cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 2: of Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone
Creators: name: Ruiz-Blanco, Yasser
name: Guillermin Agüero-Chapin
name: García-Hernández, Enrique
name: Álvarez, Orlando
name: Antunes, Agostinho
name: Green, James
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Inorganic Chemistry

description: Supplementary figures (Figure SI-I and SI-2) and Tables (Table SI-1 to Table SI-13). Figure SI-1 Dot plot of the pairwise amino acid identity matrix expressed in percentage (colour bar) for the D&D dataset. (A) Global all-vs-all sequence alignments using the Needleman-Wunsch (NW) algorithm (B) Local all-vs-all sequence alignments using the Smith-Waterman (SW) algorithm. Figure SI-2 Structural diversity summary of the D&D dataset according to SCOP database. Table SI-1 Compendium of structural and chemical-physical amino acid properties. Table SI-2 Formulae and description of Thermodynamics Indices for Protein Sequences. Table SI-3 Formulae and description of Topographic Indices. Table SI-4 Formulae and description of 3D–Thermodynamics Indices. Table SI-5 Summary of the definitions of amino acid groups. Table SI-6 Aggregation operators: Norms (Metrics) Invariants. Table SI-7 Aggregation operators: Mean (First Statistical Moment) Invariants. Table SI-8 Aggregation operators: Statistical (Highest Statistical Moments) Invariants. Table SI-9 Aggregation operators: Information-Theory-based Invariants. Table SI-10 Structural diversity summary of the D&D enzyme subset according to SCOP hierarchal database. Table SI-11 Structural diversity summary of the D&D enzyme subset according to SCOP hierarchal database. Table SI-12 Structural information of the selected ProtDCal’s features from the different families of descriptors (0D, 1D & 3D). Table SI-13 Detailed information about the benchmark annotation dataset and the prediction performed for each method/protein. Misclassified cases are highlighted in red font. (PDF 1850 kb)
Syneches tenebricus Menezes & Ale-Rocha
Creators: name: Soares, Matheus M. M.
name: Freitas-Silva, Rafael A. P.
name: Ale-Rocha, Rosaly
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Hybotidae
Syneches
Syneches tenebricus

description: Syneches tenebricus Menezes & Ale-Rocha
(Figs 44A–E, 54)
Syneches tenebricus Menezes & Ale-Rocha, 2016: 431–432, figs 87–91, 114, 123. Type locality: Manaus, Amazonas, Brazil.
Diagnosis. Medium size (3.5 mm) (Fig. 44A). Antenna yellow (Fig. 44C). Scutum rounded, as broad as mesopleuron in lateral view, dark brown, covered with reddish brown pruinescence (Fig. 44B). Foreleg from coxa to basal 2/3 of femur brown and apex of hind femur with a small brown spot, otherwise yellow (Figs 44A, D). Wing brown; pterostigma oval, dark brown, extended from apex of R 1, ending near to the apex of cell r 1; second section of M 1 slightly longer than crossvein r-m; cell bm longer than cells br and cua (Fig. 44E).
Type examined material. HOLOTYPE ♂ (INPA) labelled: “ BRASIL, Amazonas, Manaus, F [Fazenda] Esteio, BR-174, KM 41” “ 17–20.xii.1993, F.F. Xavier ” “Holótipo, Syneches tenebricus Menezes & Ale-Rocha ”. Holotype condition: left wing damaged, hind left leg broken off; not dissected.
Additional examined material. Same data as holotype (1 ♂, INPA).
Distribution. Brazil (Amazonas and Roraima) (Fig. 54). The species is recorded only from two very contrasting landscapes in the Amazon biome, namely from Manaus (central Amazon, State of Amazonas) and Pacaraima (northern Amazon, state of Roraima). However, it is interesting to note that both localities are composed of essentially different vegetation types; while the landscape nearby Manaus is predominantly of close canopy rainforest, Pacaraima shows a predominantly open savanna-like landscape.
Remarks. Syneches tenebricus is similar to S. fuscus sp. nov., differing from it due to the antenna and femora being predominantly yellow (except fore femur mostly brown), while in S. fuscus sp. nov. the antenna is dark brown and the fore and mid femora have more extensive brown markings (see also “Remarks” under S. fuscus sp. nov.).
description: Published as part of Soares, Matheus M. M., Freitas-Silva, Rafael A. P. & Ale-Rocha, Rosaly, 2021, Review of Brazilian species of Syneches Walker (Diptera, Hybotidae, Hybotinae), with description of ten new species, pp. 1-84 in Zootaxa 5049 (1) on page 68, DOI: 10.11646/zootaxa.5049.1.1, http://zenodo.org/record/5560580
Lithobius aeruginosus L. Koch 1862
Creators: name: Zarei, Roghaieh
name: Rahimian, Hassan
name: Mirmonsef, Hassan
name: Bonato, Lucio
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Chilopoda
Lithobiomorpha
Lithobiidae
Lithobius
Lithobius aeruginosus

