cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Particulate flows and heteroaggregation studied by optical imaging and fluorescence spectroscopy
Creators: name: Deshpande, Kapil V.
Publisher: name: No Publisher Supplied
Year: 2014

description: The production of multiscale heteroaggregates of microparticles coated with nanoparticles has generated renewed interest in recent literature due to the wide-ranging applications of such structured particles.  These applications include particle stabilization, nanotemplating, and drug delivery, among others.  In the past, the majority of heteroaggregation studies and associated applications have involved rigid, spherical particles. However, as part of a multiscale heteroaggregate, hydrophilic hydrogel particles can be used to open a whole range of new applications.  These hydrogel particles have also been of great interest recently due to their significant microencapsulation capabilities and variety of delivery mechanisms.  This dissertation is focused on gaining understanding of the heteroaggregation of hydrogel microparticles and nanoparticles and of particulate flows that could potentially be used to influence aggregate formation.     First, concentrated noncolloidal particle suspensions undergoing oscillatory torsional flow between parallel plates were studied using optical imaging.  Much of the work focuses on the effect of moderate strain amplitude and frequency on particle migration.  Also explored were various effects that can lead to enhanced or reduced particle migration in the flow.     Next, a new quantitative application of fluorescence spectroscopy was developed in order to study the interaction of oppositely charged hydrogel microparticles and nanoparticles in suspensions.  Optical microscopy was first used to determine the type of aggregate morphology formed by mixtures of alginate microparticles and fluorescently tagged chitosan nanoparticles at different concentration levels.  It was hypothesized that due to fluorophore and particle interaction properties that fluorescence spectroscopy would be able to quantify the boundaries between different types of interactions in the system.  With this new technique, the effect of the concentration ratio of nanoparticles to microparticles and the total overall particle concentration was also explored.   Finally, after developing the application of fluorescence spectroscopy for quantifying particle interaction, varying the pH of the interaction environment where heteroaggregation occurs was studied.  pH is an important parameter in hydrogel microcapsule and nanocapsule delivery and in heteroaggregation behavior.  The change in interaction behavior of alginate and chitosan particles was explored and the capabilities and limits of fluorescence spectroscopy were determined.
Nucleotide-Guanidinonucleoside Conjugates as Anti-HIV Agents
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 rapid appearance of resistant HIV-1 strains, adverse effects on contemporary drugs, recent indications for HIV “superinfections” and disappointing results with experimental vaccines, all necessitate the continuous development of independent therapeutic strategies to combat HIV infection. The goals of the proposed project are to design, synthesize and evaluate novel nucleotide-guanidinoglycoside conjugates as potential anti HIV-1 agents. The basic hypothesis guiding the proposed strategy is that the anti HIV efficacy of nucleoside-based Reverse Transcriptase inhibitors can be enhanced by covalently conjugating their corresponding monophosphates to guanidinoglycosides, a novel family of cellular uptake vehicles that also exhibit high affinity to viral RNA sequences. Two objectives are therefore concomitantly met: (a) Reverse Transcriptase inhibitors are actively transported into the cell and then released in a semi-activated form, and (b) essential regulatory events involving viral-specific protein–RNA interactions are inhibited.
Perceptual interactions between cooling and flavors
Creators: name: DeLaura, Christie
Publisher: name: No Publisher Supplied
Year: 2014

