G protein-coupled receptors (GPCR) are the largest family of cell surface receptors in vertebrates. Their abundance and role in nearly all physiological systems make GPCR the largest protein family ...targeted for development of pharmaceuticals. Ligand discovery aimed at identification of chemical tools and drug leads is aided by molecular docking simulations that allow critical analysis of the potential interactions between small molecules and proteins in resulting complexes. However, blind assessments of ligand pose quality and affinity prediction have thus far not provided broadly generalizable performance expectations for docking into experimentally-characterized GPCR targets. Likewise, the relative importance of receptor activation state and ligand function differences have also not been systematically assessed. This study compares performance when docking ligands of varied function into varied GPCR activation states in the absence of extensive resampling of the input GPCR structure, and only limited sidechain flexibility after ligand placement. Simulations were performed using 37 experimental structures of 11 Class A GPCR crystallized in multiple activation states (giving rise to 37 self-docking and 68 cross docking simulations). Our results show that one specific subset of cross-docking simulations gave results of similar quality to self-docking. Median ligand RMSD values for top-scored poses were 1.2 Å and 2.0 Å for self-docking and StateMatch/FunctionMatch cross-docking, respectively. The distributions of ligand RMSD values were not statistically different for these two conditions, according to a Kolmogorov-Smirnov test. Therefore, docking performance against GPCR targets can be estimated in advance based on docking target structure activation states, with higher accuracy expected when docking agonists into active state structures and inverse agonists or antagonists into inactive state structures. Receptor conformational sampling in advance of docking or receptor conformational adjustment after docking are more likely to produce substantial improvements for other pairings of receptor activation state and ligand function.
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•GPCR binding pocket structural similarity is high between matched activation states•GPCR ligands recognizing common activation states exhibit variable structural similarity•Docking pose accuracy is strongly impacted by GPCR activation state
The Muir-Torre syndrome variant of Lynch syndrome is characterized by the presence of sebaceous neoplasms (adenoma, epithelioma/sebaceoma, carcinoma) and Lynch syndrome-associated cancers (colon, ...endometrial, and others). Several clinical scoring systems have been developed to identify patients with colon cancer at high risk of Lynch syndrome. However, no such system has been described for patients presenting with sebaceous neoplasms.
Based on logistic regression analysis, a scoring system was developed for patients with sebaceous neoplasm to identify those with the highest likelihood of having Muir-Torre syndrome. The final version of the scoring system included variables such as age at presentation of initial sebaceous neoplasm, total number of sebaceous neoplasms, personal history of a Lynch-related cancer, and family history of Lynch-related cancers.
Patients with a score of 3 or more were more likely to have Muir-Torre syndrome (28 of 29 patients), those with a score of 2 had intermediate likelihood (12 of 20 patients), and no patient with a score of 0 or 1 was diagnosed with Muir-Torre syndrome.
The Mayo Muir-Torre syndrome risk scoring system appears to identify whether patients who present with sebaceous neoplasms are in need of further Lynch syndrome evaluation using easily ascertained clinical information. Abnormal mismatch repair gene immunohistochemistry of a sebaceous neoplasm is a poor predictor in regard to diagnosing Lynch syndrome.
Aims
Rhabdomyosarcomas of bone are extremely rare, with fewer than 10 reported cases. A very rare subtype of spindle cell/sclerosing rhabdomyosarcoma harbouring a FUS–TFCP2 fusion and involving both ...soft tissue and bone locations has been reported very recently. We report only the fourth case of this unusual, clinically aggressive rhabdomyosarcoma.
Material and results
A previously well 72‐year‐old male presented with a destructive lesion of the mandible. Morphological and immunohistochemical study of a needle biopsy and the subsequent resection showed a spindle cell rhabdomyosarcoma. RNA‐seq, RT–PCR and FISH confirmed the presence of the FUS–TFCP2 fusion.
Conclusions
Spindle cell rhabdomyosarcomas carrying the FUS–TFCP2 fusion are very rare rhabdomyosarcoma variants with osseous predilection. The classification and differential diagnosis of this unusual molecular variant of spindle cell/sclerosing rhabdomyosarcoma are discussed.
