cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Atheta (Dimetrota) chartersensis Klimaszewski and Webster
Creators: name: Klimaszewski, Jan
name: Chandler, Donald S.
name: Davies, Anthony
name: Bourdon, Caroline
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Atheta
Atheta chartersensis

description: 36. Atheta (Dimetrota) chartersensis Klimaszewski and Webster
(Illustrations in Klimaszewski et al. 2018), Table 1
References. Webster et al. 2016. Klimaszewski et al. 2018.
Distribution. Nearctic. Canada: NB. USA (NCR): NH (NSR).
Collection and Habitat data. The NH specimens were found in leaf litter below a birch sap drip, and in leaf litter under a fallen spruce. Collected in May and September. In Canada most specimens were captured from a pile of decaying moldy corncobs and cornhusks near a composter next to a mixed forest in a residential area; two adults were sifted from coyote dung in an old jack pine forest, and another from a decayed mushroom in a mixed forest (Webster et al. 2016, Klimaszewski et al. 2018).
Material. USA, New Hampshire, Coos Co.: Norton Pool, 2 mi E East Inlet Dam, 7.IX.1984, D.S. Chandler, leaf litter under fallen spruce, 1 female. Rockingham Co.: Jct. 1A & 1B, nr. Foyes Corner, 12.V.1982, D.S. Chandler, sift oak & beech litter, 1 female. Strafford Co.: 1 mi SW Durham, 21.V.1982, D.S. Chandler, sift leaf litter, birch sap drip, 3 males, 2 females.
description: Published as part of Klimaszewski, Jan, Chandler, Donald S., Davies, Anthony & Bourdon, Caroline, 2023, Aleocharine rove beetles of New Hampshire, USA: new taxa and new records (Coleoptera, Staphylinidae, Aleocharinae), pp. 1-141 in Zootaxa 5364 (1) on page 24, DOI: 10.11646/zootaxa.5364.1.1, http://zenodo.org/record/10145460
Africonus antoniaensis Cossignani & Fiadeiro 2014
Creators: name: Tenorio, Manuel J.
name: Abalde, Samuel
name: Pardos-Blas, José R.
name: Zardoya, Rafael
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Gastropoda
Neogastropoda
Conidae
Africonus
Africonus antoniaensis

description: Africonus antoniaensis Cossignani & Fiadeiro, 2014
Fig. 3A
Africonus antoniaensis Cossignani & Fiadeiro, 2014a: 16.
Africonus padarosae Cossignani & Fiadeiro, 2018a: 18. syn. nov.
Material examined
Holotype
CABO VERDE • 15.6 mm; Boa Vista Island, Baía Antónia; 0.5 to 5 m depth on rocky bottom; MMM.
Other material
CABO VERDE • 14.5 mm; Boa Vista Island, Água Doce; 16º12′29″ N, 22º44′7″ W; 19 Apr. 2015; MNCN exped.; GenBank mitochondrion, partial genome: MF491587; MNCN 15.05/79889 (Fig. 3A) • 13.4 mm, holotype of Africonus padarosae; Boa Vista Island, Baixa de Padaroso; MMM.
Geographical distribution
North of Boa Vista Island, Cabo Verde Archipelago, from Ponta do Sol towards the east, including Derrubado area.
Conservation status in IUCN Red List
Not evaluated.
Remarks
The specimen sequenced from this recently described taxon appears closely related to A. damottai, but at a genetic distance consistent with its consideration as a valid species. The shell of the recently described A. padarosae is morphologically very close to that of A. antoniaensis, and separation at the species level is unsupported, as it falls within the morphological variability of the latter. As it happens with many other recently named cone snails endemic to the Cabo Verde Archipelago, the species separation criterion was based mainly on the type locality, and on subtle conchological differences, which were never statistically tested. In this particular case, the authors claimed that the A. padarosae could be separated from A. antoniaensis based upon “different spire profile and more elongated shape” without any statistically supported morphometric analysis. We therefore propose to consider A. padarosae as a mere form of A. antoniaensis.
description: Published as part of Tenorio, Manuel J., Abalde, Samuel, Pardos-Blas, José R. & Zardoya, Rafael, 2020, Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation, pp. 1-89 in European Journal of Taxonomy 663 (663) on page 10, DOI: 10.5852/ejt.2020.663, http://zenodo.org/record/3890442
Institutional Repositories serve the interests of research funders
Creators: name: Havemann, Jo
Publisher: name: My University
Year: 2024
Subjects: AfricArXiv
Funding
Research in Africa
FAIR Principles
Persistent Identifiers

description: Presentation held at the Africa PID Alliance (africapidalliance.org) Webinar: How effective FAIR data management aids in the visibility of African funding output "Effective FAIR data management significantly aids in the visibility of African funding outputs by making research more discoverable, accessible, interoperable, and reusable. This not only boosts the profile of African research on the global stage but also fosters collaborations, enhances credibility, informs policy, and attracts further funding. For more on how we have been doing this please join our partners Crossref and Research Organization Registry(ROR) as we take you through what we have been doing and listen to some of the African funders case studies from National Research Fund Kenya and National de la Recherche et de l’Innovation pour le Développement - FONRID (Burkina Faso) in addition with the contributions from Association of African Universities and African Open Science Platform who will share the research management and policy-making implications on making African funders output accessible."
The Role of Task Events, Environmental Uncertainty, and Striatal Activity in Modulating Decision Strategies
Creators: name: Badyna, Julia
Publisher: name: Carnegie Mellon University
Year: 2024
Subjects: classificationCode: 319999
subject: Other biological sciences not elsewhere classified

description:  To maximize rewards, organisms must adapt their decision strategies to  environmental events and conditions. For example, one might hypothesize that rewarded  actions should be repeated, whereas behavior should become more variable following  unrewarded actions. The level of outcome responsivity, however, should shift depending on  the environmental conditions, such as the stability of the environment or reliability of  action-outcome contingencies. We propose that all decision strategies can be described  along this outcome responsivity axis.  These strategies range from highly outcome  responsive (such as the win-stay, lose-shift strategy described above) to various low  responsivity strategies (such as biased choices or random exploration). This thesis  investigates specific task events and environmental conditions that trigger these distinct  strategies.  Second, we highlight the striatum as a key brain region for modulating the  “knob” of outcome responsivity.  Finally, the thesis puts forth the notion of cognitive effort to-reward ratio maintenance as an explanation for the observed strategy shifts.
Africonus antoniomonteiroi
Creators: name: Tenorio, Manuel J.
name: Abalde, Samuel
name: Pardos-Blas, José R.
name: Zardoya, Rafael
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Gastropoda
Neogastropoda
Conidae
Africonus
Africonus antoniomonteiroi

