate opportunities given to the agriculture sector. In this line a project has been designed, working together with a Non-Profit Organization (NPO). The present research paper analyses the factors which determine the farmers’ socio-economic, educational and nutrition commitments to design an assignment criterion in the frame of a rural development project in Ethiopia where all the families are surveyed. The donated wells are intended to make possible their access to safe water and the creation of a small vegetable garden with the final goal of improving their living standard. However, because the number of wells to donate was limited, it was crucial to identify assignment criteria to maximize the outcomes of the project. The selected families must help in the building of additional wells to other families and improving social status of the village through commitment to (i) return a percentage of exceeding crops for the community, (ii) assist to continuous training in agriculture, budgeting and nutrition and (iii) enroll their children in school. The article seeks to understand which socio-demographic and economic variables determine families’ different commitments. A descriptive analysis of the sample is made and different multivariate techniques are applied. Interesting results were observed such as women income, having an animal for transportation and owning a mobile, which are variables that determine these commitments.
Behavior of soil heave inside stiffened caissons being installed in clay

The length of suction caisson anchors has been increasing to support increasing dimensions and weight of floating facilities, which necessitates employing horizontal ring stiffeners at intervals along the inner wall of the thin skirt of caissons to ensure structural integrity. The addition of these stiffeners has created significant uncertainties regarding soil flow mechanisms, in particular soil heave inside the caisson, which may reduce the caisson final penetration depth and influence the process of installation due to the need to avoid inside soil suction in the pumping equipment. This paper reports results of large-deformation finite element (LDFE) analyses investigating soil heave inside stiffened caissons during installation in nonhomogeneous clay deposits, with the corresponding evolution of soil flow mechanisms and penetration resistance profiles reported by Zhou et al. in 2016. The LDFE analyses have simulated continuous penetration of stiffened caissons from the seabed surface. A detailed param.
AIS Electronic

Privacy risk is increasingly entering the public consciousness when it comes to use of information technology (IT). To gain insight into the role of risk in the technology adoption process, we studied the use of information systems for student registration and schedule management at two major U.S. universities. We extended the Technology Acceptance Model (TAM) with perceptual measures of privacy risk harm and privacy risk likelihood which apply to the extended model and predict students’ intentions to use technology. Privacy risk factors are found to negatively influence intention and contribute substantially to model predictiveness. This finding underlines the growing importance of privacy risk in the use of IT.
The Asymmetric Effect of Web Site Attribute Performance on Web Satisfaction: An Empirical Study

The purpose of this study is to examine the asymmetrical effects of negative and positive Web site attribute performance on satisfaction. An online survey of satisfaction with an e-portal was conducted, and a total of 515 usable questionnaires were collected. Psychometric properties of the measures were examined, and a dummy-variable regression model was used to estimate the regression coefficients. Results show that the importance of asymmetrical effect is different for different attributes, where the negative performance on information reliability and usefulness had a more significant impact on satisfaction than their positive performance. On the other hand, the positive performance on information understandability and system navigation had a more significant impact on satisfaction than their negative performance. This difference of asymmetrical effect is an important area calling for future investigation.
Why Do Multi-Stream , Multi-Band and Multi-Modal Approaches Work on Biometric User Authentication Tasks ?

Multi-band, multi-stream and multi-modal approaches have proven to be very successful both in experiments and in real-life applications, among which speech recognition and biometric authentication are of particular interest here. However, there is a lack of a theoretical study to justify why and how they work, when one combines the streams at the feature or classifier score levels. In this paper, we attempt to cast a light onto the latter subject. Our findings suggest that combining several experts using the mean operator, Multi-Layer-Perceptrons and Support Vector Machines always perform better than the average performance of the underlying experts. Furthermore, in practice, most combined experts using the methods mentioned above perform better than the best underlying expert.
Experience from a Course in Game Theory: Pre- and Post-class Problem Sets as a Didactic Device

The paper summarizes my experience in teaching an undergraduate course in game theory in 1998. Students were required to submit two types of problem sets: pre-class problem sets, which served as experiments, and post-class problem sets, which require the students to study and apply the solution concepts taught in the course. The sharp separation between the two types of problem sets emphasizes the limited relevance of game theory as a tool for making predictions and giving advice. The paper summarizes the results of 41 experiments which were conducted during the course. It is argued that the crude experimental methods produced results which are not substantially different from those obtained at much higher cost using stricter experimental methods (This abstract was borrowed from another version of this item.) (This abstract was borrowed from another version of this item.)
Poissons d'eaux douces et saumâtres de basse Guinée, ouest de l'Afrique centrale : volume 1 = The fresh and brackish water fishes of lower Guinea, west-central Africa : volume 1

répartition des poissons d’eaux douces et saumâtres de l’ouest de l’Afrique centrale (province ichtyologique de basse Guinée). L’étude couvre la région allant de la rivière Cross, au sud-est du Nigeria, jusqu’à la République du Congo, en incluant le Cabinda. La basse Guinée possède sa propre identité ichtyologique, avec une diversité faunistique regroupant quelque 580 espèces dont beaucoup sont endémiques. Cet ouvrage fait suite à la faune des poissons d’Afrique de l’Ouest publiée en 2003 dans cette collection. Le classement taxinomique est donné par famille avec un ensemble de clefs communes à tous les genres. Pour chaque espèce, le lecteur trouvera une description illustrée des caractéristiques morphologiques essentielles ainsi qu’une carte de répartition pour les espèces dulçaquicoles.
Extreme temperature and precipitation changes associated with four degree of global warming above pre‐industrial levels