description: Lithobius aeruginosus L. Koch, 1862
Lithobius aeruginosus L. Koch, 1862: 75
Literature records. Attems (1951): Khoramabad (Mazandaran Province). Zapparoli (1986): 1♀, Kuhenjan (Fars Province).
Distribution: from central Europe, thorugh Anatolia, to Iran.
description: Published as part of Zarei, Roghaieh, Rahimian, Hassan, Mirmonsef, Hassan & Bonato, Lucio, 2020, Geophilomorpha from Alborz Mountains and a checklist of Chilopoda from Iran, pp. 132-146 in Zootaxa 4780 (1) on page 138, DOI: 10.11646/zootaxa.4780.1.6, http://zenodo.org/record/3839630
Non-bifurcating phylogenetic tree inference via the adaptive LASSO
Creators: name: Zhang, Cheng
name: Dinh, Vu
name: Matsen, Frederick A.
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special features, including sampled ancestors in which we sequence a genotype along with its direct descendants, and polytomies in which multiple descendants arise simultaneously. These features are apparent after identifying zero-length branches in the tree. However, current maximum-likelihood based approaches are not capable of revealing such zero-length branches. In this paper, we find these zero-length branches by introducing adaptive-LASSO-type regularization estimators for the branch lengths of phylogenetic trees, deriving their properties, and showing regularization to be a practically useful approach for phylogenetics.
Niceforonia nana Goin and Cochran 1963
Creators: name: Cruz-Rodríguez, Cristian
name: Lynch, John D.
name: Cárdenas, Julieth S.
name: Caicedo-Portilla, José Rancés
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Amphibia
Anura
Strabomantidae
Niceforonia
Niceforonia nana

description: Niceforonia nana Goin and Cochran, 1963.
Holotype MLS 142. “ Colombia, Santander, Páramo de la Rusia ”.
Remarks: This specimen is currently at the United States National Museum (now National Museum of Natural History; Smithsonian Institution) with the catalog number USNM 150643.
description: Published as part of Cruz-Rodríguez, Cristian, Lynch, John D., Cárdenas, Julieth S. & Caicedo-Portilla, José Rancés, 2021, Type specimens housed in the herpetological collections at Museo de La Salle Bogotá and their historical importance for the consolidation of herpetology in Colombia, pp. 261-292 in Zootaxa 4965 (2) on page 267, DOI: 10.11646/zootaxa.4965.2.3, http://zenodo.org/record/4749961
Planetary Caring Politics in the Chthulucene
Creators: name: Bushy, Anna R.
Publisher: name: Washington State University
Year: 2024
Subjects: care
caring politics
ecofeminism
planetarity
Gender studies

description: In a context of rapidly increasing connections around the globe, Ursula Heise claims that “what is crucial for ecological awareness and environmental ethics is arguably not so a much a sense of place but a sense of planet,” or “a sense of how political, economic, technological, social, cultural, and ecological networks shape daily routines” (Sense 55). In this thesis, I develop the concept of a planetary caring politics, a material-discursive practice that considers how systems and structures such as heteropatriarchy, the nuclear family, racial capitalism, colonialism, and technology intersect and consequently shape the situated knowledges that inform how we conceptualize and practice care, and for whom we conceptualize and practice care. I offer interdisciplinary readings of selected literary texts to analyze their representations of planetary caring politics, as well as how these texts function on a narratological plane to shape how the reader understands the role of planetary caring politics in their own life.
Additional file 3: of Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone
Creators: name: Ruiz-Blanco, Yasser
name: Guillermin Agüero-Chapin
name: García-Hernández, Enrique
name: Álvarez, Orlando
name: Antunes, Agostinho
name: Green, James
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Experiments leading to the selection of the SVM and kernel parameters. (PDF 310 kb)
Lithobius antipai Matic 1969
Creators: name: Zarei, Roghaieh
name: Rahimian, Hassan
name: Mirmonsef, Hassan
name: Bonato, Lucio
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Chilopoda
Lithobiomorpha
Lithobiidae
Lithobius
Lithobius antipai

description: Lithobius antipai Matic, 1969
Lithobius antipai Matic, 1969: 94
Literature records. Matic (1969): 5♀, Damavand and Gajereh, 2600-4400 m (Tehran and Alborz Provinces). Distribution: Iran, Azerbaijan.
description: Published as part of Zarei, Roghaieh, Rahimian, Hassan, Mirmonsef, Hassan & Bonato, Lucio, 2020, Geophilomorpha from Alborz Mountains and a checklist of Chilopoda from Iran, pp. 132-146 in Zootaxa 4780 (1) on page 138, DOI: 10.11646/zootaxa.4780.1.6, http://zenodo.org/record/3839630
Intrinsic wavelet regression for curves of Hermitian positive definite matrices
Creators: name: Chau, Joris
name: von Sachs, Rainer
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Space Science
subject: Medicine
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Intrinsic wavelet transforms and wavelet estimation methods are introduced for curves in the non-Euclidean space of Hermitian positive definite matrices, with in mind the application to Fourier spectral estimation of multivariate stationary time series. The main focus is on intrinsic average-interpolation wavelet transforms in the space of positive definite matrices equipped with an affine-invariant Riemannian metric, and convergence rates of linear wavelet thresholding are derived for intrinsically smooth curves of Hermitian positive definite matrices. In the context of multivariate Fourier spectral estimation, intrinsic wavelet thresholding is equivariant under a change of basis of the time series, and nonlinear wavelet thresholding is able to capture localized features in the spectral density matrix across frequency, always guaranteeing positive definite estimates. The finite-sample performance of intrinsic wavelet thresholding is assessed by means of simulated data and compared to several benchmark estimators in the Riemannian manifold. Further illustrations are provided by examining the multivariate spectra of trial-replicated brain signal time series recorded during a learning experiment.
Auto-G-Computation of Causal Effects on a Network
Creators: name: Tchetgen, Eric J. Tchetgen
name: Fulcher, Isabel R.
name: Shpitser, Ilya
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Medicine
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Statistics
subject: FOS: Mathematics
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology
subject: Cardiology