description: Africonus antoniomonteiroi (Rolán, 1990)
Fig. 3B
Conus antoniomonteiroi Rolán, 1990: 47, pl. 1, fig. 16.
Conus antoniomonteiroi – Monteiro et al. 2004: 25, pl. 123.
Conus cuneolus form F – Röckel et al. 1980a (not C. cuneolus Reeve, 1843): 107, pl. 3, row 6a, c–f.
Material examined
Holotype
CABO VERDE • 16.8 mm; Sal Island, Parda; 0.5 to 1 m depth; E. Rolán leg.; MNCN 15.05/1100 (Fig. 3 B).
Other material
CABO VERDE • 1 spec.; Sal Island, Pedra Lume; 16º45′44″ N, 22º53′2″ W; 7 Apr. 2014; MNCN exped.; GenBank mitochondrion, partial genome: MF491578; MNCN 15.05/79794.
Geographical distribution
East coast of Sal Island in the Cabo Verde Archipelago, from a point approximately 6 km north to 8 km south of the locality of Pedra Lume.
Conservation status in IUCN Red List
Least concern.
Remarks
Prior to its introduction as a full species by Rolán (1990), it was referred to as Conus cuneolus form F in Röckel et al. (1980a). In the phylogeny this taxon is certainly a member of the cuneolus clade, but the genetic distances and age divergence estimates are consistent with its consideration as a valid species with habitat restricted to the east coast of Sal Island.
description: Published as part of Tenorio, Manuel J., Abalde, Samuel, Pardos-Blas, José R. & Zardoya, Rafael, 2020, Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation, pp. 1-89 in European Journal of Taxonomy 663 (663) on pages 10-11, DOI: 10.5852/ejt.2020.663, http://zenodo.org/record/3890442
Atheta circulicollis Lohse 1990
Creators: name: Klimaszewski, Jan
name: Chandler, Donald S.
name: Davies, Anthony
name: Bourdon, Caroline
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Atheta
Atheta circulicollis

description: 37. Atheta circulicollis Lohse
(Illustrations in Klimaszewski et al. 2018), Table 1
References. Lohse et al. 1990. Klimaszewski et al. 2011, 2021, 2018. Brunke et al. 2012. Webster et al. 2012.
Distribution. Nearctic, transcontinental in Canada, reported from A/S (Klimaszewski et al. 2021). Canada: LB, NB, NF, NT, ON, QC. USA: AK, NH (NSR).
Collection and Habitat data. In NH captured by FITs in a secondary boreal forest and a mixed forest, and in pine litter. In Canada found in leaf litters: in NB in old-growth eastern white cedar swamps in moss and leaves under alders on brook margin and among moist leaves at base of tree, and in mixed forest in a Pleurotus sp. on the side of a log; in NF found in pitfall traps in fir forests, riparian forests, and a recently burned coniferous forest. Specimens from southern ON were taken by flight intercept traps in a flooded mixed forest and other unspecified forests (Klimaszewski et al. 2018). Lohse et al. (1990) reported it from northern boreal forest localities in QC as far north as tree line.
Material. USA, New Hampshire, Coos Co.: 1 mi NE East Inlet Dam, 12–24.VI.1986, D.S. Chandler, FIT, 1 female. Strafford Co.: Kingman Farm, 3.5 km N Durham, 47m, 3–17.IX.2009, forest, FIT, 1 female. 3 mi E Durham, 17.XI.1981, DS Chandler, sift pine litter, 1 male.
description: Published as part of Klimaszewski, Jan, Chandler, Donald S., Davies, Anthony & Bourdon, Caroline, 2023, Aleocharine rove beetles of New Hampshire, USA: new taxa and new records (Coleoptera, Staphylinidae, Aleocharinae), pp. 1-141 in Zootaxa 5364 (1) on page 24, DOI: 10.11646/zootaxa.5364.1.1, http://zenodo.org/record/10145460
Socio-cultural conditions of Japan reflected by factors inducing recent Japanese immigration to Canada
Creators: name: Nagoshi, Mariko
Publisher: name: University of British Columbia
Year: 2008

description: This dissertation examines the socio-cultural conditions of Japanese society as reflected in factors that induce recent Japanese immigration to Canada. The examination is based on interview research done with six female and six male Japanese immigrants living in Vancouver, who arrived in Canada after the mid-1990s. While previous migration studies emphasized political-economic conditions as the causes of migration flow, the narratives of these interviewees reveal a different migratory pattern that is motivated by spiritual well-being and life values. In order to encapsulate the complexity of contemporary migration flow, the push/pull factors that induced interviewees' emigration are thematically categorized and analyzed within a frame that emphasizes both these factors' interdependence with the interrelationships of Japanese social systems that have swayed the interviewees' decision to emigrate from Japan, and the nature of complexity in Japanese society. Showing the pluralism of these factors, they are categorized into nine themes: 1)physical environment; 2) spiritual enrichment and a stress-reduced life style; 3) socio-cultural constraints; 4) family life; 5) education; 6) age restrictions; 7) gender roles; 8)diversification, and 9) self-actualization. Luhmann's theory of social systems and Foucault's notion of governmentality serve as touchstones for the re-interpretation of the push/pull factors based on the examination of the interrelations among three Japanese social systems of family, education, and employment. The analysis reveals the complexity of the push/pull factors. Moreover, the interviewees' image of a "simple Canada," which also contributes to their decision to immigrate, is explained in terms of the "double complexity" of Japanese society stemming from both the complexity of modern society and the complexity of an amalgam of "modern" and "pre-modern" elements in Japanese society. Through an extensive examination of the correlations between the experiences of contemporary Japanese migrants and Japanese social systems, this study brings new insights to discussions on tensions between human agency and social structure, and the importance of intangible, mental images in the ways people shape their lives.
Atheta (Dimetrota) crenuliventris Bernhauer 1907
Creators: name: Klimaszewski, Jan
name: Chandler, Donald S.
name: Davies, Anthony
name: Bourdon, Caroline
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Atheta
Atheta crenuliventris

