cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Centrosome abnormalities, Chlamydia and HPV
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Cervical cancer is caused by human papillomavirus (HPV), but only develops in a subset of women infected with HPV. Chlamydia trachomatis, the most common cause of bacterial sexually transmitted infection, is proposed as a co-factor for HPV, but the mechanism is not understood. In this application, we will examine if Chlamydia contributes to oncogenesis by enhancing HPV-induced centrosome abnormalities. Overexpression of HPV oncoproteins E6 and E7 cause centrosome amplification indirectly or through effects on Cdk2. Work from my lab and another group showed that C. trachomatis also induces centrosome abnormalities. This finding provides biologic plausibility for Chlamydia’s role in cancer development because centrosome abnormalities cause genomic instability, trigger invasive behavior and are a hallmark of most human cancers. We hypothesize that co-infection with HPV and Chlamydia may promote oncogenesis by causing cooperative or synergistic dysregulation of centrosome number and organization. In parallel experiments, we will compare centrosome dysregulation caused by HPV and Chlamydia alone and in combination. We will induce HPV-associated centrosome abnormalities by transiently expressing HPV E6 and/or E7 from high-risk HPV type 16 in HPV-negative cervical cell lines. We will also infect such cells with C. trachomatis in the presence and absence of HPV oncoproteins. We will use methods that my lab has developed to quantify centrosome abnormalities in Chlamydia-infected cells. For example, we will measure the proportion of cells with supernumerary centrosomes, average centrosome number per cell and morphologic changes using immunofluorescence and transmission electron microscopy. We will assay for defects in the ability of supernumerary centrosomes to nucleate and organize microtubules and to form a bipolar spindle in mitosis, and will detect chromosomal segregation errors by FISH analysis. We will also measure the activity of the small GTPase Rac1, which has been shown to promote invasive behavior of cells with amplified centrosomes. Finally, we will assay for malignant transformation by testing if cells can grow in the absence of adhesion in a soft agar transformation assay. These studies of Chlamydia and HPV’s combined effects on the centrosome may provide a molecular mechanism for Chlamydia as a co-factor for HPV in the development of cervical cancer.
Additional file 1: of All things to all people: trade-offs in pursuit of an ideal modeling tool for maternal and child health
Creators: name: Roberton, Timothy
name: Litvin, Kate
name: Self, Andrew
name: Stegmuller, Angela
Publisher: name: Figshare
Year: 2017
Subjects: subject: Molecular Biology
subject: Sociology
subject: FOS: Sociology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Science Policy
subject: Computational Biology

description: Qualitative survey. (PDF 33 kb)
Photothermal Therapy of Oral Squamous Cell Carcinoma
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Actively targeted photothermal therapy (PTT) is a new and highly promising medical modality for cancer imaging and treatment. Oral cancer is the ninth most common cancer worldwide, and its prognosis remains poor in comparison to other cancer types, representing a continuing challenge in biomedicine. We propose to use a novel photothermal agent based on peptide-conjugated hollow gold nanospheres (P-HGNs) to actively target and treat oral squamous cell carcinoma (OSCC). The P-HGNs are designed with optimal size, shape, strong near infrared (NIR) light absorption, conjugation length, and high photothermal conversion efficiency. Instead of using antibody for targeting, we propose to use short peptides to reduce the distance between the HGNs and cancer cell or tissue to enhance heat transport and thereby PTT efficiency. Moreover, peptides, as recognition elements, are highly specific, yet inexpensive to produce, thus improving the translational potential of our constructs. We will conduct in vitro studies to validate the hypothesis that P-HGNs are highly effective for PTT applications, which lays the foundation for future in vivo studies.
Centropomidae Poey 1967
Creators: name: Angulo, Arturo
name: Betts, Joel T.
name: González-Alemán, Néstor J.
name: Castañeda, Edgar
name: Berghe, Eric Van Den
name: Elías, Diego J.
name: Mcmahan, Caleb D.
name: Matamoros, Wilfredo A.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Centropomidae

description: Family Centropomidae Poey 1967 (Fig. 3L). Snooks; Róbalos, Gualajes
Description: Body oblong, elongate and slightly compressed; up to 120 cm in length; head pointed, with forehead oblique to concave; mouth large and protractile; lower jaw strongly protruding; margin of preopercle serrated; scales rough, large; lateral line, which usually is dark, extends to the end of the tail fin; two well separated dorsal fins, the first one with eight spines and the second one with one spine and 8–11 rays; anal fin short, with three strong spines and 5–8 soft rays; pelvic fins insert a little behind pectoral base, with one strong spine and five rays; caudal fin strongly forked (Robertson & Allen 2015). Distribution: Marine (often brackish) and freshwater; tropical and subtropical waters of America (Nelson et al. 2016). One genus and eleven species in Nicaraguan freshwaters.
description: Published as part of Angulo, Arturo, Betts, Joel T., González-Alemán, Néstor J., Castañeda, Edgar, Berghe, Eric Van Den, Elías, Diego J., Mcmahan, Caleb D. & Matamoros, Wilfredo A., 2023, Continental fishes of Nicaragua: diversity, distribution and conservation status; with an annotated and illustrated checklist of species and an identification guide to families, pp. 1-89 in Zootaxa 5376 (1) on page 39, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Yagansia lajaensis Zicsi & Csuzdi 2001
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Acanthodrilidae
Yagansia
Yagansia lajaensis