description: There are many studies on the perceptual interactions between taste and smell, however, few studies have focused on interactions between flavor and cooling sensations.   To examine the interactions between these sensations, two studies were conducted. The objective of the first study was to determine whether perceptual interactions exist between cooling and flavors, whether these interactions are dependent on the congruency (appropriate pairing) of the flavor with cooling, and how this influences perceived intensity of cooling and flavor attributes. Based on studies of interactions between taste and smell, the expectation was that congruent pairings would enhance cooling and flavor intensities, while incongruent pairings would suppress or have no influence on attribute intensities. The objective of the second study was to understand how cooling compounds influence liking and emotions when added to congruent and incongruent flavored model beverages.     Concentrations corresponding to moderate and low cooling intensities were determined with a dose-response study of WS-3 (N-Ethyl-5-methyl-2-(1-methylethyl) cyclohexanecarboxamide). WS-3 concentrations were varied in flavored model beverages (apple, spearmint, caramel). Intensity scales were employed to study the effects of the mixtures on cooling and flavor intensities using ScentMove® and affective scales to study the hedonics and emotions related to these mixtures.   Results indicated that moderate intensity WS-3 significantly increased perceived intensity of spearmint flavor (a congruent pairing) over the flavor alone for a period of 2 minutes from tasting, while there was no influence of cooling intensity on apple or caramel intensities (incongruent pairings).  For apple and caramel, increasing levels of WS-3 corresponded with decreased liking and positive emotions, as well as higher disgust. For spearmint, moderate intensity WS-3 slightly decreased positive emotions and slightly increased disgust.  Results suggest that congruency has an impact on perceptual interactions involving cooling. Cooling congruent flavor intensity can be boosted using a cooling agent. It is important to use caution in product design, as liking and emotional profiles are influenced by cooling intensities. Even with a congruent flavor, there is an optimal cooling intensity level.
Additional file 1: Figure S1. of Erv1 of Arabidopsis thaliana can directly oxidize mitochondrial intermembrane space proteins in the absence of redox-active Mia40
Creators: name: Peleh, Valentina
name: Zannini, Flavien
name: Backes, Sandra
name: Rouhier, Nicolas
name: Herrmann, Johannes
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Related to Fig.Â 1. Alignment of members of the Erv1 family. The sequences were compared using Clustal Omega with standard settings of the program. (DOCX 1001 kb)
Neuroimaging of CNS Targeted Penetrating ART in HNCI
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: HIV affects the central nervous system (CNS) (brain and spinal cord) and can lead to cognitive impairment, increased mortality, and a decreased quality of life. The cognitive disorders due to HIV associated neurocognitive impairment (HNCI) are characterized by impairments in memory, attention, and reasoning. HNCI patients can be classified as having either mild motor cognitive deficits (MCMD) or HIV associated dementia (HAD). HIV almost immediately after infection affects the brain and is protected from medications and natural host defenses because of the blood-brain barrier. Thus, HIV has a reservoir in the brain and can easily replicate within the CNS. Treatment with Anti-Retroviral Therapy (ART) has decreased the incidence but not prevalence of HNCI. HIV patients are now living longer with the disease with many eventually developing HNCI. Differences exist in the degree of CNS targeted (CNS-T) ART penetration across the blood brain barrier. No consensus exists as to which ART regimen is best for HNCI patients. Currently, neuropsychological testing and lumbar punctures are performed for classifying HNCI patients and determining the efficacy of ART regimens. This UARP proposed to use non-invasive neuroimaging methods as a biomarker for determining the effects of CNS-T ART on cerebral blood flow (CBF) in HNCI patients of California. Specific Aim 1 will use arterial spin labeling magnetic resonance imaging (ASL-MRI) to obtain quantitative measurements of baseline CBF (ml/mg/min) within controls (n=10) and HNCI patients (n=20). An effect of the degree of CNS-T penetration of ART regimens will be investigated in MCMD (n=10) and HAD (n=10) patients. Specific Aim 2 will assess CBF response due to a simple functional task using blood oxygen level dependent functional magnetic imaging (BOLD-fMRI) within controls and HNCI patients. The effect of the degree of CNS-T penetration of ART regimens will be analyzed in MCMD (n=10) and HAD (n=10). These results will provide a more complete profile of the effects of CNS-T ART on CBF and may influence the choice of regimens administered to HNCI patients in California. It is hypothesized that higher CNS-T ART regimens should be used for HNCI patients in California. These higher penetrating CNS-T ART regimens will lead to a greater normalization of baseline CBF and CBF responses to functional stimulation in HNCI patients. These observed changes most likely reflect a greater reduction in inflammation and neuronal loss that accompanies these regimens.
Targets of transcription inhibition by the antibiotics lipiarmycin, GE230&&, and salinamide
Creators: name: Degen, David D.
Publisher: name: No Publisher Supplied
Year: 2014