description: 39. Atheta (Dimetrota) crenuliventris Bernhauer
(Illustrations in Klimaszewski et al. 2018, 2021), Table 1
References. Bernhauer 1907. Lohse et al. 1990. Majka and Klimaszewski 2008. Klimaszewski et al. 2005 a, 2018, 2021. Webster et al. 2016.
Distribution. Nearctic. Canada: LB, MB, NB, NF, NS, ON, QC, SK. USA: ME, NH (NSR).
Collection and Habitat data. Specimens in NH were captured from June to September by FIT and pitfall traps in maple litter along a stream in a forest, and at pig dung in a bog and a pasture. Collected from June to September. In Canada found in various forested and open habitats, often in decaying organic materials: in compost near mixed forest, in dung in entrance to fox den in a pasture, in decaying sea wrack on sea beach, under dung on margin of lake, in litter on roof of an abandoned beaver lodge occupied by muskrats, in decaying moist litter in Carex marsh, and from unbaited pitfall traps in a red spruce forest (Webster et al. 2016). In SK in compost, wrack on lakeshore; in NF captured in carrion-baited pitfall traps and flight intercept traps in conifer-dominated and mixed forests, and at coastal barrens in LB (Klimaszewski et al. 2021).
Material. USA, New Hampshire, Coos Co.: 1 mi NE East Inlet Dam, 12–24.VI.1986, FIT, 1 female; 8– 21.VIII.1986, D.S. Chandler, FIT, 1 female. Grafton Co.: Bedell Bridge St. Park @ Oliverian Brook, 3.VII.1992, D.S. Chandler, berlese maple litter along stream in forest, 1 male; 3.VII.1992, D.S. Chandler, sift silver maple by stream, 1 male; 15–26.VII.1992, D.S. Chandler, FITrap, 1 male. Rockingham Co.: 2 mi SE Epping, Rockingham Co. Farm, 31.VII.1986, S.C. Sherman, pig dung in pasture, 1 male. Strafford Co.: 1 mi SW Durham, 7–20.VIII.1987, D.S. Chandler, FIT, 2 males. Spruce Hole, 3 mi SW Durham, 29.VII.1986, 1 male; 31.VII.1986, S.C. Sherman, pig dung in bog, 1 male. UNH Dudley Lot, 1 km W[E] Lee, 4–18.IX.2008, old field, pitfall trap, 1 male.
description: Published as part of Klimaszewski, Jan, Chandler, Donald S., Davies, Anthony & Bourdon, Caroline, 2023, Aleocharine rove beetles of New Hampshire, USA: new taxa and new records (Coleoptera, Staphylinidae, Aleocharinae), pp. 1-141 in Zootaxa 5364 (1) on page 25, DOI: 10.11646/zootaxa.5364.1.1, http://zenodo.org/record/10145460
Africonus bellulus
Creators: name: Tenorio, Manuel J.
name: Abalde, Samuel
name: Pardos-Blas, José R.
name: Zardoya, Rafael
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Gastropoda
Neogastropoda
Conidae
Africonus
Africonus bellulus

description: Africonus bellulus (Rolán, 1990)
Fig. 3C
Conus bellulus Rolán, 1990: 44, pl. 1, fig. 14.
Conus bellulus – Monteiro et al. 2004: 28, pl. 85.
Material examined
Holotype
CABO VERDE • 18.9 mm; Santa Luzia Island, Curral; E. Rolán leg.; MNCN 15.05/1098 (Fig. 3 C).
Paratype
CABO VERDE • 1 spec.; Santa Luzia Island, Curral; E. Rolán leg.; MJT.
Geographical distribution
Santa Luzia (Curral) and São Vicente (Saragaça), Cabo Verde Archipelago.
Conservation status in IUCN Red List
Data deficient.
Remarks
No specimens of this species have been molecularly examined. Very few specimens have surfaced in the last 30 years, and most of them have been collected as empty shells. Clearly, more studies are needed in order to confirm the status of this taxon. Given the fact that most of the species described from the islands of São Vicente and Santa Luzia have shown relative large genetic divergences, we provisionally consider this as a valid species.
description: Published as part of Tenorio, Manuel J., Abalde, Samuel, Pardos-Blas, José R. & Zardoya, Rafael, 2020, Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation, pp. 1-89 in European Journal of Taxonomy 663 (663) on page 11, DOI: 10.5852/ejt.2020.663, http://zenodo.org/record/3890442
Atheta (Dimetrota) districta Casey 1911
Creators: name: Klimaszewski, Jan
name: Chandler, Donald S.
name: Davies, Anthony
name: Bourdon, Caroline
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Atheta
Atheta districta

