bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence of Endolymphatic Hydrops in Cochlear Implant Candidates with Idiopathic Profound Sensorineural Hearing Loss
Authors: Mosimann Eva , Bächinger David , Eckhard Andreas , Reddiess Philipp , Veraguth Dorothe , Röösli Christof , Huber Alexander , De Vere-Tyndall Anthony , Winklhofer Sebastian , Dlugaiczyk Julia , Dalbert Adrian
Published: August 2022

Objective

To determine the prevalence of endolymphatic hydrops (EH) in cochlear implant (CI) candidates with idiopathic profound sensorineural hearing loss (SNHL) and its influence on the preservation of audiovestibular function after cochlear implantation.

Study Design

Prospective case series.

Setting

Tertiary referral center.

Patients

CI candidates with idiopathic progressive SNHL, but without classic EH-associated symptoms.

Interventions

Delayed intravenous gadolinium-enhanced inner ear fluid-attenuated inversion recovery magnetic resonance imaging as well as pure-tone audiograms, video head impulse tests, and vestibular evoked myogenic potentials before and 4 weeks after cochlear implantation.

Main Outcome Measures

Prevalence of EH before cochlear implantation, audiovestibular function before and after surgery in hydropic and nonhydropic ears.

Results

Thirty-two ears in 16 CI candidates were included. Nine ears (28%) with EH were detected. Although preoperative hearing thresholds, utricular function, and semicircular canal function were not different between the two groups, saccular function was reduced in hydropic ears. Ten subjects received a unilateral CI. Of these, 3 (30%) showed EH on the implanted side. There was no difference regarding postoperative hearing loss between the two groups, but the results point toward a higher vulnerability of hydropic ears with respect to loss of otolith function after cochlear implantation.

Conclusions

This is the first study showing that EH can be assumed in about one third of CI candidates with idiopathic profound SNHL, but no classic EH-associated symptoms. Preliminary results suggest that EH has no influence on the preservation of cochlear function but could be a risk factor for loss of otolith function after cochlear implantation.
Geographic Variations in Medicare Cochlear Implantations in the United States
Authors: Fujiwara Rance J. T. , Wong Emily C. , Ishiyama Akira
Published: August 2022

Objective

To describe national practice patterns and detail geographic and temporal changes in cochlear implantations (CIs) in the Medicare population.

Study Design

Cross-sectional analysis.

Setting

Medicare B Public Use Files.

Patients

Medicare B fee-for-service patients who underwent CI from 2012 to 2019.

Intervention(s)

Cochlear implantations (Current Procedural Terminology code 69930).

Main Outcome Measures

Medicare Part B Public Use Files were used to identify all individual providers who performed CIs from 2012 to 2019. The total number of CIs performed annually was calculated for hospital referral regions (HRRs) as well as U.S. census regions to describe geographic variations and changes over the study period. Average Medicare reimbursement rates were tabulated.

Results

From 2012 of 2019, the number of CIs performed in the Medicare population increased from 1,239 to 2,429, representing a 96.0% increase. In each of the four U.S. census regions, there was a statistically significant increase in the number of CIs performed over the study period. However, of 306 HRR in the United States, cochlear implants were performed in only 117 (38.2%), with the median number of CIs in each HRRs 16.7 (interquartile range, 13–24.2) per year. The median weighted average Medicare reimbursement was $1205.49 (interquartile range, 1161.65–1253.46).

Conclusions

The number of CIs in the Medicare population has increased from 2012 to 2019. However, widespread geographic variations continue to persist in the United States and represent opportunities toward identifying and acting on the etiologies of persistent disparities in CI.
De novo interstitial deletion of 11q14.3q22 in a boy with mild intellectual disability and short stature
Authors: Kurt Colak Fatma , Eyerci Nilnur , Lafci Naz Guleray
Published: August 2022

Background

Interstitial deletions of the 11q region are infrequent. Nonrecurrent chromosomal rearrangements are observed with high variability in size and precise breakpoints of the deleted area. Moreover heterogeneous clinical findings are observed in those harboring 11q interstitial deletions. Main clinical features associated with these deletions include mild dysmorphic findings intellectual disability and moderate developmental or speech delay

Method

Conventional high-resolution karyotyping along with microarray studies were performed for the index patient who was found to be a carrier of a de novo interstitial deletion in the long arm of chromosome 11 which is located between the 11q14 and 11q22 band regions. We also investigated the homologous chromosome with next-generation sequencing technology to search for unmasked recessive variants in genes on the nondeleted contralateral allele.