In 2012, the World Bank released a report and stated that a 4 °C increase in global temperature relative to the pre‐industrial levels would be devastating. However, there is a lack of scientific literature on the changes in climate associated with a 4 °C temperature increase. Based on the daily temperature and precipitation data from the Coupled Model Intercomparison Project Phase 5 (CMIP5), we project the global terrestrial changes in the extreme values of temperature and precipitation in association with a warming of 4 °C above the pre‐industrial levels using the Representative Concentration Pathways 8.5 (RCP8.5) scenario. The results indicated that cold extremes will decrease and warm extremes will increase. More remarkable signals in temperature extremes based on daily minimum temperature are expected, and local changes in temperature extremes generally extend beyond the natural internal variability. Significant signals in the frequency of temperature extremes appear in low latitudes, while the temperature changes of the coldest and hottest days are great in northern high latitudes. Large signal‐to‐noise ratios for warm extremes mainly occur in low latitudes, while those of cold extremes are not uniformly distributed. More intense and frequent heavy precipitation is also projected. Signals in high‐precipitation extremes are prominent in high latitudes and usually exceed the local natural internal variability. Changes in extreme dry events are high in the extratropics and generally lie within the background noise. Relative to the 1.5 °C global warming scenario, there would be more violent temperature and precipitation extremes with the 4 °C warming level, and these extremes would pose more threats to natural and human systems. Additionally, small inter‐model uncertainty occurs in the regions with remarkable signals for high precipitation‐related extremes and cold days and nights, while the opposite trend is seen for extreme dry events and other temperature extremes.
Demo: how long to wait?: predicting bus arrival time with mobile phone based participatory sensing

The bus arrival time is primary information to most city transport travelers. Excessively long waiting time at bus stops often discourages the travelers and makes them reluctant to take buses. In this paper, we present a bus arrival time prediction system based on bus passengers' participatory sensing. With commodity mobile phones, the bus passengers' surrounding environmental context is effectively collected and utilized to estimate the bus traveling routes and predict bus arrival time at various bus stops. The proposed system solely relies on the collaborative effort of the participating users and is independent from the bus operating companies, so it can be easily adopted to support universal bus service systems without requesting support from particular bus operating companies. Instead of referring to GPS enabled location information, we resolve to more generally available and energy efficient sensing resources, including cell tower signals, movement statuses, audio recordings, etc., which bring less burden to the participatory party and encourage their participation. We develop a prototype system with different types of Android based mobile phones and comprehensively experiment over a 7 week period. The evaluation results suggest that the proposed system achieves outstanding prediction accuracy compared with those bus company initiated and GPS supported solutions. At the same time, the proposed solution is more generally available and energy friendly.
On the Dynamic Fragmentation and Lubrication of Coseismic Landslides

The three‐dimensional discrete element method has been employed to analyze the dynamic fragmentation and lubrication mechanisms of coseismic Tangjiashan landslide induced by the 2008 Ms 8.0 Wenchuan earthquake. The numerical results show that the internal rock damage occurs and propagates gradually along the basal failure plane due to seismic shaking. At the peak seismic shaking, a sudden increase of tensile and shear stresses can lead to the complete breakage of basal bonds. This is associated with a sudden relief of overburden stress and rapid decrease of basal stress ratio. Thus, the slope fails as a whole and moves quickly downslope. In this process, several large transversal cracks develop at the middle and upper rear regions, disintegrating the slope mass into several large blocks. During landslide propagation, the thickness of basal fragmented layer increases progressively due to intense shearing, and the basal stress ratio reduces accordingly from 0.68 to 0.28. The reduction of landslide basal stress ratio occurs when the strong basal resistance is overcome by seismic‐ and gravity‐induced shear forces together with intense particle rearrangements. It can be quantified by vibrational and rotational granular temperatures of the basal shear layer, with the peak values of 35.2 and 11.6 m2/s2, respectively. The widespread internal slope fragmentation and subsequent lubrication have been identified as the key mechanisms governing landslide motion, which appear to be the intrinsic features of landslide irrespective of its triggering mechanism. The seismic shaking is more relevant to the detachment than to the spreading of landslide mass.