description: Methods for inferring average causal effects have traditionally relied on two key assumptions: (i) the intervention received by one unit cannot causally influence the outcome of another; and (ii) units can be organized into nonoverlapping groups such that outcomes of units in separate groups are independent. In this article, we develop new statistical methods for causal inference based on a single realization of a network of connected units for which neither assumption (i) nor (ii) holds. The proposed approach allows both for arbitrary forms of interference, whereby the outcome of a unit may depend on interventions received by other units with whom a network path through connected units exists; and long range dependence, whereby outcomes for any two units likewise connected by a path in the network may be dependent. Under network versions of consistency and no unobserved confounding, inference is made tractable by an assumption that the networks outcome, treatment and covariate vectors are a single realization of a certain chain graph model. This assumption allows inferences about various network causal effects via the auto-g-computation algorithm, a network generalization of Robins’ well-known g-computation algorithm previously described for causal inference under assumptions (i) and (ii). Supplementary materials for this article are available online.
EXPLORATION OF ARABICA COFFEE GROUND WASTE FOR SUSTAINABLE TEXTILE DYEING AND APPAREL DESIGN
Creators: name: Durán, Nehemiah Stone
Publisher: name: Washington State University
Year: 2024
Subjects: Coffee Waste
Environment
Natural Dye
Sustainability
Textiles

description: Coffee is one of most well known beverages in the world as throughout the last century, the consumption has increased creating more waste from the coffee grounds that eventually ends up in the landfills. Even though coffee is a natural cellulosic product that is biodegradable, with current consumption practices, much of the coffee grounds ends up at landfills unable to be decomposed correctly. A new application of using coffee ground waste, sustainable textile dyeing, is explored in this research, with the goal of diverting used coffee grounds from landfills and utilizing its beneficial functional properties. In the first part of the study, an experiment is carried out to examine the viability of coffee ground waste for textile dyeing, including examination of different coffee types, fabric types, and dyebath conditions. Second part involves development of a garment to illustrate the utility of coffee ground waste-dyed fabrics for wearable apparel. The findings showed that using coffee ground waste for textile dyeing has potential, providing a range of browns based on the regional location of the coffee bean cultivation.
title: DECODING THE FASHION QUOTIENT
title: AN EMPIRICAL STUDY OF KEY FACTORS INFLUENCING GENERATION Z’S PURCHASE INTENTION TOWARD FAST FASHION
titleType: Subtitle
Creators: name: Wojdyla, Weronika
Publisher: name: Washington State University
Year: 2024
Subjects: fashion
fast fashion
Generation z
Theory of planned behavior

description: With a reputation for offering stylish and on-trend clothing at pocket-friendly prices, fast fashion brands resonate with the economic realities faced by many Generation Z consumers. Generation Zers are not just a target consumer market but are a driving force shaping the future of the fashion industry. Their preferences, values, and behaviors impact trends, reshape retail practices, and influence the overall trajectory of the fashion landscape. The evolving discourse surrounding sustainability and conscious consumerism suggests that the future may see a recalibration of the fashion landscape, with Generation Zers at the forefront of demanding more responsible and transparent practices from the fashion industry. Therefore, this study aims to identify the factors significantly influencing U.S. Gen Z consumers’ intention to purchase fast fashion. Building on the theory of planned behavior (TPB), a research model for understanding Gen Z consumers’ intention to buy fast fashion products is proposed. Attitude, subjective norms
description: (SN), perceived behavioral control (PBC), environmental knowledge (EK), need for uniqueness (NFU), materialism (M), and fashion leadership (FL) are investigated as predictors. In addition, attitude is proposed as a mediator between environmental knowledge (EK), need for uniqueness (NFU), materialism (M), and fashion leadership (FL) and Gen Z consumers’ intention to purchase fast fashion products. Through a Qualtrics online survey, 528 eligible responses were gathered for analysis. The psychometric properties of the proposed model were examined, and the multiple regression method was applied to test the hypotheses. Attitude, perceived consumer effectiveness, environmental knowledge, and fashion leadership significantly affected Generation Z consumers’ intentions to shop fast fashion. Attitude plays a mediating role between Generation Z consumers’ environmental knowledge, need for uniqueness, fashion leadership, and their intention to shop fast fashion. The proposed research model exhibited good explanatory power, accounting for 68.9% of the variance in Generation Z consumers’ purchase intention toward fast fashion.
Hylaeus Fabricius 1793
Creators: name: Dathe, Holger H.
name: Proshchalykin, Maxim Yu.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Colletidae
Hylaeus