description: 41. Atheta (Dimetrota) districta Casey
(Illustrations in Klimaszewski et al. 2018), Table 1
References. Casey 1911. Klimaszewski et al. 2005 a, 2018. Majka and Klimaszewski 2008.
Distribution. Nearctic. Canada: AB, BC, LB, MB, NB, NF, NS, ON, QC, SK. USA (NCR): ME (NSR), NH (NSR).
Collection and Habitat data. The NH specimens were found in leaf litter at a birch sap drip in deciduous forests and in an old burned field. Collected in May and August–October by window and flight intercept traps, and by sifting rotting lawn clippings. In Canada found in various forest types, usually in dung or decaying mushrooms: eastern white cedar swamp in moose dung, mature red spruce and eastern white cedar forest in deer dung, mixed forest in bear dung, in decaying (moldy) corncobs and cornhusks near mixed forest, regenerating mixed forest in decaying mushrooms, near lakeshore in decaying fungi, and in an old jack pine forest in rotten Boletus mushrooms. Also taken in a red maple swamp in leaf litter near a stream, and by pitfall traps in a red spruce forest A few specimens were collected at UV lights (Klimaszewski et al. 2018).
Material. USA, Maine, Piscataquis Co.: Mt. Katahdin, 5200’, 3.IX.1939, 1 male. York Co.: West Lebanon, 7–13.V.1991, 1 male; 10–16.VII.1990, 1 male; 17–23.VII.1990, 1 male; 21–27.VIII.1990, 25–30.IX.1990, 1 female, D.W. Barry, FIT, 1 male, 1 female. New Hampshire, Carroll Co.: 6 mi NW Bartlett Nancy Brook Trail, 1500’, 9.IX.1987, Y. Bousquet (CNC), 1 sex? Crawford Notch, 3–5.IX.1970, S. Peck, deciduous forest, human dung trap (CNC), 1 male, 1 female. Coos Co.: 8 mi E Gorham, 800’, 14.VIII.1976, J.M. and B.A. Campbell (CNC), 3 sex? 8 mi E Gorham, 800’, 15.VIII.1976, J.M. and B.A. Campbell (CNC) 8 sex? Strafford Co.: 1 mi SW Durham, 21.V.1982, D.S. Chandler, sift leaf litter birch sap drip, 1 male, 1 female. Durham, 26.V.1987, W.J. Morse, rotting lawn clippings, 1 female. 4 mi W Durham, 19–21.V.1982, R.M. Reeves, window trap, 1 male. East Foss Farm, 32m, 1 km S Durham, 21.IX–4.X.2007, ZOOL 745/845 class, FIT, old burned field, 1 male, 1 female.
description: Published as part of Klimaszewski, Jan, Chandler, Donald S., Davies, Anthony & Bourdon, Caroline, 2023, Aleocharine rove beetles of New Hampshire, USA: new taxa and new records (Coleoptera, Staphylinidae, Aleocharinae), pp. 1-141 in Zootaxa 5364 (1) on page 26, DOI: 10.11646/zootaxa.5364.1.1, http://zenodo.org/record/10145460
College students with learning disabilities: a developmental perspective on conceptions of learning, learning disability, and others in learning
Creators: name: Pacheva, Daniela Jivkova
Publisher: name: University of British Columbia
Year: 2008

description: A call for the design of programs focused on the development of self-awareness skills permeates the field of research and practice on postsecondary students with learning disabilities (LD). Important components of self-awareness are students' advanced understanding of learning, LD, and the social context (peers, instructors, classmates) of college learning. This study explores students with LD's conceptual understanding of learning and LD by situating it within developmental theoretical frameworks delineating the form and content of adult reasoning. Twelve female and five male college-students with LD participated in two-hour interviews. Students' thinking about others was explored by asking participants to reason about the behaviors, intentions, feelings and traits of the characters in two scenarios depicting typical dilemmas faced by students with LD. Students' conceptual understanding of learning and LD was elicited by means of open-ended questions followed by prompts. Students' responses were scored for level of cognitive complexity and coded for conceptual content. Overall, the students reasoned abstractly about learning and LD at a level of complexity expected from college-age population. They demonstrated well-developed understanding of others' expectations and motivations especially as they relate to the themes of self-identification, seeking accommodations, and understanding of LD. Students' conceptions of learning and LD presented qualitatively different variations on main themes. These variations paralleled the increase in complexity and were associated with experience(number of years of education). The overarching understanding of learning as acquiring knowledge transitioned from understanding learning as an external, given task to learning as an internal, personal-development process. The common understanding of LD as a difference transitioned from a difference related to an external label and an imposed constraint, to meaning of "difference" as a special ability, an asset, and a source of identity. These results indicate a possible progression in the evolution of the concepts of learning and LD throughout the college career of students with LD. The approach to this conceptual content and its description can inform and serve as starting points in the development of programs that foster the conceptual understanding of learning, LD, and the social-context of the educational enterprise, as a way of building these students' self-awareness skills.
Atheta cranberriensis Klimaszewski and Webster
Creators: name: Klimaszewski, Jan
name: Chandler, Donald S.
name: Davies, Anthony
name: Bourdon, Caroline
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Atheta
Atheta cranberriensis

description: 38. Atheta cranberriensis Klimaszewski and Webster
(Illustrations in Webster et al. 2016, Klimaszewski et al. 2018), Table 1
References. Webster et al. 2016. Klimaszewski et al. 2018.
Distribution. Nearctic. Canada: NB. USA (NCR): NH (NSR).
Collection and Habitat data. In NH specimens were captured by window, flight intercept, and pitfall traps. Also taken in Rhododendron litter, beech litter, rotten wood, in a pine-oak barrens, and by sweeping Maianthemum canadense Desf. Adults were taken from April to June and from September to October. In Canada collected in Lindgren funnel traps in a red oak forest and a hardwood woodland near a seasonally flooded marsh; some flying individuals were collected with a net in a mixed forest opening; four were sifted from litter at the entrance of a groundhog (Marmota monax) burrow (Webster et al. 2016).
Material. USA, New Hampshire, Cheshire Co.: Rhododendron St. Park, 22.IV.1982, D.S. Chandler, sift Rhododendron litter, 1 male. Grafton Co.: Hubbard Brook Exp. Forest, Bear Brook, 1500’, 15.X.1982, D.S. Chandler, sift rotten wood, 1 male. Merrimack Co.: 1 mi E Concord, Concord Airport, CZ-4a, 13–26.VI.2001, C. Anderson, pine-oak barrens, pitfall trap, 1 female. Rockingham Co.: Jct. 1A & 1B, near Foyes Corner, 4.V.1982, D.S. Chandler, sweep Maianthemum canadense, 1 male. Odiorne Point, 18–25.V.1983, window trap, D.S. Chandler, 1 male. Strafford Co.: 4 mi W Durham, 14–17.V.1982, R.M. Reeves, window trap, 7 females. East Foss Farm, 1 km S Durham, 26m, 2.IX–4.X.2007, ZOOL 745/845 class, pitfall trap, 1 male. Spruce Hole, 3 mi SW Durham, 12.VI.1982, D.S. Chandler, sift beech litter, 1 female. West Foss Farm, 1 km S Durham, 43 07.370, -70 56.639, 2–16.IX.2004, ZOOL 745/845 class, fl. trap, forest, 1 male.
Comments. Some Atheta alesi and A. cranberriensis were collected in the same trap during the same time period. The two can be readily separated by the different shape of the male tergite VIII (for illustrations see Klimaszewski et al. 2018).
description: Published as part of Klimaszewski, Jan, Chandler, Donald S., Davies, Anthony & Bourdon, Caroline, 2023, Aleocharine rove beetles of New Hampshire, USA: new taxa and new records (Coleoptera, Staphylinidae, Aleocharinae), pp. 1-141 in Zootaxa 5364 (1) on pages 24-25, DOI: 10.11646/zootaxa.5364.1.1, http://zenodo.org/record/10145460
Africonus boavistensis
Creators: name: Tenorio, Manuel J.
name: Abalde, Samuel
name: Pardos-Blas, José R.
name: Zardoya, Rafael
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Gastropoda
Neogastropoda
Conidae
Africonus
Africonus boavistensis