Babesiosis is a protozoal, tick transmitted disease found worldwide in humans, wildlife and domesticated animals. Commonly used approaches to diagnose babesiosis include microscopic examination of ...peripheral blood smears, detection of circulating antibodies and PCR. To screen and differentiate canine Babesia infections many PCR assays amplify the 18S rRNA gene. These sequences contain hypervariable regions flanked by highly conserved regions allowing for amplification of a broad-range of Babesia spp. However, differences in the 18S rRNA gene sequence of distantly related clades can make it difficult to design assays that will amplify all Babesia species while excluding the amplification of other eukaryotes. By targeting Babesia mitochondrial genome (mtDNA), we designed a novel three primer qPCR with greater sensitivity and broader screening capabilities to diagnose and differentiate Babesia spp.
Using 13 Babesia mtDNA sequences, a region spanning two large subunit rRNA gene fragments (lsu5-lsu4) was aligned to design three primers for use in a qPCR assay (LSU qPCR) capable of amplifying a wide range of Babesia spp. Plasmid clones were generated and used as standards to determine efficiency, linear dynamic range and analytical sensitivity. Animals naturally infected with vector-borne pathogens were tested retrospectively and prospectively to determine relative clinical sensitivity and specificity by comparing the LSU qPCR to an established 18S rDNA qPCR.
The LSU qPCR efficiencies ranged between 92 and 100% with the limit of detection at five copies/reaction. The assay did not amplify mammalian host or other vector-borne pathogen gDNA except Cytauxzoon felis (a feline protozoal pathogen). The LSU qPCR assay amplified 12 different Babesia. sp. and C. felis from 31/31 (100%) archived samples, whereas the 18S qPCR amplified only 26/31 (83.9%). By prospective analysis, 19/394 diagnostic accessions (4.8%) were LSU qPCR positive, compared to 11/394 (2.8%) 18S rDNA qPCR positive.
We have developed a more sensitive qPCR assay with a more expansive range of Babesia spp. detection by targeting a highly conserved region of mtDNA, when compared to an established 18S qPCR.
A 2‐year‐old female intact pregnant Beagle was evaluated after the owner surrendered her to a shelter. Prepartum and 2 months postpartum at the time of routine spay, the dam was whole‐blood ...polymerase chain reaction (PCR) positive for Ehrlichia ewingii. She was also whole‐blood PCR positive for Mycoplasma haemocanis prepartum and continuously for 5 months thereafter. The dam delivered 5 healthy puppies, 1 of which was whole‐blood PCR positive for M. haemocanis. All 5 puppies had antibodies against Ehrlichia spp. at 1 month of age but not thereafter, and all puppies were Ehrlichia spp. PCR negative for 5 months of follow‐up. Therefore, this study supports a potential role for vertical transmission in the maintenance of M. haemocanis in dogs as reservoir hosts. In contrast, in this case there was no evidence that E. ewingii was transmitted transplacentally or during the perinatal period.
Background
Babesiosis is an important cause of thrombocytopenia and hemolytic anemia in dogs. Babesia vulpes, reported in European dogs and North American foxes, rarely has been reported in domestic ...North American dogs. Newly optimized polymerase chain reaction (PCR) primers facilitate more sensitive amplification of B. vulpes DNA.
Objectives
To determine the prevalence of Babesia sp. infections in dogs being tested for Babesia infection, and to describe co‐infections and clinicopathologic abnormalities in B. vulpes positive dogs.
Animals
Dog blood or tissue samples (n = 9367) submitted to a diagnostic laboratory between June 2015 and June 2018 were tested using an optimized Babesia PCR assay.
Methods
Comprehensive canine vector‐borne disease diagnostic testing was performed on convenience samples.
Results
Babesia sp. DNA was amplified from 269/9367 (2.9%) North American dogs. Babesia sp. infections included B. gibsoni monoinfection (157; 1.7%), B. vulpes monoinfection (19; 0.20%), and B. gibsoni and B. vulpes coinfection (29; 0.31%). Forty‐three of the 48 total B. vulpes‐infected dogs were American Pit Bull Terrier‐type breeds, of which 36 historically were involved with dog fights. Coinfections with Mycoplasma, Dirofilaria immitis, or Wolbachia and coexposures to Bartonella, Ehrlichia, and Rickettsia spp. were documented in B. vulpes‐infected dogs. Clinicopathologic data in B. vulpes‐infected dogs both with and without coinfections included anemia, thrombocytopenia, hyperglobulinemia, hypoalbuminemia, and proteinuria.
Conclusions and Clinical Importance
Babesia vulpes infection in domestic North American dogs is commonly found in conjunction with other coinfections, including B. gibsoni and hemotropic Mycoplasma. Similar to B. gibsoni, dog‐to‐dog transmission of B. vulpes may be a frequent mode of transmission.