description: Genus Hylaeus Fabricius, 1793
Hylaeus Fabricius, 1793: 302. Type species: Prosopis annulata Fabricius, 1804 = Apis annulata Linnaeus, 1758, by designation of Latreille 1810: 438.
description: Published as part of Dathe, Holger H. & Proshchalykin, Maxim Yu., 2016, The genus Hylaeus Fabricius in Mongolia, an updated species inventory (Hymenoptera: Apoidea, Colletidae), pp. 351-382 in Zootaxa 4121 (4) on page 357, DOI: 10.11646/zootaxa.4121.4.1, http://zenodo.org/record/256897
Bolitoglossa vallecula Brame 1963
Creators: name: Cruz-Rodríguez, Cristian
name: Lynch, John D.
name: Cárdenas, Julieth S.
name: Caicedo-Portilla, José Rancés
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Amphibia
Caudata
Plethodontidae
Bolitoglossa
Bolitoglossa vallecula

description: Bolitoglossa vallecula Brame and Wake, 1963.
Holotype MLS 8 a (fig. 15), paratypes MLS 8 B, 8C, 8D, 8E, 8F, 8G, 8H, 5, 5A, 5B, 9, 10, 10A and 10B (= actual numbers MLS 2, 3, 4, 5, 6, 7, and 8) (fig. 16). “Yarumal, 2300 meters, Departamento de Antioquia, Colombia.” Brother Nicéforo María, Jan. 1963.
Remarks: The paratypes MLS 8B, 8C, 8D, 8E, 8F, 8G, 8H were collected by Brother José Ignacio Izasa. The paratypes MLS 5, 5a, 5b, 9, 10, 10A and 10B are not present in the collection and are probably lost. Specimen MLS 2, 3, 4, 5, 7 and 8 are hydrated and in good state of preservation and specimen MLS 6 is hydrated and presents slight decay.
description: Published as part of Cruz-Rodríguez, Cristian, Lynch, John D., Cárdenas, Julieth S. & Caicedo-Portilla, José Rancés, 2021, Type specimens housed in the herpetological collections at Museo de La Salle Bogotá and their historical importance for the consolidation of herpetology in Colombia, pp. 261-292 in Zootaxa 4965 (2) on page 268, DOI: 10.11646/zootaxa.4965.2.3, http://zenodo.org/record/4749961
Mecistocephalus
Creators: name: Zarei, Roghaieh
name: Rahimian, Hassan
name: Mirmonsef, Hassan
name: Bonato, Lucio
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Chilopoda
Geophilomorpha
Mecistocephalidae
Mecistocephalus

description: Mecistocephalus sp.
New records: 2♀, Gazor Khan, Alamut Mountain (Qazvin Province).
Notes. The species identity of these specimens is uncertain. Mecistocephalus species are mainly found in tropical and subtropical regions, and Iranian populations are at the northern border of their distribution in south-western Asia.
description: Published as part of Zarei, Roghaieh, Rahimian, Hassan, Mirmonsef, Hassan & Bonato, Lucio, 2020, Geophilomorpha from Alborz Mountains and a checklist of Chilopoda from Iran, pp. 132-146 in Zootaxa 4780 (1) on page 137, DOI: 10.11646/zootaxa.4780.1.6, http://zenodo.org/record/3839630
Transformed Dynamic Quantile Regression on Censored Data
Creators: name: Chu, Chi Wing
name: Sit, Tony
name: Xu, Gongjun
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: Ecology
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: We propose a class of power-transformed linear quantile regression models for time-to-event observations subject to censoring. By introducing a process of power transformation with different transformation parameters at individual quantile levels, our framework relaxes the assumption of logarithmic transformation on survival times and provides dynamic estimation of various quantile levels. With such formulation, our proposal no longer requires the potentially restrictive global linearity assumption imposed on a class of existing inference procedures for censored quantile regression. Uniform consistency and weak convergence of the proposed estimator as a process of quantile levels are established via the martingale-based argument. Numerical studies are presented to illustrate the outperformance of the proposed estimator over existing contenders under various settings.
Additional file 3: Figure S1. of Characterization of background noise in capture-based targeted sequencing data
Creators: name: Gahee Park
name: Park, Joo
name: Shin, Seung-Ho
name: Hyo-Jeong Jeon
name: Nayoung Kim
name: Kim, Yeon
name: Hyun-Tae Shin
name: Eunjin Lee
name: Lee, Kwang
name: Dae-Soon Son
name: Woong-Yang Park
name: Donghyun Park
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biophysics
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Developmental Biology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: 60506 Virology
subject: Computational Biology