description: Africonus boavistensis (Rolán & Fernandes in Rolán, 1990)
Fig. 3D
Conus boavistensis Rolán & Fernandes in Rolán, 1990: 23, pl. 1, fig. 17.
Africonus barrosensis Cossignani & Fiadeiro, 2017a: 27. syn. nov.
Africonus varandinhensis Cossignani & Fiadeiro, 2017a: 33. syn. nov.
Conus boavistensis – Monteiro et al. 2004: 29, pl. 121.
Material examined
Holotype
CABO VERDE • 13.2 mm; Boa Vista Island, Morro de Areia; E. Rolán leg.; MNCN 15.05/1089 (Fig. 3 D).
Other material
CABO VERDE • 1 spec.; Boa Vista Island, Baía do Ervatão; 16º12′3″ N, 22º54′43″ W; 2 Jul. 2013; MNCN exped.; GenBank mitochondrion, partial genome: MF491563; MNCN 15.05/80413 • 1 spec., 11 mm, holotype of Africonus barrosensis; Boa Vista Island, João Barrosa; MMM • 1 spec, 10.6 mm, holotype of Africonus varandinhensis; Boa Vista Island, Varandinha; MMM.
Geographical distribution
Multiple localities around Boa Vista Island, Cabo Verde Archipelago.
Conservation status in IUCN Red List
Least concern.
Remarks
This small species is widely distributed around the island of Boa Vista. It is very variable, and it has given rise to the introduction of several names (applied to representative specimens from certain local populations from the southwest and south coasts of the island), which are hereby considered junior synonyms. In the molecular tree, it appears as sister to A. diminutus, with a short genetic distance. Both species belong to a clade in which all the individuals have medium-sized and very broad radular teeth. The specimens in the type series of A. barrosensis and A. varandinhensis exhibit shell coloration, pattern and shape consistent with the morphological variability of A. boavistensi s.
description: Published as part of Tenorio, Manuel J., Abalde, Samuel, Pardos-Blas, José R. & Zardoya, Rafael, 2020, Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation, pp. 1-89 in European Journal of Taxonomy 663 (663) on pages 11-12, DOI: 10.5852/ejt.2020.663, http://zenodo.org/record/3890442
Atheta (Datomicra) dadopora Thomson
Creators: name: Klimaszewski, Jan
name: Chandler, Donald S.
name: Davies, Anthony
name: Bourdon, Caroline
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Atheta
Atheta dadopora

description: 40. Atheta (Datomicra) dadopora Thomson *
(Illustrations in Lee and Ahn, 2017, Klimaszewski et al. 2018), Table 1
References. Thomson 1867. Casey 1910. Gusarov 2003. Majka and Sikes 2009. Lee and Ahn 2017. Klimaszewski et al. 2018.
Distribution. Holarctic, recorded from Europe, China, India, Japan and South Korea. Canada: AB, BC, LB, MB, NB, NF, NS, NT, ON, PE, QC, SK, YT. USA: AK, MA?, NH (NSR), NY, PA, RI.
Collection and Habitat data. Specimens in NH were captured by window traps, and were found in fungi and in leaf litter at a birch sap drip. Collected from May to September. In Canada found in various mixed, coniferous, and hardwood forest types, usually in decaying materials such as decaying fungi and carrion. Collected by: Lindgren funnel traps in red spruce forest with red maple and balsam fir, unbaited pitfall traps in red spruce forest, spruce forest in decaying fleshy fungi, mixed forests on Pleurotus sp. on Populus log, red oak and red maple forest in gilled mushrooms, alder swamp on remains of dead deer, and rich Appalachian hardwood forest in fleshy fungi in various stages of decay. Also in compost, poplar/spruce litter, carrion, bison and caribou dung, and under the bark of decaying spruce logs (Klimaszewski et al. 2018).
Material. USA, New Hampshire, Strafford Co.: 4 mi W Durham, 7–10.V.1982, 10–13.VI.1982, 9–12.VII.1982, 29.VII–1.VIII.1982, window trap, R.M. Reeves, 6 females, 1 sex?; 10.V.1982, D.S. Chandler, mushrooms, 1 female. Barrington, 6.IX.1986, fungus, W.J. Morse, 1 female. 1 mi SW Durham, 21.V.1982, sift leaf litter birch sap drip, D.S. Chandler, 1 male, 2 females, 19 sex? Kingman Farm, 3.5 km N Durham, 47m, 3–17.IX.2009, ZOOL 745/845 class, forest, FIT, 1 female. Spruce Hole, 3 mi SW Durham, 21–23.VII.1987, 10–23.VII.1987, D.S. Chandler, FIT, 2 males.
description: Published as part of Klimaszewski, Jan, Chandler, Donald S., Davies, Anthony & Bourdon, Caroline, 2023, Aleocharine rove beetles of New Hampshire, USA: new taxa and new records (Coleoptera, Staphylinidae, Aleocharinae), pp. 1-141 in Zootaxa 5364 (1) on page 25, DOI: 10.11646/zootaxa.5364.1.1, http://zenodo.org/record/10145460
Atheta (Tetropla) frosti Bernhauer
Creators: name: Klimaszewski, Jan
name: Chandler, Donald S.
name: Davies, Anthony
name: Bourdon, Caroline
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Atheta
Atheta frosti