description: Yagansia lajaensis Zicsi & Csuzdi, 2001
Yagansia lajaensis Zicsi & Csuzdi, 2001 Ber. nat-med. Verein Innsbruck 88: 136.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 14, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Impact of Diet on Myeloproliferative Neoplasm
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Myeloproliferative neoplasm (MPN) is a hematologic malignancy characterized by the clonal outgrowth of hematopoietic cells with a somatically acquired mutation most commonly in JAK2 (JAK2V617F). This mutation endows upon myeloid progenitors cytokine independent growth and consequently leads to excessive production of myeloid lineage cells. Chronic inflammation is a characteristic feature of MPN, inflammation contributes to disease initiation, progression, transformation, thrombosis, and symptomatology. The traditional approach to therapy in MPN is to reduce the risk of thrombosis, manage symptoms, and observe for progression of the disease. This leaves many early stage MPN patients to be managed with aspirin alone and simply observed for progression. Currently there are no therapeutic options that delay or halt disease progression. There is a critical need for interventions in early stage patients that impact MPN disease progression, particularly interventions with minimal risk given that MPN clinical course may range from indolent to aggressive. Additionally, disease interventions that allow patients to self-manage their MPN symptoms are lacking. Nutrition modification is a well-accepted intervention to reduce thrombosis and improve symptoms in cardiovascular disease. To date no interventions evaluating nutrition have been evaluated in the MPN population. We hypothesize that targeting inflammation early during the MPN disease course may relieve symptom burden and retard progression of MPN. Our overarching goal is to develop a low-risk nutritional intervention among MPN patients that may ultimately lead to better-controlled disease by reducing inflammatory cytokines. To test the effect of altering the inflammatory milieu via dietary intervention we will expose a JAK2V617F mutated mouse model to a high inflammatory (high fat) or low inflammatory (Mediterranean) diet and measure the impact on the MPN phenotype. We will also prospectively test the feasibility of a Mediterranean diet intervention which emphasizes foods rich in anti-inflammatory properties in MPN patients and determine the impact on plasma inflammatory cytokines, MPN symptom burden, and peripheral blood counts.
MOESM6 of Population structure and genomic inbreeding in nine Swiss dairy cattle populations
Creators: name: Signer-Hasler, Heidi
name: Burren, Alexander
name: Neuditschko, Markus
name: Frischknecht, Mirjam
name: Garrick, Dorian
name: Stricker, Christian
name: Gredler, Birgit
name: Bapst, Beat
name: Flury, Christine
Publisher: name: Figshare
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Additional file 6: Table S3. F ST-values with 95% confidence interval in brackets in the lower triangular part.
Wind-forced upwelling over high latitude submarine canyons
Creators: name: Statscewich, Hank
Publisher: name: No Publisher Supplied
Year: 2014

description: Analytical and numerical models of circulation over submarine canyons are presented where parameters such as stratification and canyon geometric scale closely mimic the Mackenzie Canyon located in the Beaufort Sea. The analytical model represents the linear, inviscid dynamics that take place during a geostrophic adjustment. The numerical model contains a full representation of the Navier-Stokes equations and is forced by a wind stress. Comparisons between the analytical and numerical simulations show that both models accurately represent simple coastal flow patterns in the vicinity of a coastal canyon.     Numerical simulations of a wind forced upwelling event on a shelf with a canyon and a shelf without a canyon differ drastically. For the shelf without a canyon, upwelled waters are confined to within 5-6 km of the coast and a uniform along-shore coastal jet develops within 3 days of steady forcing. For the shelf with a canyon, vertical velocities are much stronger within the canyon, and there is an isolated region of upwelled waters that is confined to the coast along the axis of the canyon. Also, onshore trans ort is five times greater than offshore transport along the axis of the canyon indicating that canyons facilitate cross-shelf mixing during wind-forced upwelling events.     Simulations of the coastal ocean's response to passing frontal systems reach an adjusted state after 5 days of continuous forcing. Alongshore transport dominates the system with a minimal amount of net on shore or off shore transport taking place in either of the model runs. Upon cessation of the winds, near-inertial oscillations take place in both simulations.
Calliptaminae Jacobson 1905
Creators: name: Sultana, Riffat
name: Song, Hojun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Acrididae