description: The antibiotics lipiarmycin (Lpm), GE230&& (GE), and salinamide (Sal) function by inhibiting bacterial RNA polymerase (RNAP). In this work, the targets (and mechanisms) of transcription inhibition by Lpm, GE, and Sal are identified and characterized through a combination of genetic, biochemical, and structural approaches. Each of these compounds functions through a different target on the enzyme that does not significantly overlap the targets of other bacterial RNAP inhibitors. Elucidation of these targets may prove useful for antibacterial drug discovery and design.       To define the functional target of Lpm, we isolated and sequenced 160 Lpm-resistant mutants. In the structure of RNAP, sites of substitutions conferring Lpm-resistance cluster to define the “Lpm target,” which includes residues in the RNAP switch-region, as well as one wall of the RNA exit channel. Biochemical experiments show that Lpm inhibits the RNAP-DNA interaction, and appears to function by trapping the RNAP clamp in a fully-to-partially closed state.       To define the functional target of GE, we isolated and sequenced 35 GE-resistant mutants. In the structure of RNAP, sites of substitutions conferring GE-resistance cluster to define the “GE target,” which includes residues in the RNAP active-center subregions, the “β D2-loop” and the “link region.” Biochemical experiments reveal that GE inhibits nucleotide addition during transcription initiation, after open complex formation, but prior to phosphodiester bond formation. The crystal structure of RNAP in complex with GE confirms that GE binds to the GE target, and indicates that GE functions by  precluding the binding of NTP substrates to the RNAP active-center "i site" and "i+1 site.”       To define the functional target of Sal, we isolated and sequenced 4& Sal-resistant mutants. In the structure of RNAP, sites of substitutions conferring Sal-resistance cluster to define the “Sal target,” which includes residues in the RNAP active-center subregions: the “bridge-helix N-terminal hinge” (BH-HN), the “F-loop,” and the “link region.”       Biochemical experiments reveal that Sal inhibits nucleotide addition during both transcription initiation and elongation. The crystal structure of RNAP in complex with Sal confirms that Sal binds to the Sal target, and suggests that Sal functions by trapping the BH-HN in a straight (unbent) conformation.
Polytoreutus pocsorum Zicsi 1996
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Eudrilidae
Polytoreutus
Polytoreutus pocsorum

description: Polytoreutus pocsorum Zicsi, 1996
Polytoreutus pocsorum Zicsi, 1996 Mitt. Hamb. Zool. Mus. Inst. 93: 29.
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 19, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Additional file 1: of The role of human rights litigation in improving access to reproductive health care and achieving reductions in maternal mortality
Creators: name: Dunn, Jennifer
name: Lesyna, Katherine
name: Zaret, Anna
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Open peer review. (PDF 165 kb)
Role of circadian rhythm gene homolog PER3 in breast 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: Emerging evidence suggests that disruption of circadian rhythms (i.e., the 24-hour cycle involved in biochemical, physiological or behavioral processes) and underlying genes may play a significant role in cancer. Women with disrupted sleep cycles are more likely to develop breast cancer. In fact, Period 3 (PER3), a mammalian homolog of the Drosophila (fruit fly) circadian rhythm gene period, contains a coding polymorphism that is associated with an increased risk of breast cancer in younger women. Interestingly, Per3 is not required for central regulation of circadian rhythms in mice since targeted disruption of Per3 result in minimal circadian abnormalities. However, our preliminary data indicate that when Per3-deficient mice are exposed to carcinogens, they are more prone to develop cancer, in particular breast tumors. In addition, mice with Her2/neu overexpression have an accelerated course of developing malignant breast cancer when Per3 is also disrupted. We have found that low levels of PER3 correlate with poor prognosis in patients with estrogen receptor (ER) positive but not ER-negative invasive ductal carcinomas. Of note, in humans PER3 is located on the short arm of chromosome 1 (1p36), a locus that is commonly lost in human cancers including breast cancer.

 Our research will further examine the mechanism by which loss of Per3 can lead to breast tumor formation in mice and determine whether Per3 is useful prognostic biomarker. To address these aims, we will: (1) Characterize the molecular defects that contribute to breast tumor development in Per3-deficient mice when exposed to genotoxic stresses (DNA damage); (2) evaluate the utility of PER3 expression as a prognostic marker for ER-positive invasive ductal carcinoma; and (3) determine the effects of PER3 expression on estrogen and tamoxifen sensitivity. Using mouse models, we will examine various aspects of the genotoxic stress response including proliferative activity, ability to elicit cell cycle arrest, extent of apoptosis, and ability to repair DNA and maintain genomic stability following DNA damage. Similar work will be performed in human breast cancer cell lines that either overexpress PER3 or have PER3 knocked-down by short hairpin RNA (shRNA) inhibition. Next, we will also determine the mRNA level of PER3 in a panel of approximately 400 primary human breast cancer specimens to validate whether PER3 expression is a prognostic marker in human ER-positive invasive ductal carcinoma. Finally, we will examine the effects of PER3 on hormone sensitivity in human breast cancer cell lines.