description: 44. Atheta (Tetropla) frosti Bernhauer
(Illustrations in Klimaszewski et al. 2018), Table 1
References. Bernhauer 1909. Casey 1910, 1911 (as 10 junior synonyms). Gusarov 2003. Majka and Klimaszewski 2008. Klimaszewski et al. 2018, 2020, 2021.
Distribution. Nearctic, transcontinental in Canada, reported from A/S (Klimaszewski et al. 2021). Canada: AK, BC, LB, MB, NB, NS, ON, QC, SK. USA: AK, IA, MA, NC, NH, NY, PA, RI, VT, WV.
Collection and Habitat data. In NH captured by window and Malaise traps, and found in beech and unspecified forest litters; collected from June to November. In Canada found in various coniferous, mixed, and hardwood forests in decaying fungi/mushrooms where it is often common; in pitfall trap in red spruce forest and some in decaying (moldy) corncobs and cornhusks near a mixed forest Also from pitfall traps in an open spruce forest with sandy soil and Cladina lichen cover, in birch-dominated forests, and in polypore fungus in a coniferous forest (Klimaszewski et al. 2018).
Material. USA, New Hampshire, Carroll Co.: 2 mi NW Jackson, 11.IX.1981, D.S. Chandler, berlese forest litter, 1 female. Coos Co.: 8 mi E Gorham, 800’, 14.VIII.1976, J.M. and B.A. Campbell (CNC), 2 males, 9 sex? White Mts., Crawford Notch, Silver Cascade, 17.VIII.1976, J.M. Campbell (CNC), 1 sex? Pinkham Notch, near Lost Pond, 11.IX.1987, Y. Bousquet (CNC), 1 sex? Strafford Co.: 4 mi W Durham, 20.X–1.XI.1982, R.M. Reeves, window trap, 1 female; 29.VII–1.VIII.1982, R.M. Reeves, malaise trap, 1 male. Spruce Hole, 3 mi SW Durham, 10–23.VII.1987, FIT, 1 male; 12.VI.1982, D.S. Chandler, sift beech litter, 1 male. UNH Dudley Lot, 1 km W[E] Lee, 11.IX.2008, J.A. Feehily, sift forest litter, 1 female.
description: Published as part of Klimaszewski, Jan, Chandler, Donald S., Davies, Anthony & Bourdon, Caroline, 2023, Aleocharine rove beetles of New Hampshire, USA: new taxa and new records (Coleoptera, Staphylinidae, Aleocharinae), pp. 1-141 in Zootaxa 5364 (1) on page 27, DOI: 10.11646/zootaxa.5364.1.1, http://zenodo.org/record/10145460
Africonus borgesi
Creators: name: Tenorio, Manuel J.
name: Abalde, Samuel
name: Pardos-Blas, José R.
name: Zardoya, Rafael
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Gastropoda
Neogastropoda
Conidae
Africonus
Africonus borgesi

description: Africonus borgesi (Trovão, 1979)
Fig. 3E
Conus borgesi Trovão, 1979: 6, pl. 1, fig. 4.
Africonus wandae Cossignani, 2014: 22. syn. nov.
Africonus pedrofiadeiroi Cossignani & Fiadeiro, 2015a: 18. syn. nov.
Conus borgesi – Monteiro et al. 2004: 30, pl. 116–117.
Material examined
Holotype
CABO VERDE • 26.1 mm; Boa Vista Island, Baía das Gatas; 2 m depth; NHMUK 1986196.
Other material
CABO VERDE • 1 spec., 30.5 mm; Boa Vista Island, Derrubado; 16º13′31″ N, 22º47′32″ W; 29 Jun. 2013; MNCN exped.; MNCN 15.05 /88646 (Fig. 3E) • 1 spec.; Boa Vista Island, Porto Ferreira; 16º7′45″ N, 22º40′17″ W; MNCN exped.; GenBank mitochondrion, partial genome: NC_013243; MNCN ADN/6990 • 1 spec., 27.4 mm, holotype of Africonus wandae; Boa Vista Island, Baía Grande; MMM • 1 spec., 24.7 mm, holotype of Africonus pedrofiadeiroi; Boa Vista Island, Curral Velho to Ilhéu de Galeão; 1 to 5 m depth; MMM.
Geographical distribution
Multiple localities around Boa Vista Island, Cabo Verde Archipelago.
Conservation status in IUCN Red List
Least concern.
Remarks
This species is widely distributed around the island of Boa Vista. Differences in color pattern have been invoked for the introduction of new names for certain local populations from the southeast and south coasts of the island without further justification. We hereby consider these names as synonyms. Thus, specimens matching the type material of Africonus wandae were studied in detail in Tenorio et al. (2014), and their haplotypes (cox1 gene fragment) showed to be identical with that of A. borgesi. The holotype of Africonus pedrofiadeiroi exhibits a white middle band patterned with minute brown zigzag markings, a feature characteristic of A. borgesi, which is considered conspecific.
Africonus borgesi and A. josephinae are very closely related according to the phylogeny. They belong to a lineage that contains species from Boa Vista and Maio islands, and is the sister group to the remaining Africonus.
description: Published as part of Tenorio, Manuel J., Abalde, Samuel, Pardos-Blas, José R. & Zardoya, Rafael, 2020, Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation, pp. 1-89 in European Journal of Taxonomy 663 (663) on pages 12-14, DOI: 10.5852/ejt.2020.663, http://zenodo.org/record/3890442
Atheta (Microdota) festinans ON, QC
Creators: name: Klimaszewski, Jan
name: Chandler, Donald S.
name: Davies, Anthony
name: Bourdon, Caroline
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Atheta
Atheta festinans