Results:

Cytogenetic analysis revealed a de novo interstitial deletion on the long arm of chromosome 11 46XYdel(11) (q14q22). Microarray analysis confirmed the deletion of 11.2Mb in length mapping from 11q14.3 to 11q22.2 [arr (GRCh37) 11q14.3q22.1(90549863_101833022)x1 dn]. Whole-exome sequencing did not detect any other genetic variant (single nucleotide variant) on the nondeleted allele.

Conclusion

This study gave us the opportunity for an attempt to define the smallest region of overlap for frequently observed clinical findings by reviewing the literature.
Advances in oral tongue reconstruction: a reconstructive paradigm and review of functional outcomes
Authors: Thompson Joshua A. , Vakharia Kalpesh T. , Hatten Kyle M.
Published: August 2022

Purpose of review

Glossectomy remains a common treatment of oral tongue malignancies, which has a range of functional impacts depending on the extent of resection. This review aims to categorize and provide context for the approach to reconstructing these defects using recent evidence.

Recent findings

The reconstruction method of choice should be tailored to the size and location of the glossectomy defect with special consideration to replace tongue volume and preserve mobility. There has been an increasing focus on patient-reported outcomes in oral tongue reconstruction. For defects beyond one-third of the tongue, free tissue reconstruction, and more recently, the submental artery island flap yield excellent results. Advances in reconstruction of larger defects have included preoperative soft tissue planning and assessment of outcomes in total glossectomy patients with laryngeal preservation.

Depending on the defect, the appropriate reconstruction may range from healing by secondary intention to large volume free tissue transfer. In general, functional outcomes diminish with increasing size and complexity of the defect regardless of the reconstructive technique.
The role of pH-impedance monitoring in swallowing disorders
Authors: Bobin Francois , Lechien Jerome R.
Published: August 2022

Purpose of review

To review the current evidence about the usefulness and the place of pH study in the management of patients with swallowing disorders.

Recent findings

Gastroesophageal reflux disease (GERD) and laryngopharyngeal reflux (LPR) are found in approximately 30% of patients with esophageal or oropharyngeal dysphagia. Patients with suspected GERD may benefit from gastrointestinal endoscopy and proton pump inhibitors according to guidelines. The diagnosis of LPR in patients with oropharyngeal dysphagia is more controversial because there are no gold standard and diagnostic guidelines. The clinical diagnosis based on empirical therapeutic trial is a reasonable first-line strategy, but many dysphagic patients should not respond to treatment. These patients require hypopharyngeal-esophageal multichannel intraluminal impedance-pH monitoring (HEMII-pH), which is the most effective examination providing important information on GERD and LPR features. At the HEMII-pH, GERD patients often report upright (daytime) and supine (nighttime) liquid acid esophageal events with significant esophageal distal acid exposure time. LPR patients have more frequently upright (daytime) gaseous weakly acid or nonacid pharyngeal reflux events without distal esophageal acid exposure abnormalities in many times. The features of reflux at the HEMII-pH may indicate a personalized treatment for dysphagic patients combining proton pump inhibitors, alginate/magaldrate or gastroprokinetic in cases of esophageal dysmotility.

GERD and LPR are prevalent causes of dysphagia. The large number of reflux patients who do not respond to empirical treatment makes important the awareness of otolaryngologists about pH-impedance monitoring indication, features, and interpretation.
Expanded Paramedian Forehead Flap for Nasal Reconstruction Following Congenital Nevus Excision
Authors: Sahu Ranjit Kumar , Acharya Sudeshna , Midya Manojit , Chakraborty Sourabh Shankar
Published: August 2022

In this report, we discuss the excision of a large congenital nevus covering the nose and face and the reconstruction of the defect using an expanded forehead flap, in a 24-year-old man. We observed that after incorporating specific modifications including tissue expansion, thinning of the distal part of the flap, and placing the pedicle over the cutaneous branch of the supratrochlear artery, we were able to provide excellent aesthetic results using this time-tested paramedian forehead flap for nasal reconstruction. After we inset the flap, there was negligible donor site morbidity during a 33-month follow-up period.
Epidemiology of Clefts in Kwazulu Natal: Comparison With Systematic Review Analysis, Similarities, and Differences
Authors: Madaree Anil
Published: August 2022

Preamble:

The incidence and accuracy of cleft epidemiology is variable depending on geographical region, population group, and country being assessed. Confounding factors are rendered more accurate if consecutive patients seen in a unit over a prolonged period are reported.