description: Calliptaminae
(Fig.2)
Geographical Distribution: Pakistan (Ahmad 1958, 1983; Moeed 1971; Wagan 1990; Malik 1993; Suhail 1999; Wagan & Sultana 2013; Sultana & Wagan 2015; Sultana 2020)
description: Published as part of Sultana, Riffat & Song, Hojun, 2024, Annotated catalogue of Pakistani Acrididae (Orthoptera: Caelifera: Acridoidea), pp. 1-47 in Zootaxa 5486 (1) on page 20, DOI: 10.11646/zootaxa.5486.1.1, http://zenodo.org/record/13209743
The protection of ultraviolet sensitive molecules through polymeric encapsulation and proximity
Creators: name: Steeley, Kristin Gilida
Publisher: name: No Publisher Supplied
Year: 2014

description: Exposure to ultraviolet (UV) radiation causes many materials to undergo chemical reactions leading to degradation. While the negative impact of UV radiation on human skin remains in the spotlight, many commercial products have also proven to be photosensitive, leading to the desire to protect molecules from photodegradation. The most common method of UV protection is to add protective materials such as UV absorbers or antioxidants to a formulation. Encapsulation of a photosensitive molecule is also a proven method of photoprotection. In this work, novel UV protective systems were created by encapsulating a photosensitive molecule, beta-carotene, in various polymer particle geometries with protectant molecules. The goal of this dissertation was to use such systems to examine the effect of proximity between photosensitive and UV protecting molecules.   Uniform particles were initially created in order to quantify the effect of encapsulation and to study the result of encapsulating beta-carotene with UV absorbers (oxybenzone, avobenzone, and octyl-4-methoxycinnamate (OMC)) and an antioxidant (vitamin E) in a polymer matrix. Particles were synthesized by the solvent evaporation method. UV protection was found to be dependent on the protectant added and the concentration of the protectant, except in the case of OMC. The most effective particle formulation contained both oxybenzone and vitamin E.   Experimental designs were created to discover the proper composition and procedure for synthesizing various core-shell particle geometries. These core-shell particles were used to study the effect of proximity on UV protection. The core-shell particles themselves offered more protection than the uniform particles, and in most cases the addition of a protectant increased UV protection. Splitting the protectant concentration between the core and shell did not have a significant effect in most cases. The optimal formulation consisted of a suspension of polymer particles containing vitamin E and beta-carotene in the particle core and a UV absorber in the particle shell. Other particle characteristics were studied, including particle size and shell thickness, and were found to have minimal effect. The core-shell particles provide a new protective system for photosensitive molecules as well as a method of studying the effect of proximity on UV protection.
Yagansia parinacotana Zicsi 1989
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Acanthodrilidae
Yagansia
Yagansia parinacotana

description: Yagansia parinacotana Zicsi, 1989
Yagansia parinacotana Zicsi, 1989a Acta Zool. Hung. 35 (3/4): 427.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 14, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Catantopinae Brunner von Wattenwyl 1893
Creators: name: Sultana, Riffat
name: Song, Hojun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Acrididae

description: Catantopinae
(Fig.3)
Geographical Distribution: Pakistan (Ahmad 1958; Moeed 1971; Wagan 1990; Malik 1993; Suhail 1999; Wagan & Sultana 2013; Sultana & Wagan 2015; Sultana 2020)
description: Published as part of Sultana, Riffat & Song, Hojun, 2024, Annotated catalogue of Pakistani Acrididae (Orthoptera: Caelifera: Acridoidea), pp. 1-47 in Zootaxa 5486 (1) on page 21, DOI: 10.11646/zootaxa.5486.1.1, http://zenodo.org/record/13209743
Defining targetable pro-tumor effects of neutrophils in GBM
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: The growth and treatment refractoriness of glioblastoma (GBM), a brain tumor with a devastatingly short survival of under two years, derives from the dynamic interplay between tumor cells and cells in the tumor microenvironment. Our lab has demonstrated the previously underappreciated importance of neutrophils in this microenvironment. Neutrophils, the most abundant leukocytes in blood, are the first line of defense during inflammation. Like macrophages, tumor-associated neutrophil (TAN) subtypes have been proposed: N1 neutrophils possessing “anti-tumoral” activity and N2 pro-tumoral neutrophils, with little known about subtype-specific markers. We have found that GBM cells secrete leukotriene B4 (LTB4), a chemoattractant which recruits circulating neutrophils. Using single cell sequencing, we defined two TAN gene expression profiles with functional analysis revealing them to be ant-tumoral N1 vs. pro-tumoral N2 TANs. We also found that tumor-secreted factors promote gene expression changes in recruited circulating neutrophils, driving them towards an N1 state in low-grade gliomas and an N2 state in high-grade gliomas. And we found that pro-tumoral N2 TAN osteopontin secretion increases tumor cell and tumor stem cell proliferation. Here, we will build upon this data by investigating our central hypothesis that GBM cells secrete LTB4 to recruit circulating neutrophils and polarize them into N2 TANs in a TGF-ß-dependent manner, with N2 TANs exerting osteopontin-driven pro-tumoral effects on GBM cells and the GBM microenvironment. We will investigate this hypothesis through two aims: Aim 1 – Define the mechanisms by which GBM recruits and polarizes neutrophils; and Aim 2 – Define the role of osteopontin in pro-tumoral "N2" TAN effects on GBM cells and the tumor microenvironment in culture and in vivo. To accomplish these goals, we will use single cell-technology, site-directed biopsies, and mouse models. Our studies will discover novel mechanisms by which tumor cells regulate their microenvironment to make it more hospitable for tumor growth. This work will challenge conventional thinking by showing that neutrophils are not bystanders passively accumulating in a growing tumor but active participants in the growth of the tumor, as well as a novel therapeutic target.
Centropomus armatus Gill 1863
Creators: name: Angulo, Arturo
name: Betts, Joel T.
name: González-Alemán, Néstor J.
name: Castañeda, Edgar
name: Berghe, Eric Van Den
name: Elías, Diego J.
name: Mcmahan, Caleb D.
name: Matamoros, Wilfredo A.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Centropomidae
Centropomus
Centropomus armatus