Variants of uncertain significance (VUS) are a common result of diagnostic genetic testing and can be difficult to manage with potential misinterpretation and downstream costs, including time ...investment by clinicians. We investigated the rate of VUS reported on diagnostic testing via multi-gene panels (MGPs) and exome and genome sequencing (ES/GS) to measure the magnitude of uncertain results and explore ways to reduce their potentially detrimental impact.
Rates of inconclusive results due to VUS were collected from over 1.5 million sequencing test results from 19 clinical laboratories in North America from 2020 to 2021.
We found a lower rate of inconclusive test results due to VUSs from ES/GS (22.5%) compared with MGPs (32.6%; P < .0001). For MGPs, the rate of inconclusive results correlated with panel size. The use of trios reduced inconclusive rates (18.9% vs 27.6%; P < .0001), whereas the use of GS compared with ES had no impact (22.2% vs 22.6%; P = ns).
The high rate of VUS observed in diagnostic MGP testing warrants examining current variant reporting practices. We propose several approaches to reduce reported VUS rates, while directing clinician resources toward important VUS follow-up.
Background:
Black women involved in the legal system disproportionately experience intimate partner violence (IPV); however, current research does not satisfactorily describe the risk and protective ...factors associated with IPV among Black women under community supervision.
Methods:
We conducted a subgroup analysis of Black women (
N
= 128) using data from a randomized controlled trial that evaluated the feasibility and efficacy of two IPV screening and prevention programs for women under community supervision. Participants in the original study were randomized into two IPV prevention conditions—computerized or case manager Women Initiating New Goals of Safety (WINGS). In this study, we examine the effects of that study's two conditions on linkage to IPV services and secondary outcomes, specifically among Black participants who experienced physical, sexual, and psychological IPV.
Results:
Both conditions showed significant reductions in days of substance use abstinence over the 3-month period among Black women who experienced sexual or verbal IPV. Participants in the case manager arm were 14 times more likely to receive IPV services in the past 90 days—from baseline to the 3-month follow-up (adjusted odds ratio = 14.45, 95% confidence interval CI = 1.25 to 166.51,
p
= 0.032). Participants in the computerized arm were significantly more likely to report receiving social support from baseline to the 3-month follow-up assessment (regression coefficient
b
= 2.27, 95% CI = 0.43 to 4.11,
p
= 0.015).
Conclusions:
Although both conditions showed significant reductions in the number of days of abstinence from substance use among this subgroup of Black women, the findings showed differential effectiveness between the computerized WINGS arm and the case manager WINGS arm in improving social support and linkage to services. These findings may indicate that different modalities of WINGS may work better for specific activities and point to the need for a hybrid format that optimizes the use of distinct modalities for delivering activities.
In rural Bangladesh, India and elsewhere, pour-flush pit latrines are the most common sanitation system. When a single pit latrine becomes full, users must empty it themselves and risk exposure to ...fresh feces, pay an emptying service to remove pit contents or build a new latrine. Double pit pour-flush latrines may serve as a long-term sanitation option including high water table areas because the pits do not need to be emptied immediately and the excreta decomposes into reusable soil.
Double pit pour-flush latrines were implemented in rural Bangladesh for 'hardcore poor' households by a national NGO, BRAC. We conducted interviews, focus groups, and spot checks in two low-income, rural areas of Bangladesh to explore the advantages and limitations of using double pit latrines compared to single pit latrines.
The rural households accepted the double pit pour-flush latrine model and considered it feasible to use and maintain. This latrine design increased accessibility of a sanitation facility for these low-income residents and provided privacy, convenience and comfort, compared to open defecation. Although a double pit latrine is more costly and requires more space than a single pit latrine the households perceived this sanitation system to save resources, because households did not need to hire service workers to empty pits or remove decomposed contents themselves. In addition, the excreta decomposition process produced a reusable soil product that some households used in homestead gardening. The durability of the latrine superstructures was a problem, as most of the bamboo-pole superstructure broke after 6-18 months of use.
Double pit pour-flush latrines are a long-term improved sanitation option that offers users several important advantages over single pit pour-flush latrines like in rural Bangladesh which can also be used in areas with high water table. Further research can provide an understanding of the comparative health impacts and effectiveness of the model in preventing human excreta from entering the environment.
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