Materials and Methods:

Plastic surgery charts at Inkosi Albert Luthuli Central Hospital (IALCH) were reviewed from 2003 to 2019. Appropriate International Classification of Diseases (ICD) cleft codes were used to obtain a cleft database of all cleft patients. The review revealed 1487 cleft patients. Data extracted included sex, race, extent of cleft lip or palate, laterality, and birth month.

Results:

Overall, there was an almost equivalent sex distribution with 745 females and 742 males. There were 390 cleft lip only (26%), 505 cleft lip with palate (CLP) (34%), and 592 cleft palate only (40%). In the cleft lip only group, Black females were affected in 54% and males in 46%, whereas in the Asian group, females were affected in 33% and males in 67% (P=0.022). In the CLP group, Asian and Colored females were affected more (56% and 60%, respectively), while in the Black and White groups, females were less affected (40% and 26%, respectively). Cleft palate only was the most common category in Black (44%) and Colored (55%), while the CLP category was most common in Asian (49%) and White (42%).

Conclusions:

Demographics of cleft lip and palate in KwaZulu Natal is different from other series in certain aspects. In addition, there are differences in the race groups when analyzing certain aspects. The differences may be based on genetic or environmental factors and warrants further investigation.
70 Years of Human Cingulate Cortex Stimulation. Functions and Dysfunctions Through the Lens of Electrical Stimulation
Authors: Pelliccia Veronica , Del Vecchio Maria , Avanzini Pietro , Revay Martina , Sartori Ivana , Caruana Fausto
Published: August 2022

In this review, we retrace the results of 70 years of human cingulate cortex (CC) intracerebral electrical stimulation and discuss its contribution to our understanding of the anatomofunctional and clinical aspects of this wide cortical region. The review is divided into three main sections. In the first section, we report the results obtained by the stimulation of the anterior, middle, and posterior CC, in 30 studies conducted on approximately 1,000 patients from the 1950s to the present day. These studies show that specific manifestations can be reliably associated with specific cingulate subfields, with autonomic, interoceptive, and emotional manifestations clustered in the anterior cingulate, goal-oriented motor behaviors elicited from the anterior midcingulate and a variety of sensory symptoms characterizing the posterior cingulate regions. In the second section, we compare the effect of CC intracerebral electrical stimulation with signs and manifestations characterizing cingulate epilepsy, showing that the stimulation mapping of CC subfields provides precious information for understanding cingulate epileptic manifestations. The last section tackles the issue of the discrepancy emerging when comparing the results of clinical (electrical stimulation, epilepsy) studies—revealing the quintessential affective and motor nature of the CC—with that reported by neuroimaging studies—which focus on high-level cognitive functions. Particular attention will be paid to the hypothesis that CC hosts a “Pain Matrix” specifically involved in pain perception, which we will discuss in the light of the fact that the stimulation of CC (as well as cingulate epileptic seizures) does not induce nociceptive effects.
DExH/D-box helicases at the frontline of intrinsic and innate immunity against viral infections
Authors: Bonaventure Boris , Goujon Caroline
Published: August 2022