description: Centropomus armatus Gill 1863. Armed Snook, Long-Spine Snook; Róbalo Armado, Róbalo Espina Larga
Vouchers: Not available. Distribution: Eastern Pacific Ocean; from the Gulf of California, Mexico, to northern Peru; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) PN and Ni (Pacific); 0–6 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2019), population trend unknown. Literature: Villa (1982: 161; detailed description, including illustrations and an identification key, and information on distribution and ecology), Robertson & Allen (2015: 1086; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 40; listed, including information on distribution).
description: Published as part of Angulo, Arturo, Betts, Joel T., González-Alemán, Néstor J., Castañeda, Edgar, Berghe, Eric Van Den, Elías, Diego J., Mcmahan, Caleb D. & Matamoros, Wilfredo A., 2023, Continental fishes of Nicaragua: diversity, distribution and conservation status; with an annotated and illustrated checklist of species and an identification guide to families, pp. 1-89 in Zootaxa 5376 (1) on page 39, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Xestospongins: total synthesis of IP3R inhibitors in cancer
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: A gram scale total synthesis of desmethyl xestospongin B (dm Xe B) is proposed. dm Xe B is a leading chemical tool in the study of inositol 1,4,5-triphosphate receptors (IP3Rs), which are ligand-gated calcium channels that control calcium signaling between the endoplasmic reticulum and mitochondria. There is a growing body of evidence that xestospongins trough interaction with IP3Rs have a major impact on mitochondrial metabolism in cancer cells, enabling selective destruction of cancer cells with minimal impact on normal cells. Because natural sources of xestospongins are exhausted, a total synthesis of the natural products is necessary to continue research on IP3Rs. We propose a general synthetic platform to access these valuable compounds on scale.
Multifunctional nanomaterials for advanced molecular imaging and cancer therapy
Creators: name: Subramaniam, Prasad
Publisher: name: No Publisher Supplied
Year: 2014

description: Nanotechnology offers tremendous potential for use in biomedical applications, including cancer and stem cell imaging, disease diagnosis and drug delivery. The development of nanosystems has aided in understanding the molecular mechanisms of many diseases and permitted the controlled nanoscale manipulation of biological phenomena. In recent years, many studies have focused on the use of several kinds of nanomaterials for cancer and stem cell imaging and also for the delivery of anticancer therapeutics to tumor cells. However, the proper diagnosis and treatment of aggressive tumors such as brain and breast cancer requires highly sensitive diagnostic agents, in addition to the ability to deliver multiple therapeutics using a single platform to the target cells. Addressing these challenges, novel multifunctional nanomaterial-based platforms that incorporate multiple therapeutic and diagnostic agents, with superior molecular imaging and targeting capabilities, has been presented in this work.    The initial part of this work presents the development of novel nanomaterials with superior optical properties for efficiently delivering soluble cues such as small interfering RNA (siRNA) into brain cancer cells with minimal toxicity.  Specifically, this section details the development of non-toxic quantums dots for the imaging and delivery of siRNA into brain cancer and mesenchymal stem cells, with the hope of using these quantum dots as multiplexed imaging and delivery vehicles. The use of these quantum dots could overcome the toxicity issues associated with the use of conventional quantum dots, enabled the imaging of brain cancer and stem cells with high efficiency and allowed for the delivery of siRNA to knockdown the target oncogene in brain cancer cells.      The latter part of this thesis details the development of nanomaterial-based drug delivery platforms for the codelivery of multiple anticancer drugs to brain tumor cells. In particular, this part of the thesis focuses on the synthesis and use of a biodegradable dendritic polypeptide-based nanocarrier for the delivery of multiple anticancer drugs and siRNA to brain tumor cells. The co-delivery of important anticancer agents using a single platform was shown to increase the efficacy of the drugs manyfold, ensuring the cancer cell-specific delivery and minimizing dose limiting toxicities of the individual drugs. This would be of immense importance when used in vivo.
Amphiphilic macromolecule therapeutics to manage cardiovascular disease
Creators: name: Lewis, Daniel Raiken
Publisher: name: No Publisher Supplied
Year: 2014