description: Single nucleotide polymorphism concordance between plasma and PBL DNA samples. Figure S2. The distribution of base quality scores from generated sequencing data. Figure S3. The proportion of consistent/inconsistent errors between paired reads 1 and 2. Figure S4. Background allele frequencies of 12 substitution classes. Figure S5. Mutagenic DNA lesions are associated with high DNA-shearing conditions. Figure S6. Background allele frequencies around the DNA break point. Figure S7. Normalized mononucleotide frequencies around the DNA break point. Figure S8. Dinucleotide frequencies around the DNA break point. Figure S9. Comparison of dinucleotide frequencies around the DNA break point between PBL and plasma DNA samples. Figure S10. Density plot of allelic background rate. Figure S11. Mononucleotide frequencies of plasma DNA fragments around the DNA break point. Figure S12. Analysis of the DNA break point. Figure S13. Analysis of background allele frequency in â  hotspotâ   mutations. (PDF 1649 kb)
Amphisbaena elbakyanae Torres-Ramirez, Angarita-Sierra and Vargas-Ramirez 2021
Creators: name: Cruz-Rodríguez, Cristian
name: Lynch, John D.
name: Cárdenas, Julieth S.
name: Caicedo-Portilla, José Rancés
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Reptilia
Squamata
Amphisbaenidae
Amphisbaena
Amphisbaena elbakyanae

description: Amphisbaena elbakyanae Torres-Ramírez, Angarita-Sierra and Vargas-Ramírez 2021.
Holotype MLS 1901 (fig. 17), male. “ El Porvenir farm, Vereda La Colombina, municipality of Paz de Ariporo, department of Casanare,
Colombia, N 6.043472222, W –71.09283333); elevation 140 m. a.s.l”. 20 Aug. 2012. Paratype MLS 1902 (fig. 18), female. “Caño El Socorro, between veredas Aguaverde and La Virgen, municipality of Orocué, department of Casanare, Colombia, (N 5.02901, W –71.18037); elevation 128 m. a.s.l.”. Dec 2012
Remarks: MLS 1901 was collected by Teddy Angarita-Sierra, Marvin Anganoy-Criollo and John Jairo and MLS 1902 was collected by Marvin Anganoy-Criollo. Both specimens are hydrated and in good state of preservation.
description: Published as part of Cruz-Rodríguez, Cristian, Lynch, John D., Cárdenas, Julieth S. & Caicedo-Portilla, José Rancés, 2021, Type specimens housed in the herpetological collections at Museo de La Salle Bogotá and their historical importance for the consolidation of herpetology in Colombia, pp. 261-292 in Zootaxa 4965 (2) on pages 269-270, DOI: 10.11646/zootaxa.4965.2.3, http://zenodo.org/record/4749961
Additional file 3: of ADHD-related symptoms and attention profiles in the unaffected siblings of probands with autism spectrum disorder: focus on the subtypes of autism and Aspergerâ  s disorder
Creators: name: Chien, Yi-Ling
name: Miao-Chun Chou
name: Yen-Nan Chiu
name: Wen-Jiun Chou
name: Wu, Yu-Yu
name: Wen-Che Tsai
name: Gau, Susan
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: Science Policy
subject: Mental Health

description: Comparison of CCPT performance between probands with autism, unaffected siblings of autism probands, and typically developing controls. Comparison of CCPT performance between probands with autism, unaffected siblings of autism probands, and typically developing controls adjusting for sex and age. (PDF 103 kb)
Hessebius barbipes
Creators: name: Zarei, Roghaieh
name: Rahimian, Hassan
name: Mirmonsef, Hassan
name: Bonato, Lucio
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Chilopoda
Lithobiomorpha
Lithobiidae
Hessebius
Hessebius barbipes

description: Hessebius barbipes (Porat, 1893)
Lithobius barbipes Porat, 1893: 66
Literature records. Eason (1981): 1♂, 1♀, Shiraz (Fars Province); 1♂, Bushehr (Bushehr Province); 3♂, 4♀, Shah Bazan (Khuzestan Province); 3♂, 1♀, Anjedan (Markazi Province). Zapparoli (1986): 1♂, 1♀, Ardakan (Fars Prov- ince); 2♂, 1♀, Deh Sheykh (Fars Province).
Distribution: from the eastern Mediterranean region, throught the Middle East, to central Asia.
description: Published as part of Zarei, Roghaieh, Rahimian, Hassan, Mirmonsef, Hassan & Bonato, Lucio, 2020, Geophilomorpha from Alborz Mountains and a checklist of Chilopoda from Iran, pp. 132-146 in Zootaxa 4780 (1) on page 137, DOI: 10.11646/zootaxa.4780.1.6, http://zenodo.org/record/3839630
Covariate Regularized Community Detection in Sparse Graphs
Creators: name: Yan, Bowei
name: Sarkar, Purnamrita
Publisher: name: Taylor & Francis
Year: 2020
Subjects: Environmental Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Mathematical Sciences not elsewhere classified
Science Policy

description: In this article, we investigate community detection in networks in the presence of node covariates. In many instances, covariates and networks individually only give a partial view of the cluster structure. One needs to jointly infer the full cluster structure by considering both. In statistics, an emerging body of work has been focused on combining information from both the edges in the network and the node covariates to infer community memberships. However, so far the theoretical guarantees have been established in the dense regime, where the network can lead to perfect clustering under a broad parameter regime, and hence the role of covariates is often not clear. In this article, we examine sparse networks in conjunction with finite dimensional sub-Gaussian mixtures as covariates under moderate separation conditions. In this setting each individual source can only cluster a nonvanishing fraction of nodes correctly. We propose a simple optimization framework which improves clustering accuracy when the two sources carry partial information about the cluster memberships, and hence perform poorly on their own. Our optimization problem can be solved by scalable convex optimization algorithms. With a variety of simulated and real data examples, we show that the proposed method outperforms other existing methodology. Supplementary materials for this article are available online.
Lithobius buxtoni Brolemann 1921
Creators: name: Zarei, Roghaieh
name: Rahimian, Hassan
name: Mirmonsef, Hassan
name: Bonato, Lucio
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Chilopoda
Lithobiomorpha
Lithobiidae
Lithobius
Lithobius buxtoni