DExH/D-box helicases are essential nucleic acid and ribonucleoprotein remodelers involved in all aspects of nucleic acid metabolism including replication, gene expression and post-transcriptional modifications. In parallel to their importance in basic cellular functions, DExH/D-box helicases play multiple roles in viral life cycles, with some of them highjacked by viruses or negatively regulating innate immune activation. However, other DExH/D-box helicases have recurrently been highlighted as direct antiviral effectors or as positive regulators of innate immune activation. Innate immunity relies on the ability of Pathogen Recognition Receptors to recognize viral signatures and trigger the production of interferons (IFNs) and pro-inflammatory cytokines. Secreted IFNs interact with their receptors to establish antiviral cellular reprogramming via expression regulation of the interferon-stimulated genes (ISGs). Several DExH/D-box helicases have been reported to act as viral sensors (DDX3, DDX41, DHX9, DDX1/DDX21/DHX36 complex), and others to play roles in innate immune activation (DDX60, DDX60L, DDX23). In contrast, the DDX39A, DDX46, DDX5 and DDX24 helicases act as negative regulators and impede IFN production upon viral infection. Beyond their role in viral sensing, the ISGs DDX60 and DDX60L act as viral inhibitors. Interestingly, the constitutively expressed DEAD-box helicases DDX56, DDX17, DDX42 intrinsically restrict viral replication. Hence, DExH/D-box helicases appear to form a multilayer network of primary and secondary factors involved in both intrinsic and innate antiviral immunity. In this review, we highlight recent findings on the extent of antiviral defences played by helicases and emphasize the need to better understand their immune functions as well as their complex interplay.
Prevalence of Helicobacter pylori resistance to clarithromycin in Tunisia
Authors: Chtourou Lassaad , Moalla Manel , Mnif Basma , Smaoui Hend , Gdoura Hela , Boudabous Mona , Mnif Leila , Amouri Ali , Hammami Adnene , Tahri Nabil
Published: August 2022

Background.

Helicobacter pylori

(H. pylori) resistance to clarithromycin is increasing worldwide. Data on the prevalence of

H. pylori

resistance are limited in Tunisia.

Gap statement. Given that

H. pylori

resistance to clarithromycin has not been studied in Tunisia since 2010, there was a need to determinate its prevalence and the principal mutations implicated in this resistance.

Aim. The aims were to define the prevalence of

H. pylori

infection among symptomatic patients and to determinate the level of clarithromycin resistance among these patients and the main mutations conferring this resistance.

Methods. We conducted a cross-sectional study from March 2017 to February 2020 in the Hepato-Gastroenterology Department of Hedi Chaker University Hospital in Sfax that included 124 Tunisian patients who underwent gastroduodenal endoscopy with biopsies. Mutations conferring resistance to clarithromycin were detected using the Allplex

H. pylori

and ClariR PCR Assay.

Results. Out of 124 biopsies, 101 (81.5 2 %) were PCR-positive for

H. pylori

. Mutations conferring resistance to clarithromycin were detected in 30/95 (31.6 %) of patients. The rate of primary resistance was 25.3 % and of secondary resistance 62.5 %. The most frequently detected mutation was A2143G (86, 90%) followed by A2142G (11, 36%). Seven patients had a double mutation A2143G–A2142G. The factors independently associated with resistance to clarithromycin were diabetes, high blood pressure, the presence of a bulbar ulcer on endoscopy and the presence of gastric atrophy on histology.

Conclusion. Detection of more than 25 % of strains with clarithromycin resistance mutations makes the

H. pylori

first-line treatment with clarithromycin questionable in our setting, and a review of empirical treatment of

H. pylori

is urgently needed.
Systematic Review and Meta-Analysis of the Effect of Adverse Childhood Experiences (ACEs) on Brain-Derived Neurotrophic Factor (BDNF) Levels
Authors: Vyas Neha , Wimberly Courtney E. , Beaman M. Makenzie , Kaplan Samantha J. , Rasmussen Line J.H. , Wertz Jasmin , Gifford Elizabeth J. , Walsh Kyle M.
Published: August 2022