description: The hypothesis of this research is that atherosclerosis, the principal pathology underlying vascular occlusive disease, can be targeted and moderated using Amphiphilic Macromolecules (AMs). By mimicking the amphiphilicity and charge distribution of oxidized LDL, AMs can mitigate its downstream consequences by competitively blocking interaction with scavenger receptors. This work evaluated the ability of AM of various chemical compositions and architectures to reduce lipid accumulation in macrophages. Insights from these studies were used in conjunction with 3D molecular descriptors to identify the features of AM with most anti-atherogenic potency. To further develop AM as a viable therapeutic modality, these features were incorporated into kinetically fabricated nanoparticles (NPs) that are non-inflammatory and resist serum binding. An atherosclerotic animal model was established and used to examine the in vivo biodistribution and pharmacokinetic profile of systemically circulating AM NPs in addition to their ability to localize to lesions and stabilize plaques. Collectively, these outcomes establish AM as a multimodal nanotherapeutic platform designed to target atherosclerotic lesions and inhibit inflammation and atherogenesis.  This thesis is comprised of three principal research aims: 1) To determine quantitative structure-activity relationships between Amphiphilic Macromolecule architecture and in vitro reductions in oxidized LDL uptake and lipid accumulation in macrophages; 2) To develop AM into non-inflammatory serum-stable nanoparticles (AM NPs); 3) To study the in vivo dynamics of systemically injected AM NPs and examine their ability to target atherosclerotic lesions and mitigate plaque development.
Novel small-molecule inhibitors of mycobacterial RNAP "AAPS"
Creators: name: Mandal, Soma
Publisher: name: No Publisher Supplied
Year: 2014

description: Tuberculosis global epidemics is a serious threat to human population, the disease  is estimated to be the second highest cause of death due to infection. In this study   we present a lead hit-compound “AAP1” identified through high-throughput screening   performed against Mycobacterium tuberculosis RNA polymerase (RNAP). AAP1   displays great potential as a mycobacterial RNAP inhibitor and mycobacterial growth   inhibitor.    AAP1 can be synthesized from commercially available precursors in single reaction step.   AAP1 has a modular structure, facilitating the synthesis of novel AAP1 analogs and   facilitating the interpretation of structure-activity relationships for novel AAP1 analogs.   Currently, more than 400 AAP1 analogs have been synthesized and tested and based   on improved characteristics, an AAP1 analog AAP12 is used in this study with AAP1   (AAPs).    By isolating, sequencing, and characterizing spontaneous resistant mutants, we have   shown that mycobacterial RNAP is the functional cellular target for the antibacterial   activity of AAPs     By isolating, sequencing, and characterizing resistant mutants, we have shown AAPs   function through a site on RNAP that is different from, and does not overlap with the   binding sites for rifamycins. The site is located at the base of RNAP " lobe" and N’-   terminal of β’ bridge helix and corresponds, essentially exactly, to the site for CBR&03, a   compound that does not inhibit mycobacterial RNAP and does not inhibit mycobacterial   growth. It appears that AAPs are mycobacterial-specific ligands of RNAP β lobe and   that CBR&03 is a Gram-negative-specific ligand of the RNAP β lobe.    By observing the effect of AAPs on individual transcription step, we have shown that   AAPs affect the nucleotide addition cycle of RNAP. Based on the fact that AAPs   interfere with the nucleotide addition cycle of the RNAP without making any contact with   the active center residues we propose that AAPs function allosterically by binding at   the N-terminal sub-region of β’ bridge helix, and by interfering with its conformational   dynamics     In our current work, we are systematically preparing and evaluating novel AAP1 analogs.   The objectives are to increase the antimycobacterial potency, to improve physical and   pharmacological properties, and to identify compounds suitable for evaluation in an   animal model of tuberculosis.
Yagansia villarricai Zicsi & Csuzdi 2001
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Acanthodrilidae
Yagansia
Yagansia villarricai

description: Yagansia villarricai Zicsi & Csuzdi, 2001
Yagansia villarricai Zicsi & Csuzdi, 2001 Ber. nat.-med. Verein Innsbruck 88: 137.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 14, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
A strategy for classifying a set of dissimilar channels bytheir a priori channel occupancy probability
Creators: name: Sugrim, Shridatt
Publisher: name: No Publisher Supplied
Year: 2014