 These studies will allow us to better understand PER3 function and its relationship to breast cancer, breast cancer prognosis, and hormone sensitivity in ER-positive breast tumors.
The role of HuD, a post-transcriptional regulator, in the development and function of the murine neocortex
Creators: name: DeBoer, Erik Michael
Publisher: name: No Publisher Supplied
Year: 2014

description: The neocortex is a unique six-layered brain region composed of an array of morphologically and functionally distinct subpopulations of primary projection neurons forming complex circuits across the central nervous system. The developmentally progressive specification, differentiation, and signaling of these distinct subpopulations of neocortical projection neurons is critical to mammalian cognitive and sensorimotor abilities.   Recent research points to mRNA metabolism as a key regulator of this development and maturation process.  Hu antigen D (HuD), an RNA binding protein has been implicated in the establishment of neuronal identity and neurite outgrowth in vitro.  Therefore, we investigated the role of HuD loss of function on neuron specification and dendritogenesis in vivo using a mouse model.  We found that loss of HuD early in development results in a defective early dendritic overgrowth phase as well as pervasive deficits in neuron specification in the lower neocortical layers, as well as defects in dendritogenesis in the CA3 region of the hippocampus.  Subsequent behavioral analysis revealed a deficit in performance of a hippocampal dependent task: the Morris water maze.  Further, HuD knockout (KO) mice exhibited lower levels of anxiety than wild type counterparts, and were overall less active.  Last, we found that HuD KO mice are more susceptible to auditory-induced seizures, often resulting in death.  I have also discovered that HuD itself is heavily regulated at the post-transcriptional level, and is expressed in four transcript variants which encode 4 functionally distinct protein isoforms.  Specifically, my data indicate that HuD4 is translated during early neocortical neurogenesis when lower layers are formed, where HuD3 is specifically translated during late neocortical neurogenesis.  Further, early HuD3 overexpression drives the production of upper layer neurons, where HuD4 overexpression drives the fate of lower layer neurons.  Using a conditional transgenic line as well as in-vitro cell cycle analysis, I also determined that the translational regulation of HuD3 is dependent upon NT-3 arriving from the thalamic afferents to the neocortex.  This trophic source appears to only affect those stem cells distal to the ventricle when they are in S-phase.
Teleudrilus dewittei Zicsi & Csuzdi 2000
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Eudrilidae
Teleudrilus
Teleudrilus dewittei

description: Teleudrilus dewittei Zicsi & Csuzdi, 2000
Teleudrilus dewittei Zicsi & Csuzdi, 2000 Ber. nat.-med. Verein Innsbruck 87: 123.
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 19, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Design and synthesis of novel small molecule modulators of KEAP1-NRF2-ARE pathway
Creators: name: Chen, Lin
Publisher: name: No Publisher Supplied
Year: 2014

description: Keap1-Nrf2-ARE system represents a key signaling pathway in the regulation of cellular defense mechanisms against oxidative stress and inflammation. Activation of Keap1-Nrf2-ARE system can induce the expression of a number of antioxidant defense enzymes and proteins critical for preventing oxidative damage, inflammation and tumorigenesis.    Curcumin exhibits antioxidant, anti-inflammatory and anti-carcinogenic properties and is demonstrated as an indirect inhibitor of Keap1-Nrf2 protein-protein interaction. Novel classes of iminothiazinylbutadienols and divinylpyrimidinethiones were designed and synthesized as analogs of curcumin with its β-diketone moiety masked as a heterocyclic adduct with thiourea. The chemical stability of these novel heterocyclic compounds was improved as compared to curcumin. The biological activity evaluations revealed that some of these new curcumin analogs are more effective ARE activators than curcumin and isothiocyanates.    Most available modulators of Keap1-Nrf2-ARE pathway modify the cysteine sulfhydryl groups of Keap1 for ARE activation. There are safety concerns about these thiol-reactive compounds. A high-throughput screen (HTS) of the MLPCN library identified the first-in-class inhibitor specifically for the direct inhibition of the Keap1-Nrf2 protein-protein interaction. The HTS hit has three chiral centers and the active stereoisomer was designated as LH601A and its stereochemistry was confirmed by X-ray crystallography and stereospecific synthesis. Various analogs of LH601A were designed and synthesized to improve the binding affinity. The obtained structure activity relationships (SAR) provided guidance for further structural optimization. Several analogs showed to be more potent than LH601A. These direct Keap1-Nrf2 inhibitors can mimic the actions of electrophiles in the induction of cytoprotective enzymes but are more selective and specific. Therefore, these direct inhibitors of Keap1-Nrf2 protein-protein interaction have great potential to be developed into innovative therapeutic agents for many diseases and conditions involving oxidative stress.
Object category recognition through visual-semantic context networks
Creators: name: Chakraborty, Ishani
Publisher: name: No Publisher Supplied
Year: 2014