description: 43. Atheta (Microdota) festinans (Erichson)
(Illustrations in Klimaszewski et al. 2018), Table 1
References. Erichson 1839. Bernhauer 1907. Blatchley 1910. Casey 1910. Gusarov 2003. Majka and Sikes 2009. Brunke et al. 2012. Klimaszewski et al. 2015c, 2018.
Distribution. Nearctic. Canada: ON, QC. USA: AZ, CT, IA, IN, KS, MA, ME, MI, NH, NY, PA, RI.
Collection and Habitat data. In NH three females were captured by sweeping a lawn in October. In Canada taken by a pitfall trap in a hedgerow (ON), and from woody debris in a sandy pit in association with a Dyschirius sp. (Carabidae) (QC) (Brunke et al. 2012, Klimaszewski et al. 2018).
Material. USA, New Hampshire, Strafford Co.: Bellamy Road, 3.2. km S Dover, 15.X.2020, D.S. Chandler, sweep lawn, 3 females.
Comments. Gusarov (2003 a) remarked that all specimens seen of this species were females, and suggested that this species may be parthenogenetic. Congruently, the Ontario, Quebec (Klimaszewski et al. 2018), and New Hampshire specimens were also females.
description: Published as part of Klimaszewski, Jan, Chandler, Donald S., Davies, Anthony & Bourdon, Caroline, 2023, Aleocharine rove beetles of New Hampshire, USA: new taxa and new records (Coleoptera, Staphylinidae, Aleocharinae), pp. 1-141 in Zootaxa 5364 (1) on page 27, DOI: 10.11646/zootaxa.5364.1.1, http://zenodo.org/record/10145460
Atheta (Dimetrota) giguereae Klimaszewski and Webster
Creators: name: Klimaszewski, Jan
name: Chandler, Donald S.
name: Davies, Anthony
name: Bourdon, Caroline
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Atheta
Atheta giguereae

description: 45. Atheta (Dimetrota) giguereae Klimaszewski and Webster
(Illustrations in Webster et al. 2016, Klimaszewski et al. 2018), Table 1
References. Webster et al. 2016. Klimaszewski et al. 2016, 2018.
Distribution. Nearctic. Canada: NB, NF, NS, ON. USA (NCR): NY (NSR)
Collection and Habitat data. In NY found in rotten wood in December. In Canada found in various coniferous, mixed, and hardwood forests, usually in moss and leaf litter near streams, brooks, and seepage areas, and from moist moss on forest floor or at bases of trees (Webster et al. 2016). In NB taken in mature and old-growth eastern white cedar forests and swamps; a few were captured in Lindgren funnel traps; in NS specimens were captured in flight intercept traps in red spruce and red spruce/hemlock forests (Webster et al. 2016).
Material. USA, New York, Franklin Co.: Jct. 30 and 192, 4.XII.1982, D.S. Chandler, sift rotten wood, 1 female.
Comments. This species has not yet been reported from NH where it is almost certainly present. We report it for the first time here from the USA from the state of NY.
description: Published as part of Klimaszewski, Jan, Chandler, Donald S., Davies, Anthony & Bourdon, Caroline, 2023, Aleocharine rove beetles of New Hampshire, USA: new taxa and new records (Coleoptera, Staphylinidae, Aleocharinae), pp. 1-141 in Zootaxa 5364 (1) on page 29, DOI: 10.11646/zootaxa.5364.1.1, http://zenodo.org/record/10145460
Atheta (Atheta) graminicola
Creators: name: Klimaszewski, Jan
name: Chandler, Donald S.
name: Davies, Anthony
name: Bourdon, Caroline
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Atheta
Atheta graminicola

description: 46. Atheta (Atheta) graminicola (Gravenhorst) *
(Illustrations in Klimaszewski et al. 2018), Table 1
References. Gravenhorst 1806. Lohse and Smetana 1985. Lohse et al. 1990. Gusarov 2003. Webster et al. 2009. Klimaszewski et al. 2011, 2015a, 2021. Brunke et al. 2021.
Distribution. Holarctic, transcontinental in Canada, listed as A/S (Klimaszewski et al. 2021). Canada: AB, BC, LB, MB, NB, NF, NT, ON, QC, SK, YT. USA: AK, NH, OR.
Collection and Habitat data. In NH captured in alder and grass leaf litter in a boreal forest, and above tree line in dwarf Salix, Vaccinium, and leatherleaf litter. Collected only in September. In Canada found in various wetland habitats: Carex marsh in emergent vegetation (treading, very common), splashing exposed bedrock next to waterfalls among cobblestones, gravel, and sand, on gravel bar near outflow of brook into a river, in hardwood forest in moist leaves on vernal pond margin, upper margin of sea beach in drift material (mostly grass litter), and two individuals were collected with an aerial net in late afternoon when snow was still present in shaded areas of the woods (Webster et al. 2009). In QC found in leaf litter next to stream; in Salix litter at two localities in the YT; and in NL taken by a flight intercept trap in a mixed forest (Klimaszewski et al. 2018).
Material. USA, New Hampshire, Coos Co.: Beaver Brook Falls, 3 mi NE Colebrook, 27.IX.1986, D.S. Chandler, sift alder and grass leaf litter, 1 female. Mt. Washington, above tree line, 5300–5700’, 10.IX.1987, J.M. Campbell and A. Davies, dwarf Salix, Vaccinium, leatherleaf litter (CNC), 1 male, 1 female, 1 sex? Mt. Washington, Alpine Garden, 5300’, 12.IX.1987, J.M. Campbell and A. Davies, sifting dwarf Salix litter (CNC), 4 males, 2 females, 1 sex?
description: Published as part of Klimaszewski, Jan, Chandler, Donald S., Davies, Anthony & Bourdon, Caroline, 2023, Aleocharine rove beetles of New Hampshire, USA: new taxa and new records (Coleoptera, Staphylinidae, Aleocharinae), pp. 1-141 in Zootaxa 5364 (1) on page 29, DOI: 10.11646/zootaxa.5364.1.1, http://zenodo.org/record/10145460
Atheta (Lamiota) keeni Casey 1910
Creators: name: Klimaszewski, Jan
name: Chandler, Donald S.
name: Davies, Anthony
name: Bourdon, Caroline
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Atheta
Atheta keeni