description: Lithobius buxtoni Brolemann, 1921 *
Lithobius buxtoni Brolemann, 1921: 169
Literature records. Brolemann (1921): 1♂, Rasht (Gilan Province). Attems (1951): Lahijan (Gilan Province). Distribution: Iran.
description: Published as part of Zarei, Roghaieh, Rahimian, Hassan, Mirmonsef, Hassan & Bonato, Lucio, 2020, Geophilomorpha from Alborz Mountains and a checklist of Chilopoda from Iran, pp. 132-146 in Zootaxa 4780 (1) on page 138, DOI: 10.11646/zootaxa.4780.1.6, http://zenodo.org/record/3839630
The Intended Uses of Automated Fact-Checking Artefacts: Why, How and Who
Creators: name: Schlichtkrull, M
name: Ousidhoum, N
name: Vlachos, A
Publisher: name: Association for Computational Linguistics
Year: 2023

description: Automated fact-checking is often presented as an epistemic tool that fact-checkers, social media consumers, and other stakeholders can use to fight misinformation. Nevertheless, few papers thoroughly discuss how. We document this by analysing 100 highly-cited papers, and annotating epistemic elements related to intended use, i.e., means, ends, and stakeholders. We find that narratives leaving out some of these aspects are common, that many papers propose inconsistent means and ends, and that the feasibility of suggested strategies rarely has empirical backing. We argue that this vagueness actively hinders the technology from reaching its goals, as it encourages overclaiming, limits criticism, and prevents stakeholder feedback. Accordingly, we provide several recommendations for thinking and writing about the use of fact-checking artefacts.
Additional file 1: Figure S1. of Childhood cancer incidence by ethnic group in England, 2001â  2007: a descriptive epidemiological study
Creators: name: Shameq Sayeed
name: Barnes, Isobel
name: Ali, Raghib
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Computational Biology

description: Sensitivity Analysis - Each cancer and all cancers by ethnicity, using imputed data. Sensitivity analyses for each cancer, and all cancers, by ethnicity (using multiple imputations of the missing ethnicity values based on age, sex, income and site of cancer). (PDF 3Â kb)
Lithobius chalusensis Matic 1969
Creators: name: Zarei, Roghaieh
name: Rahimian, Hassan
name: Mirmonsef, Hassan
name: Bonato, Lucio
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Chilopoda
Lithobiomorpha
Lithobiidae
Lithobius
Lithobius chalusensis

description: Lithobius chalusensis Matic, 1969 *
Lithobius chalusensis Matic, 1969: 105
Literature records. Matic (1969): 1♀ (holotype), Chalus, 300 m (Mazandaran Province). Mehrafrooz Mayvan & Shayanmehr (2015): 33 ex., Semeskandeh forest, Sary (Mazandaran Province).
Distribution: Iran.
Notes. The identity of the specimens reported by Mehrafrooz Mayvan & Shayanmehr (2015) cannot be evaluated, as no morphological diagnostic characters were indicated.
description: Published as part of Zarei, Roghaieh, Rahimian, Hassan, Mirmonsef, Hassan & Bonato, Lucio, 2020, Geophilomorpha from Alborz Mountains and a checklist of Chilopoda from Iran, pp. 132-146 in Zootaxa 4780 (1) on page 138, DOI: 10.11646/zootaxa.4780.1.6, http://zenodo.org/record/3839630
Bayesian Structure Learning in Multi-layered Genomic Networks
Creators: name: Ha, Min Jin
name: Stingo, Francesco Claudio
name: Baladandayuthapani, Veerabhadran
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Plant Biology