description: Understanding and interacting with one’s environment requires parsing the image of the environment  and recognizing a wide range of objects within it. Despite wide variations, such as viewpoint,  occlusion and background clutter, humans can achieve this task effortlessly and almost instantaneously.  In this thesis, we explore computational algorithms that teach computers to recognize  objects in natural scenes. Inspired by the findings in human cognition, our algorithms are based  on the notion that visual inference involves not only recognizing individual objects in isolation but  also exploiting rich visual and semantic associations between object categories that form complex  scenes. We view artificial object recognition as a fusion of information from two interconnected  representations. The first is the inter-image representation in which an image location is visually  associated with previously learnt object categories based on appearance models to find the most  likely interpretations. The second is the intra-image representation in which the objects in an image  are semantically associated with each other to find the most meaningful spatial and structural  arrangements. The two representations are interconnected in that the visual process proposes object  candidates to the semantic process, while the semantic process verifies and corrects the visual  processs hypotheses.  The primary goal of this thesis is to develop computational models for visual recognition that  characterize the visual and semantic associations and their inter-dependencies to resolve object  identities. In order to do so, we model object associations in contextual spaces. Unlike traditional  approaches for object recognition that use context as a postprocessing filter to discard inconsistent  object labels, we stratify scene generation into a Bayesian hierarchy and simultaneously learn  semantic and visual context models for objects in scenes. The semantic-visual contexts among  objects are represented through latent variables in this hierarchy. The intra-image associations  within a scene are modeled as semantic context while the inter-image relations due to appearance  similarities between object categories are modeled as visual context. To combine the complementary  information derived from the two spaces, object labels are inferred by context switching;  labels activated by appearance matches constrain semantic search while semantic coherence, in  turn, constrains object identities. We demonstrate how this novel context network for modeling  associations between objects leads to highly accurate object detection and scene understanding in  natural images, especially when training data is impoverished and negative exemplars are not easily  available.
Identifying and evaluating eastern filbert blight resistanthazelnuts (Corylus spp.) in New Jersey
Creators: name: Capik, John Michael
Publisher: name: No Publisher Supplied
Year: 2014

description: Eastern filbert blight (EFB), caused by the fungus Anisogramma anomala (Peck) E.  Müller, is a destructive disease of European hazelnut (Corylus avellana). While the wild  North American hazelnut, C. americana, only experiences minor symptoms,  commercially grown C. avellana is extremely susceptible. Anisogramma anomala,  whose range includes much of the U.S. east of the Rocky Mountains, is considered to be  the main impediment to commercial hazelnut production in the East. As such,  identifying and developing resistant C. avellana germplasm is critical to establishing an  industry in this region. To support this goal, several research projects were undertaken.  In the first study, 193 clonal hazelnut accessions spanning multiple Corylus species and  inter-specific hybrids were examined for their disease response to EFB in New Jersey. In  summary, despite the fact that many of the plants were shown to be resistant in Oregon,  some accessions developed EFB in New Jersey. These results support previous work that  suggests different isolates of the pathogen are present in the eastern U.S., and resistance  may not hold up unilaterally. A second study included searching for new sources of  resistance to EFB. New hazelnut germplasm was collected from Russia, Poland, and  Ukraine and exposed to EFB. After at least five years of exposure, plants were rated for  iii  the presence of EFB. At completion, &6 trees from 24 seed lots were found to be free of  EFB with several trees that also produced excellent quality kernels. The final study was  predicated on evaluating known resistant plants for their flowering phenology in New  Jersey. Phenological timing of flowering in hazelnuts is critical to ensure complete  pollination and high crop yields. Nineteen hazelnut accessions were evaluated compared  to daily temperatures over 4 years. Results showed that the accessions followed a similar  progression of bloom each year (both staminate and pistillate flowers), which allowed  their placement into Early, Mid-, and Late flowering groups. These findings represent  the first efforts to report on flowering and bud break phenology in New Jersey, where the  winter climate is colder and more variable than that of Oregon and other commercial  hazelnut growing regions.
Additional file 1: Tables S1 and S2. of First birth and the trajectory of women’s empowerment in Egypt
Creators: name: Goleen Samari
Publisher: name: Figshare
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology

description: (DOCX 15 kb)
Amphilophus astorquii Stauffer, McCrary & Black 2008
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
Cichlidae
Amphilophus
Amphilophus astorquii

description: Amphilophus astorquii Stauffer, McCrary & Black 2008. Black Midas Cichlid, Astorqui’s Cichlid; Cíclido Midas Oscuro, Mojarra De Astorqui
Vouchers: (other collections) AMNH 240557 (4), PSU 4518.1 (1), 4519 (4), 4520 (1), 4521 (1), 4523 (1), 4525 (1), 4526 (1), 4527 (1), 4528 (1) and 4529 (1). Distribution: Central America; endemic to the Lago Apoyo, Nicaragua; (Nicaragua) LN (Atlantic); 73– 73 masl; Sec, Pot. Occurrence and conservation status: Nat, End; CR B1ab(iii) (2020), population trend decreasing. Literature: Stauffer et al. (2008: 122; original description).
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 48, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Finite element analysis of tendon’s collagen network in three dimensions
Creators: name: Politis, Dorothea
Publisher: name: No Publisher Supplied
Year: 2014