There is continued interest in identifying dysregulated biomarkers that mediate associations between adverse childhood experiences (ACEs) and negative long-term health outcomes. However, little is known regarding how ACE exposure modulates neural biomarkers to influence poorer mental health outcomes in ACE-exposed children. To address this, we performed a systematic review and meta-analysis of the impact of ACE exposure on Brain Derived Neurotrophic Factor (BDNF) levels - a neural biomarker associated with the onset of mood disorders. Twenty-two studies were selected for inclusion within the systematic review, ten of which were included in meta-analysis. Most included studies retrospectively assessed impacts of childhood maltreatment in clinical populations. Sample size, BDNF protein levels in ACE-exposed and unexposed subjects, and standard deviations were extracted from ten publications to estimate the BDNF ratio of means (ROM) across exposure categories. Overall, no significant difference was found in BDNF protein levels between ACE-exposed and unexposed groups (ROM: 1.05; 95% CI: 0.91-1.22). Non-significant elevation of BDNF levels in ACE-exposed subjects was observed among studies specifically investigating childhood maltreatment and among studies measuring BDNF in serum, but these analyses were limited by high between-study heterogeneity. Studies that measured BDNF levels in subjects prior to age 20 revealed elevated levels in the ACE-exposed group, which was not observed in studies measuring BDNF levels later in life. These results support continued investigation into the impact of ACE exposure on neural biomarkers and highlight the potential importance of analyte type and timing of sample collection on study results.
A randomized, double-blind, Phase 1 study of IN-006, an inhaled antibody treatment for COVID-19
Authors: Moench Thomas R. , Botta Lakshmi , Farrer Brian , Lickliter Jason D. , Kang Hyunah , Park Yoona , Kim Cheolmin , Hoke Marshall , Brennan Miles , McSweeney Morgan D. , Richardson Zachary , Whelan John B. , Cho Jong Moon , Lee Soo Young , Faurot Frances , Hutchins Jeff , Lai Samuel K.
Published: August 2022

Rationale

Although COVID-19 is predominantly a respiratory tract infection, current antibody treatments are administered by systemic dosing. We hypothesize that inhaled delivery of a muco-trapping monoclonal antibody would provide a more effective and convenient treatment for COVID-19.

Objective

We investigated the safety, tolerability, and pharmacokinetics of IN-006, a reformulation of regdanvimab, an approved intravenous treatment for COVID-19, for nebulized delivery by a handheld nebulizer.

Methods

A Phase 1 study was conducted in healthy volunteers. Study staff and participants were blinded to treatment assignment, except for pharmacy staff preparing the study drug. The primary outcomes were safety and tolerability. Exploratory outcomes were pharmacokinetic measurements of IN-006 in nasal fluid and serum.

Results

Twenty-three participants were enrolled and randomized across two single dose and one multiple dose cohorts. There were no serious adverse events (SAEs). All enrolled participants completed the study without treatment interruption or discontinuation. All treatment-emergent adverse events were transient, non-dose dependent, and were graded mild to moderate in severity. Nebulization was well tolerated and completed in a mean of 6 minutes in the high dose group. Mean nasal fluid concentrations of IN-006 in the multiple dose cohort were 921 µg/g of nasal fluid at 30 minutes after dosing and 5.8 µg/g at 22 hours. Mean serum levels in the multiple dose cohort peaked at 0.55 µg/mL at 3 days after the final dose.

Conclusions

IN-006 was well-tolerated and achieved concentrations in the respiratory tract orders of magnitude above its inhibitory concentration. These data support further clinical development of IN-006.

Registration

Australian New Zealand Clinical Trials Registry: ACTRN12621001235897
Non-contact microfluidic analysis of the stiffness of single large extracellular vesicles from IDH1-mutated glioblastoma cells
Authors: Jeong Mi Ho , Im Hyungsoon , Dahl Joanna B.
Published: August 2022

In preparation for leveraging extracellular vesicles (EVs) for disease diagnostics and therapeutics, fundamental research is being done to understand EV biological, chemical, and physical properties. Most published studies investigate nanoscale EVs and focus on EV biochemical content. There is much less understanding of large microscale EV characteristics and EV mechanical properties. We recently introduced a non-contact microfluidic technique that measures the stiffness of large EVs (>1 μm diameter). This study probes the sensitivity of the microfluidic technique to distinguish between EV populations by comparing stiffness distributions of large EVs derived from glioblastoma cell lines. EVs derived from cells expressing the IDH1 mutation, a common glioblastoma mutation known to disrupt lipid metabolism, were significantly stiffer than those expressed from wild-type cells. A supporting lipidomics analysis shows that the IDH1 mutation increases the amount of saturated lipids in EVs. Taken together, these data suggest that high-throughput microfluidics is capable of distinguishing between large EV populations that differ in biomolecular composition and therefore structure. These findings advance the understanding of EV biomechanics, in particular for the less studied microscale EVs, and demonstrate microfluidics to be a promising technique to perform clinical EV mechanophenotyping.
Extreme sex chromosome differentiation, likely driven by inversion, contrasts with mitochondrial paraphyly between species of crowned sparrows
Authors: McCallum Quinn , Askelson Kenneth , Fogarty Finola , Natola Libby , Nikelski Ellen , Huang Andrew , Irwin Darren
Published: August 2022