description: Recent Changes in policy regarding the opportunistic use of licensed radio spectrum have paved the way for new innovative technologies like cognitive radio (CR). In CR systems a secondary user (SU) is allowed to use open channels if the primary user (PU) is not currently using them. Regulatory bodies like the FCC establish maximum interference requirements for SUs when making use of these channels. To comply with these requirements SUs must measure the occupancy of each of the channels they intend to use. Any strategy employed for opportunistic spectrum usage has to consider the tradeoffs between time spent searching for empty channels and time spent using those empty channels.     In most cases the spectrum sensing that is employed by a CR system starts with no prior information about the occupancy of the channels it intends to use. We propose a novel method of addressing this lack of prior knowledge by employing an efficient strategy that classifies some of the channels the SU intends to use within a fixed time limit. This classifier can be run before the SUs attempt transmission, and will provide the SUs' spectrum sensing sub-systems with a set of occupancy probabilities for some of the channels.    Our classifier will be designed around sequential probability ratio tests (SPRT) because these tests maintain bounds on classification errors while using the smallest number of samples for classification. The classifier will attempt to classify as many channels as possible within the given time limit by intelligently allocating channel measurements. We will examine the system's performance in various measurement resource regimes and identify regimes where our approach is superior to simpler classification schemes.
Additional file 1: of The Japanese version of the questionnaire about the process of recovery: development and validity and reliability testing
Creators: name: Kanehara, Akiko
name: Kotake, Risa
name: Miyamoto, Yuki
name: Kumakura, Yousuke
name: Morita, Kentaro
name: Ishiura, Tomoko
name: Shimizu, Kimiko
name: Fujieda, Yumiko
name: Shuntaro Ando
name: Kondo, Shinsuke
name: Kasai, Kiyoto
Publisher: name: Figshare
Year: 2017
Subjects: subject: Space Science
subject: Medicine
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: FOS: Biological sciences
subject: Developmental Biology
subject: Science Policy

description: Japanese version of the Questionnaire about the Process of Recovery (QPR-J). (PDF 133 kb)
Centropomus ensiferus Poey 1860
Creators: name: Angulo, Arturo
name: Betts, Joel T.
name: González-Alemán, Néstor J.
name: Castañeda, Edgar
name: Berghe, Eric Van Den
name: Elías, Diego J.
name: Mcmahan, Caleb D.
name: Matamoros, Wilfredo A.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Centropomidae
Centropomus
Centropomus ensiferus

description: Centropomus ensiferus Poey 1860. Swordspine Snook; Róbalo de Espolón, Kalwa
Vouchers: LSUMZ 15312 (1), 15332 (9), 15343 (3) and 15368 (31). Distribution: Western Atlantic Ocean; from southern Florida, USA, to Rio de Janeiro, Brazil; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) Pr, GM and Es (Atlantic); 0–11 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2019), population trend unknown. Literature: Villa (1982: 161; detailed description, including illustrations and an identification key, and information on distribution and ecology), González-Alemán (2006: 27; brief description, including an illustration, and information on distribution and ecology), van den Berghe (2015: 46, as Centropomus robalito —misidentification; listed, including an illustration and information on distribution and ecology), Robertson & Van Tassell (2019: 3457; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 40; listed, including information on distribution).
description: Published as part of Angulo, Arturo, Betts, Joel T., González-Alemán, Néstor J., Castañeda, Edgar, Berghe, Eric Van Den, Elías, Diego J., Mcmahan, Caleb D. & Matamoros, Wilfredo A., 2023, Continental fishes of Nicaragua: diversity, distribution and conservation status; with an annotated and illustrated checklist of species and an identification guide to families, pp. 1-89 in Zootaxa 5376 (1) on page 39, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Benhamiidae Michaelsen 1897
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Crassiclitellata
Benhamiidae

description: Family Benhamiidae Michaelsen, 1897
Remarks. Benhamiinae was merged into the acanthodrilid subfamily Trigastrinae by Michaelsen (1900), and resurrected by Csuzdi (1996a). Subsequent molecular studies corroborated its monophyly (Pop et al. 2005, James & Davidson 2012), and Blakemore (2005, 2015) as well as James & Gamiette (2016) suggested family rank, which is adopted here as well.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 14, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Coptacrinae Brunner von Wattenwyl 1893
Creators: name: Sultana, Riffat
name: Song, Hojun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Acrididae

description: Coptacrinae
(Fig.7)
Geographical Distribution: Pakistan: Azad Jammu & Kashmir
Comments
Coptacrinae are found in various habitats, mostly confined to open savanna, savanna woodland, and forest clearings and margins in montane to lowland rainforests. Herbaceous species are used as food plants, and several genera seem to prefer or even be confined to genera of the Asteraceae (Dirsh 1965, Johnsen 1982, Green 1997). During the present expedition, Apalacris varicornis, a single species of Coptacrinae, was reported from Hattian Bala (Azad Jammu & Kashmir), situated 40 km from Muzaffarabad city along the Jhelum River. Hattian Bala serves as the headquarters of the district and tehsil Hattian Bala (AJ&K Statistics 2019). The region is characterized by hilly and mountainous terrain with lush green plains in the Jehlum Valley along the Jehlum River. It shares boundaries with Muzaffarabad and Bagh districts in Azad Kashmir, and with Kupwara and Baramulla districts in Indian-occupied Jammu & Kashmir. The area is accessible by roads connecting it to Muzaffarabad and Bagh districts. Hattain Bala is a collection of lush, green, and beautiful valleys, including Leepa, Reshian, Bharyan, Chikkar, and Chinari, which are renowned and located along the Jehlum River. This specimen was captured from scattered leaves of the Chinar tree (Platanus orientalis) in Hattian Bala. Earlier, A. varicornis was reported by Bey-Bienko & Mistshenko (1951) from Azad Jammu & Kashmir. Notably, prior to this expedition, researchers had not reported Coptacrinae in Pakistan. The inclusion of this subfamily in the findings elevates the representation of Pakistani Acrididae to 14 subfamilies.
description: Published as part of Sultana, Riffat & Song, Hojun, 2024, Annotated catalogue of Pakistani Acrididae (Orthoptera: Caelifera: Acridoidea), pp. 1-47 in Zootaxa 5486 (1) on page 22, DOI: 10.11646/zootaxa.5486.1.1, http://zenodo.org/record/13209743
Centropomus medius Gunther 1864
Creators: name: Angulo, Arturo
name: Betts, Joel T.
name: González-Alemán, Néstor J.
name: Castañeda, Edgar
name: Berghe, Eric Van Den
name: Elías, Diego J.
name: Mcmahan, Caleb D.
name: Matamoros, Wilfredo A.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Centropomidae
Centropomus
Centropomus medius