description: Integrative network modeling of data arising from multiple genomic platforms provides insight into the holistic picture of the interactive system, as well as the flow of information across many disease domains including cancer. The basic data structure consists of a sequence of hierarchically ordered datasets for each individual subject, which facilitates integration of diverse inputs, such as genomic, transcriptomic, and proteomic data. A primary analytical task in such contexts is to model the layered architecture of networks where the vertices can be naturally partitioned into ordered layers, dictated by multiple platforms, and exhibit both undirected and directed relationships. We propose a multi-layered Gaussian graphical model (mlGGM) to investigate conditional independence structures in such multi-level genomic networks in human cancers. We implement a Bayesian node-wise selection (BANS) approach based on variable selection techniques that coherently accounts for the multiple types of dependencies in mlGGM; this flexible strategy exploits edge-specific prior knowledge and selects sparse and interpretable models. Through simulated data generated under various scenarios, we demonstrate that BANS outperforms other existing multivariate regression-based methodologies. Our integrative genomic network analysis for key signaling pathways across multiple cancer types highlights commonalities and differences of p53 integrative networks and epigenetic effects of BRCA2 on p53 and its interaction with T68 phosphorylated CHK2, that may have translational utilities of finding biomarkers and therapeutic targets.
Learning Optimal Distributionally Robust Individualized Treatment Rules
Creators: name: Mo, Weibin
name: Qi, Zhengling
name: Liu, Yufeng
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Recent development in the data-driven decision science has seen great advances in individualized decision making. Given data with individual covariates, treatment assignments and outcomes, policy makers best individualized treatment rule (ITR) that maximizes the expected outcome, known as the value function. Many existing methods assume that the training and testing distributions are the same. However, the estimated optimal ITR may have poor generalizability when the training and testing distributions are not identical. In this article, we consider the problem of finding an optimal ITR from a restricted ITR class where there are some unknown covariate changes between the training and testing distributions. We propose a novel distributionally robust ITR (DR-ITR) framework that maximizes the worst-case value function across the values under a set of underlying distributions that are “close” to the training distribution. The resulting DR-ITR can guarantee the performance among all such distributions reasonably well. We further propose a calibrating procedure that tunes the DR-ITR adaptively to a small amount of calibration data from a target population. In this way, the calibrated DR-ITR can be shown to enjoy better generalizability than the standard ITR based on our numerical studies. Supplementary materials for this article are available online.
Syneches vidali Ale-Rocha & Vieira
Creators: name: Soares, Matheus M. M.
name: Freitas-Silva, Rafael A. P.
name: Ale-Rocha, Rosaly
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Hybotidae
Syneches
Syneches vidali

description: Syneches vidali Ale-Rocha & Vieira
(Figs 47A–E, 55)
Syneches vidali Ale-Rocha & Vieira, 2008: 120, figs 29–35, 40; Menezes & Ale-Rocha, 2016: 433, fig. 123 (key, distr.). Type locality: Parque Nacional do Jaú, Amazonas, Brazil.
Diagnosis. Small size (2.6 mm) (Fig. 47A). Antenna with scape and pedicel brown, postpedicel brown on basal half and pale yellow on apical half (Fig. 47C), sometimes varying from entirely brown to entirely yellow. Scutum broader than mesopleuron in lateral view, dark brown covered with reddish brown pruinescence, except by pprn lb, dc stripe and prescutellar disc covered both with gray pruinescence; one circle of gray pruinescence on npl and other just above npl (Fig. 47B). Wing sub-hyaline, pale brown, pterostigma divided into two brown spots, one triangular, posterior to apex of R 1, and one quadrangular extended beyond the apex of cell r 1; second section of M 1 slightly longer than crossvein r-m (Fig. 47E).
Type material examined. HOLOTYPE ♂ (INPA) labelled: “ BRASIL, Amazonas, Parque Nacional [do] Jaú, 29.vii–08.viii.2001, 01°54′46″S 61°35′23″W; Arm[adilha] Malaise, campina arbustiva, Henriques & Vidal” “Holótipo, Syneches vidali Ale-Rocha & Vieira [red label]”. Holotype condition: good; not dissected.
Additional material examined. BRAZIL. Maranhão: Bom Jardim, REBIO-Res. Biol. Gurupi, Armad. Luminosa Móvel, 17–27.i.2010, F. Limeira-de-Oliveira, J.T. Câmara & M.B. Aguiar Neto, cols. (3♀, CZMA). Rio Grande do Norte: Baía Formosa, Mata Estrela, 06°23′19″S 35°01′05″W, 44 m, 24.v.2007, J.A. Rafael & F.F. Xavier F., Luz (2 ♂, INPA). Minas Gerais: Ouro Preto, 12–13.iv.1968, F.C. Val, col. (4 ♂, 1 ♀, MZUSP). São Paulo: Cássia dos Coqueiros, Mun. Cajuru, ix.1954, M.P. Barretto col. (3 ♂, MZUSP); Praia de Guaratuba, Bertioga, 1969, F.C. Val, col. (1 ♂, MZUSP).
Distribution. Brazil (Amazonas, Maranhão *, Minas Gerais *, Rio Grande do Norte *, São Paulo *) (Fig. 55). Syneches vidali was originally described from the Amazon biome and it is now recorded occurring also in the Atlantic Forest biome.
Remarks. Syneches vidali is similar to S. maculosum as mentioned above (see “Remarks” under S. maculosum). However, S. vidali can be differentiated by the pruinescence pattern on the scutum and the pterostigma extends beyond the apex of cell r 1.
description: Published as part of Soares, Matheus M. M., Freitas-Silva, Rafael A. P. & Ale-Rocha, Rosaly, 2021, Review of Brazilian species of Syneches Walker (Diptera, Hybotidae, Hybotinae), with description of ten new species, pp. 1-84 in Zootaxa 5049 (1) on pages 72-75, DOI: 10.11646/zootaxa.5049.1.1, http://zenodo.org/record/5560580
Lithobius demavendicus Matic 1969
Creators: name: Zarei, Roghaieh
name: Rahimian, Hassan
name: Mirmonsef, Hassan
name: Bonato, Lucio
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Chilopoda
Lithobiomorpha
Lithobiidae
Lithobius
Lithobius demavendicus