Sympatric species pairs provide researchers with the opportunity to study patterns of genomic differentiation during the late stages of speciation and to identify the genomic regions underlying reproductive isolation. The Golden-crowned Sparrow (Zonotrichia atricapilla) and the White-crowned Sparrow (Zonotrichia leucophrys) are broadly sympatric songbirds found in western North America. These sister species are phenotypically differentiated and largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent mitochondrial introgression. We used a genotyping-by-sequencing (GBS) approach to determine the structure of nuclear genomic differentiation between these species and also between two hybridizing subspecies of Z. leucophrys, across more than 45,000 single nucleotide polymorphisms (SNPs). The two Z. leucophrys subspecies showed moderate levels of relative differentiation, as well as patterns consistent with a history of recurrent selection in both ancestral and daughter populations. Z. leucophrys and Z. atricapilla show high levels of relative differentiation and strong heterogeneity in the level of differentiation among different chromosomal regions, with a large portion of the Z chromosome showing highly elevated differentiation. Patterns of relative and absolute differentiation and linkage disequilibrium suggest a large inversion on the Z chromosome, with inversion haplotypes that segregate between Z. atricapilla and Z. leucophrys. While mitochondrial DNA differentiation is often emphasized in studies of speciation, differentiation between these Zonotrichia sparrows appears to have occurred first in the Z chromosome and secondarily in autosomes, followed by mitochondrial introgression. This putative inversion has implications for reproductive isolation between these species and adds to a growing body of evidence for the importance of inversions and the Z chromosome in speciation.
Structures of BIRC6-Client Complexes Provide Mechanism of Smac-Mediated Release of Caspases
Authors: Hunkeler Moritz , Jin Cyrus Y. , Fischer Eric S.
Published: August 2022

Apoptosis is tightly regulated and essential for metazoan development1, 2. Excessive apoptosis contributes to neurodegenerative disease, while diminished apoptosis can lead to inflammation and cancer3. Inhibitor of apoptosis (IAP) proteins are the principal actors that restrain apoptotic activity and are thus attractive therapeutic targets4. IAPs in turn are regulated by mitochondria-derived pro-apoptotic factors such as Smac and HtrA24. Here, through a series of cryo-electron microscopy (cryo-EM) structures of full-length baculoviral IAP repeat-containing protein 6 (BIRC6) bound to Smac, caspase-3, caspase-7 and HtrA2, we provide the molecular basis for BIRC6-mediated caspase inhibition and its release by Smac. We demonstrate that BIRC6 cooperates preferentially with the non-canonical E1 enzyme UBA6 to ubiquitylate caspases and that caspase ubiquitylation is effectively inhibited by Smac through near-irreversible interactions. The dimeric arrangement of BIRC6 resolves the long-standing question of how the evolutionarily conserved single-BIR domain IAPs sequester caspases and how Smac binding antagonizes IAPs. This collection of BIRC6 structures provides critical insights into IAP-mediated apoptosis regulation, relevant for the development of current and future apoptosis-targeting cancer therapeutics.
In vitro and in vivo activity of Gepotidacin against drug-resistant mycobacterial infections
Authors: Ahmad Mohammad Naiyaz , Garg Tanu , Singh Shriya , Shukla Richa , Ramya VK , Kaur Parvinder , Chopra Sidharth , Dasgupta Arunava
Published: August 2022