description: Centropomus medius Günther 1864. Bigeye Snook, Blackfin Snook; Róbalo Aleta Manchada, Róbalo Aleta Prieta, Róbalo Ojón, Gualaje Aleta Manchada
Vouchers: Not available. Distribution: Eastern Pacific Ocean; from southern Baja California and the Gulf of California, Mexico, to northern Peru; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) PN and Ni (Pacific); 0–6 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2019), population trend unknown. Literature: Bussing (1998: 265; brief description, including illustrations and an identification key, and information on distribution, with a map, and ecology), Robertson & Allen (2015: 1088; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 40; listed, including information on distribution).
description: Published as part of Angulo, Arturo, Betts, Joel T., González-Alemán, Néstor J., Castañeda, Edgar, Berghe, Eric Van Den, Elías, Diego J., Mcmahan, Caleb D. & Matamoros, Wilfredo A., 2023, Continental fishes of Nicaragua: diversity, distribution and conservation status; with an annotated and illustrated checklist of species and an identification guide to families, pp. 1-89 in Zootaxa 5376 (1) on page 39, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Geometric figure-ground cues override standard depth from accretion-deletion
Creators: name: Tanrikulu, Ömer Dağlar
Publisher: name: No Publisher Supplied
Year: 2014

description: Accretion/deletion, where a moving texture appears from (i.e. accretion) or disappears (i.e. deletion) at a boundary, is widely considered as a reliable cue to surface depth ordering, with the accreting or deleting surface interpreted as behind the adjoining surface. However, Froyen, Feldman, and Singh (2013) showed that when accretion- deletion occurs on both sides of a contour, some accreting-deleting regions can also be perceived as in front and as self-occluding due to rotation in 3D. In this study we ask whether geometric figure-ground cues can override the standard “depth from accretion-deletion” interpretation even when accretion-deletion takes place only on one side of a contour. We used two tasks: a relative depth task (front/back), and a motion classification task (translation/rotation). We conducted two experiments, where only one set of alternating regions contained moving texture; the other set was static. In such displays the standard accretion-deletion account would unambiguously assign farther depth to the moving regions. However, when the moving regions were convex or symmetric, they tended to be perceived as figural, and rotating in 3D (with convexity > symmetry). In the second experiment, different motion directions were given to the moving regions (hence weakening motion-based grouping) and this further weakened the traditional accretion-deletion interpretation. Our results show that the standard “depth from accretion-deletion” interpretation is overridden by geometric cues to figure-ground. When this happens, the accreting-deleting surface is perceived as self-occluding due to rotation in 3D. Overall, the results demonstrate a rich interaction between accretion-deletion, figure-ground, and structure-from-motion that is not captured by existing models of depth from motion.
Cyrtacanthacridinae Kirby 1910
Creators: name: Sultana, Riffat
name: Song, Hojun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Acrididae

description: Cyrtacanthacridinae
(Fig.4)
Geographical Distribution: Pakistan (Ahmad 1958; Moeed 1971; Wagan 1990; Malik 1993; Moizuddin, 1998; Suhail 1999; Wagan & Sultana 2013; Sultana & Wagan 2015; Sultana 2020)
description: Published as part of Sultana, Riffat & Song, Hojun, 2024, Annotated catalogue of Pakistani Acrididae (Orthoptera: Caelifera: Acridoidea), pp. 1-47 in Zootaxa 5486 (1) on page 23, DOI: 10.11646/zootaxa.5486.1.1, http://zenodo.org/record/13209743
Benhamiona murithae Csuzdi & Zicsi 1994
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Octochaetidae
Benhamiona
Benhamiona murithae

description: Benhamiona murithae Csuzdi & Zicsi, 1994
Benhamiona murithae Csuzdi & Zicsi, 1994a Rev. suisse Zool. 101 (1): 222.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 14, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Centropomus mexicanus Bocourt 1868
Creators: name: Angulo, Arturo
name: Betts, Joel T.
name: González-Alemán, Néstor J.
name: Castañeda, Edgar
name: Berghe, Eric Van Den
name: Elías, Diego J.
name: Mcmahan, Caleb D.
name: Matamoros, Wilfredo A.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Centropomidae
Centropomus
Centropomus mexicanus