description: One of the most vital parts of the human body is the tendon. The main focus of this research is the development of a solid finite element model in three dimensions for the tendon’s collagenous network. Most of the previous studies use simplified approaches in two or three dimensions without including tendon’s essential network. A multi-level approach at the lower levels of hierarchy, such as the microfibrils, will be beneficial in understanding tissue function. Cross-links operate significantly at the fibril level. Thus, determining their influence on mechanical function at this level is important to appreciate the ways in which the macroscopic level is affected.  Analytical finite element models in 3D that describe the mechanical behavior of the complex collagen network and predict stresses in its individual components are still lacking. This study develops a 3D model, based on Orgel’s microfibril structure, consisting of the mineral and collagen D-bands, as well as their intermolecular crosslinks. This structure includes multiple molecules that are aligned in parallel and form the collagen fibril with a D-band repetition every 6&nm, while they are organized in a quasi-hexagonal pattern in the cross section. In this study the created collagen matrix model is subjected to tensile loads in order to estimate the stress-strain behavior and the Young’s Modulus in the elastic regime. With the use of finite element analysis this model requires less computational time than using a Molecular Dynamics Software. Furthermore, parametric analysis of the mineralization and hydration phase under tension is investigated. Results report total elastic modulus of various parametrical models that agree well with previously reported experimental and Steer Molecular Dynamics studies.
Teleudrilus lusinganensis Zicsi & Csuzdi 2000
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Eudrilidae
Teleudrilus
Teleudrilus lusinganensis

description: Teleudrilus lusinganensis Zicsi & Csuzdi, 2000
Teleudrilus lusinganensis Zicsi & Csuzdi, 2000 Ber. nat.-med. Verein Innsbruck 87: 127.
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 19, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Engineered Anti-HER2 Fragments for In Vivo Delivery
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: HER2-positive tumors account for 25-30% of all breast cancers diagnosed and are often aggressive and highly metastatic. Currently, HER2 status is determined by immunohistochemistry of a tumor biopsy, which is both invasive and time-consuming. Whole body or breast imaging of HER2-positive tumors would aid in earlier and more accurate detection and diagnosis. Trastuzumab (Herceptin), an intact “humanized” monoclonal antibody, binds HER2 and has been used to treat HER2-positive breast cancer. Due to its large molecular size and the presence of an Fc antibody region, trastuzumab has a long half-life that is ideal for therapy. However, trastuzumab has far too much “background” (non-tumor localization at any time point) for applications such as imaging.

 Antibody engineering makes it possible to tailor the size and composition of an antibody for specific purposes. We propose to create an anti-HER2 “cys-diabody”, which is one third the size of the parental trastuzumab and lacks the antibody’s Fc portion, resulting in superior pharmacokinetics (drug absorption, distribution, metabolism and excretion) for imaging applications. This molecule will contain an amino acid (cysteine) modification, enabling site-specific coupling of functional groups for imaging and therapy using simple thiol chemistry. Because a large percentage of HER2-positive tumors become refractory to trastuzumab therapy, targeted delivery of a drug via the cys-diabody presents an attractive alternative to traditional chemotherapy with higher dose delivery to the tumor, while sparing normal tissue. Thus, the aims of this study are 1) to create and characterize the anti-HER2 cys-diabody, a small antibody fragment capable of HER2 targeting and site-specific conjugation to imaging and therapeutic moieties; 2) to specifically modify anti-HER2 cys-diabodies with cargo for fluorescent imaging, and analyze their ability to demonstrate bi-functionality – HER2-binding and fluorescence; and 3) to conjugate anti-HER2 cys-diabodies to therapeutic nanoparticles and assess their effect on breast cancer cells and whole animal tumor models .