description: Lithobius demavendicus Matic, 1969 *
Lithobius demavendicus Matic, 1969: 98
Literature records. Matic (1969): 1♂ (holotype), Damavand Mountain, 3000-3200 m (Tehran Province). Distribution: Iran.
description: Published as part of Zarei, Roghaieh, Rahimian, Hassan, Mirmonsef, Hassan & Bonato, Lucio, 2020, Geophilomorpha from Alborz Mountains and a checklist of Chilopoda from Iran, pp. 132-146 in Zootaxa 4780 (1) on page 138, DOI: 10.11646/zootaxa.4780.1.6, http://zenodo.org/record/3839630
Phenacosaurus nicefori Dunn 1944
Creators: name: Cruz-Rodríguez, Cristian
name: Lynch, John D.
name: Cárdenas, Julieth S.
name: Caicedo-Portilla, José Rancés
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Squamata
Dactyloidae
Phenacosaurus
Phenacosaurus nicefori

description: Phenacosaurus nicefori Dunn 1944d.
Holotype ILS (= actual number MLS 155) (fig. 24), male. Vicinity of Pamplona, Norte de Santander, Colombia. 2340 meters elevation. Brother Nicéforo María, Dec. 1937.
Remarks: The original publication lacks the catalog number, a later publication reports that ILS 65 is the number of the type (Lazell, 1969), but this number is erroneous. Specimens MLS 155 is hydrated and in good state of preservation.
description: Published as part of Cruz-Rodríguez, Cristian, Lynch, John D., Cárdenas, Julieth S. & Caicedo-Portilla, José Rancés, 2021, Type specimens housed in the herpetological collections at Museo de La Salle Bogotá and their historical importance for the consolidation of herpetology in Colombia, pp. 261-292 in Zootaxa 4965 (2) on page 272, DOI: 10.11646/zootaxa.4965.2.3, http://zenodo.org/record/4749961
Covariate Regularized Community Detection in Sparse Graphs
Creators: name: Yan, Bowei
name: Sarkar, Purnamrita
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Space Science
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Science Policy

description: In this paper, we investigate community detection in networks in the presence of node covariates. In many instances, covariates and networks individually only give a partial view of the cluster structure. One needs to jointly infer the full cluster structure by considering both. In statistics, an emerging body of work has been focused on combining information from both the edges in the network and the node covariates to infer community memberships. However, so far the theoretical guarantees have been established in the dense regime, where the network can lead to perfect clustering under a broad parameter regime, and hence the role of covariates is often not clear. In this paper, we examine sparse networks in conjunction with finite dimensional sub-gaussian mixtures as covariates under moderate separation conditions. In this setting each individual source can only cluster a non-vanishing fraction of nodes correctly. We propose a simple optimization framework which improves clustering accuracy when the two sources carry partial information about the cluster memberships, and hence perform poorly on their own. Our optimization problem can be solved by scalable convex optimization algorithms. With a variety of simulated and real data examples, we show that the proposed method outperforms other existing methodology.
Global and Simultaneous Hypothesis Testing for High-Dimensional Logistic Regression Models
Creators: name: Ma, Rong
name: Cai, T. Tony
name: Li, Hongzhe
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Mathematical Sciences not elsewhere classified
subject: Science Policy

description: High-dimensional logistic regression is widely used in analyzing data with binary outcomes. In this paper, global testing and large-scale multiple testing for the regression coefficients are considered in both single- and two-regression settings. A test statistic for testing the global null hypothesis is constructed using a generalized low-dimensional projection for bias correction and its asymptotic null distribution is derived. A lower bound for the global testing is established, which shows that the proposed test is asymptotically minimax optimal over some sparsity range. For testing the individual coefficients simultaneously, multiple testing procedures are proposed and shown to control the false discovery rate (FDR) and falsely discovered variables (FDV) asymptotically. Simulation studies are carried out to examine the numerical performance of the proposed tests and their superiority over existing methods. The testing procedures are also illustrated by analyzing a data set of a metabolomics study that investigates the association between fecal metabolites and pediatric Crohn’s disease and the effects of treatment on such associations.
Learning Optimal Distributionally Robust Individualized Treatment Rules
Creators: name: Mo, Weibin
name: Qi, Zhengling
name: Liu, Yufeng
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Recent development in the data-driven decision science has seen great advances in individualized decision making. Given data with individual covariates, treatment assignments and outcomes, policy makers best individualized treatment rule (ITR) that maximizes the expected outcome, known as the value function. Many existing methods assume that the training and testing distributions are the same. However, the estimated optimal ITR may have poor generalizability when the training and testing distributions are not identical. In this paper, we consider the problem of finding an optimal ITR from a restricted ITR class where there is some unknown covariate changes between the training and testing distributions. We propose a novel distributionally robust ITR (DR-ITR) framework that maximizes the worst-case value function across the values under a set of underlying distributions that are “close” to the training distribution. The resulting DR-ITR can guarantee the performance among all such distributions reasonably well. We further propose a calibrating procedure that tunes the DR-ITR adaptively to a small amount of calibration data from a target population. In this way, the calibrated DR-ITR can be shown to enjoy better generalizability than the standard ITR based on our numerical studies.