description: Centropomus mexicanus Bocourt 1868. Largescale Fat Snook; Róbalo Gordo
Vouchers: Not available. Distribution: Western Atlantic Ocean; from southern Florida, USA, to southern Brazil; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) BF, IM and To (Atlantic); 0–6 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2019), population trend unknown. Literature: Robertson & Van Tassell (2019: 3458; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 41; listed, including information on distribution).
description: Published as part of Angulo, Arturo, Betts, Joel T., González-Alemán, Néstor J., Castañeda, Edgar, Berghe, Eric Van Den, Elías, Diego J., Mcmahan, Caleb D. & Matamoros, Wilfredo A., 2023, Continental fishes of Nicaragua: diversity, distribution and conservation status; with an annotated and illustrated checklist of species and an identification guide to families, pp. 1-89 in Zootaxa 5376 (1) on page 40, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Eyprepocnemidinae Brunner von Wattenwyl 1893
Creators: name: Sultana, Riffat
name: Song, Hojun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Acrididae

description: Eyprepocnemidinae
(Fig.10)
Geographical Distribution: Pakistan (Ahmed 1980; Wagan 1990; Wagan and Solangi, 1990; Mazhar 1993; Wagan & Baloch 1997; Tokhai, 1996; Yousuf, 1996; Suhail et al. 2000; Wagan & Sultana 2013; Sultana 2020)
Comments
The subfamily is widely distributed over Africa, southern and eastern Asia, and the Mediterranean, including the coasts of Spain, Italy, Greece, North Africa, Caucasus and Turkmenistan (Dirsh 1958). Currently, there are twelve described species in Pakistan, with most of them being collected from grasses, herbs, and shrubs. However, notable exceptions include Eyprepocnemis alacris, Choroedocus illustris, and Heteracris littoralis, which are found in cultivated sugarcane, maize, and jowar fields, where they are considered minor pests. Some economically significant species belong to the genera Eyprepocnemis, Heteracris, Cataloipus, and Jagoa (Rowell & Hemp 2017). Curiously, COPR (1982) lists a surprising range of plants attacked by E. plorans, spanning various grasses to cassava (Manihot), which is typically considered chemically defended against most herbivores. Choroedocus pallens is restricted to Balochistan. Eyprepocnemis rosea, easily recognizable by its small size and rose-colored hind wings, is confined to hilly regions Malamjabba (Swat) Khyber Pakhtunkhwa (KPK) and Murree in Rawalpindi (Punjab). Choroedocus illustris is widely distributed in Punjab and Azad Kashmir. It is interesting that no individual was captured from Gilgit-Baltistan. Heteracris littoralis, E. alacris alacris, and E. alacris impicta were collected from all provinces of Pakistan, including Azad Jammu & Kashmir. However, the last one was not reported from Punjab. The distribution of H. persa earlier reported from Quetta, Khuzdar and Nushki by Grunshaw (1991) but during this expedition we are unable to collect it from Baluchistan. Tylotropidius varicornis occurs in the mountainous areas of Punjab, Khyber Pakhtunkhwa, and Azad Kashmir. Choroedocus robustus is only restricted to Sindh and Punjab. At present, Cataloipus cognatus has been reported from low elevations in Sindh (13m- 50m) to high altitudes in Azad Jammu & Kashmir (1321m) and Khyber Pakhtunkhwa (871m). Two females were previously recorded from Sindh (Wagan & Sultana 2013). However, one taxon, Cataloipus thomasi is an endemic species in the southern Arabian Peninsula, specifically known only from the Dhofar region. According to Popov (1980), it is related to C. oberthuri from central-east Africa.
description: Published as part of Sultana, Riffat & Song, Hojun, 2024, Annotated catalogue of Pakistani Acrididae (Orthoptera: Caelifera: Acridoidea), pp. 1-47 in Zootaxa 5486 (1) on page 24, DOI: 10.11646/zootaxa.5486.1.1, http://zenodo.org/record/13209743
Benhamiona pitti Csuzdi & Zicsi 1994
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Octochaetidae
Benhamiona
Benhamiona pitti

description: Benhamiona pitti Csuzdi & Zicsi, 1994
Benhamiona pitti Csuzdi & Zicsi, 1994a Rev. suisse Zool. 101 (1): 224.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 14, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Additional file 1: of Lack of cytomegalovirus detection in human glioma
Creators: name: Garcia-Martinez, Araceli
name: Alenda, Cristina
name: Irles, Esperanza
name: Ochoa, Enrique
name: Quintanar, Teresa
name: Rodriguez-Lescure, Alvaro
name: Soto, Jose
name: Barbera, Victor
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Evolutionary Biology
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Computational Biology

description: Methodological details and proceduries. (DOCX 40 kb)