 The potential impact on breast cancer of the anti-HER2 cys-diabody would be to improve non-invasive detection, diagnosis, and treatment of HER2-positive breast cancer. The use of a targeted probe for imaging HER2-positive tumors, as opposed to traditional imaging methods, decreases the level of uncertainty that a physician or patient must deal with when interpreting results. More importantly, in cases of trastuzumab-refractory disease, targeted therapy using drugs or therapeutic nanoparticles conjugated to anti-HER2 cys-diabody presents an appealing alternative to systemically administered chemotherapy.
Impact of drug resistance mutation on non B HIV-1 clades
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: HIV-1 treatment with antiretroviral drugs can fail because the virus can develop resistance mutations against the drugs. However, it has been noted that some patients still have clinical benefits from treatment even when their viruses have resistance mutations. Research has shown that this benefit is related to the fact that the virus grows more poorly when it has mutations (with a reduced replicative capacity, RC). Thus, understanding the effect of resistance mutations on RC could be very important in treatment strategies where fully suppressive drug treatment is difficult or impossible. Furthermore, the persistence of drug resistance mutations also depends on RC; mutations that cause reduced RC are less likely to be spread from one person to another. This is pertinent to understanding the risk of drug resistant virus spread population-wide. A particular drug resistance mutation that is important is K103N, which makes HIV resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs). An NNRTI (nevirapine) is the basis of HIV-1 therapies being distributed in resource poor areas of the world. Although data suggest that K103N doesn’t cause reduced RC, all these data are based on a single family of HIV-1 (clade B). However, some clinical data from areas of the world where non clade B viruses predominate indicate the RC could be higher for those viruses. Understanding the impact of K103N on other strains of HIV-1 is therefore important. We hypothesize that the effect of K103N on HIV RC depends on the sequence of the virus, which differs dramatically across different strains and clades. Surprisingly, measurements of K103N effects on RC have been performed with a single strain of clade B HIV only. For this project, we plan to experimentally measure the impact of K103N on several viruses from clade B and other clades from strains circulating worldwide. The results of our experiment could be of clinical significance, since nevirapine is the most commonly used antiretroviral drug in countries with limited resources. Therefore patients who have acquired the K103N mutation are nevertheless likely to be treated with NVP since there are very limited options. If the viral fitness of non B clades is significantly decreased due to the K103N mutation, this finding could argue for continued clinical benefit despite existing drug resistance. Furthermore, if K103N causes loss of RC, this would suggest that the spread of this mutation could be a lesser problem than currently believed.
Additional file 1: of Abortion as empowerment: reproductive rights activism in a legally restricted context
Creators: name: McReynolds-PĂŠrez, Julia
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

description: Translation of 2-page clinic intake form. (PDF 34 kb)
Local roots and global wings
Creators: name: Campaiola, Jill G.
Publisher: name: No Publisher Supplied
Year: 2014

description: “Local Roots and Global Wings: Television Drama and Hybridity in Moroccan Cultural Identities” provides a snapshot of the Moroccan film and television industry in 2009 and 2010, on the eve of the Arab Uprisings. The dissertation examines how Moroccan state media elites and filmmakers struggle to instill seeds of democratic change within media structures and local media texts. It also shows how the influx of television dramas from Egypt, Syria, Turkey, and the U.S. provides an opportunity for ‘hybrid’ identities to emerge and allows viewers to interrogate the meaning of ‘modernity’ and ‘democracy’ at home and in various cultural contexts.   I examine how the process of cultural hybridization occurs through mass media. Specifically, I examine how television series coming from various locations redefine cultural boundaries in Morocco and allow individuals to form hybrid identities. Through a textual analysis of the most popular local and foreign television series shown in Morocco, as well as ethnographic fieldwork focusing on state elites, filmmakers and audiences, my dissertation reveals how local and foreign influences pervade the collective Moroccan imagination through state, production, and audience choices.   This multiperspectival approach, which looks at production, texts, and reception, allows for the examination of three phenomena: 1) How hybridity is constructed through both media production and exposure. 2) How different individuals construct their own distinctive ‘hybridities’, as state elites, filmmakers, and audiences have different patterns of socialization and interests in different cultures. 3) How the process of cultural hybridization and television viewing is not only cultural, but also deeply political, as a close look at state elites, producers, and audiences sheds light on the political tensions that emerge between these groups around questions of democracy, media censorship, and social change. As a whole, the dissertation shows how media elites use local media to disseminate dominant ideologies informed by the lingering influence of the former French colonial power and the authoritative Moroccan regime. Moreover, it highlights that many viewers watch and connect with ‘distant others’ on television as a form of passive political resistance to both local media content and policies.   After an introduction (Chapter One) and a methodology chapter (chapter Two), each chapter of the dissertation focuses on one particular aspect of the production-reception chain through the eyes of its players: states elites working at media institutions (Chapter Three), filmmakers and the local media texts they produce (Chapter Four), the influx of foreign dramas (Chapter Five), and audiences (Chapter Six). Each chapter also analyzes how culturally ‘hybrid’ identities get formed at these different stages– and for the different individuals participating– in the process of media production and reception.
The Role of CD4+ NK Cells in AIDS-Related Malignancies
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: Non-Hodgkin’s lymphoma is the sixth most common cause of cancer-related death in the United States, and HIV-associated non-Hodgkin’s lymphoma is the second most common AIDS-associated cancer. The development of non-Hodgkin’s lymphoma can be devastating to HIV-infected individuals, and appears to be linked to impairment of the immune system. Natural Killer (NK) cells play an important role in defending the body against cancer and have been shown to protect against cancer, including AIDS-associated non-Hodgkin’s lymphoma, both in the laboratory and in humans. Following HIV infection, there is NK cell dysfunction as well as an increased incidence of non-Hodgkin’s lymphoma, suggesting that NK-mediated anti-tumor immunity is critical in preventing non-Hodgkin’s lymphoma in immunocompetent individuals. We have identified NK cells that express the CD4 molecule on their surface from human tissues. We can also produce large numbers of CD4 expressing NK cells in our laboratory to study their function. These cells are highly active and are potent mediators of anti-tumor activity. CD4 expressing NK cells are also susceptible to infection with HIV, which could impact their function. Exploring the link between this reduced function and the high incidence of AIDS-associated non-Hodgkin’s lymphoma is critical and has a myriad of implications for clinical treatment strategies. This proposal describes studies aimed at determining the effectiveness of CD4 expressing NK cells in protecting against non-Hodgkin’s lymphoma and how that activity is affected by HIV infection using both laboratory and animal based models. We plan to expand our preliminary data showing that CD4 expressing NK cells effectively kill non-Hodgkin’s lymphoma cell lines by testing them against additional AIDS-associated non-Hodgkin’s lymphoma cells. We also aim to establish the mechanisms by which these cells get to sites of tumor burden within the body. We will then study how HIV infection of these cells impacts their function. Additionally, we will utilize a well-established animal model of non-Hodgkin’s lymphoma, severe combined immunodeficient (SCID) mice. By creating conditions that facilitate tumor development in these mice with no other immune defense, we can then test how our CD4+ NK cells affect disease progression, and whether HIV infection impacts the system. These studies will add to our current understanding of how the immune system protects us against tumors and the function of CD4 expressing NK cells. These cells could function as a treatment against AIDS-associated non-Hodgkin’s lymphoma, however, the implications of HIV infection of this cell type require further study as proposed in this grant.
Microchaetus braunsi Michaelsen 1899
Creators: name: Jadwiga Danuta Plisko
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Microchaetus
Microchaetus braunsi