description: 48. Atheta (Lamiota) keeni Casey
(Illustrations in Klimaszewski et al. 2020, 2021), Table 1
References. Casey 1910. Gusarov 2003. Klimaszewski and Winchester 2002a (as L. vasta). Klimaszewski et al. 2020, 2021.
Distribution. Nearctic, transcontinental in Canada, reported from A/S (Klimaszewski et al. 2021). Canada:AB, BC. USA: AK, NH (NSR), OR.
Collection and Habitat data. In NH a single female was captured in a FIT in June at a site near the border with Quebec. In AK found in forest litter of Alnus, Verathrum, and ferns (Klimaszewski et al. 2021). In BC found in a transition zone of Sitka spruce, in dung and carrion, in Alnus litter, in moss, fern, and Amelanchier litter at edge of upland pond, and in moss and leaf litter near a creek; in AB found in a Douglas fir and lodgepole pine stand with aspen and birch understory (Klimaszewski et al. 2021).
Material. USA, New Hampshire, Coos Co.: 1 mi NE East Inlet Dam, 12–24.VI.1996, D.S. Chandler, FIT, 1 female.
Comments. The record from NH should be consider as a tentative one because it is based only on single female specimen, and there is a possibility of confusion with some other species.
description: Published as part of Klimaszewski, Jan, Chandler, Donald S., Davies, Anthony & Bourdon, Caroline, 2023, Aleocharine rove beetles of New Hampshire, USA: new taxa and new records (Coleoptera, Staphylinidae, Aleocharinae), pp. 1-141 in Zootaxa 5364 (1) on page 30, DOI: 10.11646/zootaxa.5364.1.1, http://zenodo.org/record/10145460
Africonus calhetae
Creators: name: Tenorio, Manuel J.
name: Abalde, Samuel
name: Pardos-Blas, José R.
name: Zardoya, Rafael
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Gastropoda
Neogastropoda
Conidae
Africonus
Africonus calhetae

description: Africonus calhetae (Rolán, 1990)
Fig. 3F
Conus navarroi calhetae Rolán, 1990: 41, pl. 1, fig. 7.
Conus navarroi calhetae – Monteiro et al. 2004: 63, pl. 151.
Material examined
Holotype
CABO VERDE • 26.8 mm; Maio Island, Baía de Pau Seco; E. Rolán leg.; MNCN 15.05/1096 (Fig. 3F).
Other material
CABO VERDE • 1 spec.; Maio Island, Praia da Soca; 15º15′8″ N, 23º13′4″ W; 2 Apr. 2013; MNCN exped.; GenBank mitochondrion, partial genome: MF491534; MNCN 15.05/78798 • 1 spec.; same collection data as for preceding; 2 Apr. 2013; MNCN exped.; GenBank mitochondrion, partial genome: MF491533; MNCN 15.05/78787.
Geographical distribution
Between Calheta and Baía do Navío Quebrado, in the western and northwestern coast of Maio Island, Cabo Verde Archipelago.
Conservation status in IUCN Red List
Least concern.
Remarks
This taxon was initially introduced as a subspecies, i.e., Conus navarroi calhetae Rolán, 1990, due to morphological similarities in shell and radula between the populations from São Vicente and Maio islands. However, these disjunct populations are genetically distant. The closest relative according to the phylogeny is the parapatric taxon A. galeao.
description: Published as part of Tenorio, Manuel J., Abalde, Samuel, Pardos-Blas, José R. & Zardoya, Rafael, 2020, Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation, pp. 1-89 in European Journal of Taxonomy 663 (663) on pages 14-15, DOI: 10.5852/ejt.2020.663, http://zenodo.org/record/3890442
Implementation of Girsanov Reweighting in OpenMM and Deeptime
Creators: name: Schäfer, Joana-Lysiane
name: Keller, Bettina G.
Publisher: name: Freie Universität Berlin
Year: 2024
Subjects: subject: Computational chemistry
subject: Mathematical methods
subject: Molecular dynamics
subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften

description: Classical molecular dynamics (MD) simulations provide invaluable insights into complex molecular systems but face limitations in capturing phenomena occurring on time scales beyond their reach. To bridge this gap, various enhanced sampling techniques have been developed, which are complemented by reweighting techniques to recover the unbiased dynamics. Girsanov reweighting is a reweighting technique that reweights simulation paths, generated by a stochastic MD integrator, without evoking an effective model of the dynamics. Instead, it calculates the relative path probability density at the time resolution of the MD integrator. Efficient implementation of Girsanov reweighting requires that the reweighting factors are calculated on-the-fly during the simulations and thus needs to be implemented within the MD integrator. Here, we present a comprehensive guide for implementing Girsanov reweighting into MD simulations. We demonstrate the implementation in the MD simulation package OpenMM by extending the library openmmtools. Additionally, we implemented a reweighted Markov state model estimator within the time series analysis package Deeptime.
Fluorinated Protein–Ligand Complexes: A Computational Perspective
Creators: name: Wehrhan, Leon
name: Keller, Bettina G.
Publisher: name: Freie Universität Berlin
Year: 2024
Subjects: subject: Anions
subject: Fluorine
subject: Ligands
subject: Molecular mechanics
subject: Noncovalent interactions
subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften

description: Fluorine is an element renowned for its unique properties. Its powerful capability to modulate molecular properties makes it an attractive substituent for protein binding ligands; however, the rational design of fluorination can be challenging with effects on interactions and binding energies being difficult to predict. In this Perspective, we highlight how computational methods help us to understand the role of fluorine in protein–ligand binding with a focus on molecular simulation. We underline the importance of an accurate force field, present fluoride channels as a showcase for biomolecular interactions with fluorine, and discuss fluorine specific interactions like the ability to form hydrogen bonds and interactions with aryl groups. We put special emphasis on the disruption of water networks and entropic effects.
Leaf: an ultrafast filter for population-scale long-read SV detection
Creators: name: Pan, Chenxu
name: Reinert, Knut
Publisher: name: Freie Universität Berlin
Year: 2024
Subjects: subject: Filter-based pipelines
subject: Intra-read SV detection
subject: Population-scale long-read applications
subject: Generative model
subject: Extended SAM/BAM
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Advances in sequencing technology have facilitated population-scale long-read structural variant (SV) detection. Arguably, one of the main challenges in population-scale analysis is developing effective computational pipelines. Here, we present a new filter-based pipeline for population-scale long-read SV detection. It better captures SV signals at an early stage than conventional assembly-based or alignment-based pipelines. Assessments in this work suggest that the filter-based pipeline helps better resolve intra-read rearrangements. Moreover, it is also more computationally efficient than conventional pipelines and thus may facilitate population-scale long-read applications.