description: Microchaetus braunsi Michaelsen, 1899
Microchaeta Braunsi: Michaelsen 1899 a: 111; Reynolds & Cook 1976: 81. Microchaetus braunsi: Michaelsen 1900: 451; Reynolds & Cook 1993: 23; Hartwich & Kilias 1989: 255;
Plisko 1991 b: 301; 1992: 340; 1993 b: 235.
Microchaetus microchaetus var. braunsi: Michaelsen 1910: 161; 1913 a: 538; 1918: 318; Reynolds & Cook
1976: 81.
The species is known from its type locality, Port Elizabeth, Eastern Cape, and Avontuur in the eastern part of Western Cape.
description: Published as part of Jadwiga Danuta Plisko, 2006, A systematic reassessment of the genus Microchaetus Rapp, 1849: its amended definition, reinstatement of Geogenia Kinberg, 1867, and erection of a new genus Kazimierzus (Oligochaeta: Microchaetidae), pp. 31-56 in African Invertebrates 47 (1) on page 37, DOI: 10.5281/zenodo.160162
Mursia Desmarest 1823
Creators: name: Ng, Suvarna S. Devi Appukuttannair Biju Kumar Peter K. L.
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Malacostraca
Decapoda
Calappidae
Mursia

description: Genus Mursia Desmarest, 1823
Type species. Mursia cristiata H. Milne Edwards, 1837
description: Published as part of Ng, Suvarna S. Devi Appukuttannair Biju Kumar Peter K. L., 2020, Redescription of the shallow water calappid Mursia spiridonovi Karasawa, 2018 (Brachyura: Calappidae) from India, pp. 1-9 in Nauplius (e 2020015) (e 2020015) 28 on page 2, DOI: 10.1590/2358-2936e2020015, http://zenodo.org/record/14667554
Teleudrilus montanus Zicsi & Csuzdi 2000
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Eudrilidae
Teleudrilus
Teleudrilus montanus

description: Teleudrilus montanus Zicsi & Csuzdi, 2000
Teleudrilus montanus Zicsi & Csuzdi, 2000 Ber. nat.-med. Verein Innsbruck 87: 125.
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 19, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Additional file 2: of Abortion as empowerment: reproductive rights activism in a legally restricted context
Creators: name: McReynolds-PĂŠrez, Julia
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

description: Translation of 3-page clinic intake form. (PDF 97 kb)