Mycobacterial pathogens including Non-tuberculous mycobacteria (NTM) and M. tuberculosis (Mtb), are pathogens of significant worldwide interest owing to inherent drug resistance to a wide variety of FDA-approved drugs as well as causing a broad range of serious infections. Identifying new antibiotics active against mycobacterial pathogens is an urgent unmet need, especially those antibiotics that can bypass existing resistance mechanisms. In this study, we demonstrate that Gepotidacin, a first-in-class triazaacenapthylene topoisomerase inhibitor, shows potent activity against Mtb and M. fortuitum as well as against other NTMs species, including fluoroquinolone-resistant M. abscessus. Furthermore, Gepotidacin exhibits concentration-dependent bactericidal activity against various mycobacterial pathogens, synergizes with several drugs utilized for their treatment, and reduces bacterial load in macrophages in the intracellular killing assay comparable to amikacin. Additionally, M. fortuitum ATCC 6841 was unable to generate resistance to Gepotidacin in vitro. When tested in a murine neutropenic M. fortuitum infection model, Gepotidacin caused a significant reduction in bacterial load in various organs at 10 fold lower concentration than amikacin. Taken together, Gepotidacin possesses a potentially new mechanism of action that enables it to escape existing resistance mechanisms. Thus, it can be projected as a potent novel lead for the treatment of mycobacterial infections, particularly for NTM, where present therapeutic interventions are very limited.
Phat queens emerge fashionably late: body size and condition predict timing of spring emergence for queen bumble bees
Authors: Keaveny Ellen C. , Dillon Michael E.
Published: August 2022

For insects, the timing of many life history events (phenology) depends on temperature cues. Body size is a critical mediator of insect responses to temperature, so may also influence phenology. The determinants of spring emergence of bumble bee queens are not well understood, but body size is likely important for several reasons. In fall, queens accumulate energy stores to fuel overwinter survival. Accumulation of fat stores prior to and depletion of fat stores during overwintering are likely size-dependent: larger queens can accumulate more lipids and have lower mass-specific metabolic rates. Therefore, larger queens and queens in relatively better condition may have delayed depletion of energy stores, allowing for later spring emergence. To test whether timing of spring emergence is associated with body size and condition, we captured 295Bombus huntiiqueens in Laramie, WY, during the 2020 and 2021 growing seasons, weighed them, and measured intertegular width (a size metric unaffected by variation in feeding and hydration state). Early emerging queens were smaller than later emerging queens across years. Mass relative to intertegular width increased as the season progressed suggesting, as predicted, that body condition influences the timing of spring emergence for these crucial pollinators.
Evaluation of KRASG12C Inhibitor Responses in Novel Murine KRASG12C Lung Cancer Cell Line Models
Authors: Sisler Daniel J , Hinz Trista K , Le Anh T , Kleczko Emily K , Nemenoff Raphael A , Heasley Lynn E
Published: August 2022

The KRAS(G12C) mutation is the most common genetic mutation in North American lung adenocarcinoma patients. Recently, direct inhibitors of the KRASG12C protein have been developed and demonstrate clinical response rates of 37-43%. Importantly, these agents fail to generate durable therapeutic responses with median progression-free survival of ~6.5 months. To provide models for further preclinical improvement of these inhibitors, we generated three novel murine KRASG12C-driven lung cancer cell lines. The co-occurring NRASQ61L mutation in KRASG12C-positive LLC cells was deleted and the KRASG12V allele in CMT167 cells was edited to KRASG12C with CRISPR/Cas9 methods. Also, a novel murine KRASG12C line, mKRC.1, was established from a tumor generated in a genetically-engineered mouse model. The three lines exhibit similar in vitro sensitivities to KRASG12C inhibitors (MRTX-1257, AMG-510), but distinct in vivo responses to MRTX-849 ranging from progressive growth with orthotopic LLC-NRAS KO tumors to marked shrinkage with mKRC.1 tumors. All three cell lines exhibited synergistic in vitro growth inhibition with MRTX-1257 and the SHP2 inhibitor, RMC-4550 and the MRTX-849/RMC-4550 combination yielded tumor shrinkage in orthotopic LLC-NRAS KO tumors propagated in syngeneic mice. Notably, this synergistic combination response was lost in athymic nu/nu mice, supporting a growing literature demonstrating a role for adaptive immunity in the response to this class of drugs. These new models of murine KRASG12C mutant lung cancer should prove valuable for identifying improved therapeutic combination strategies with KRASG12C inhibitors.

Contribution to the Field Statement

The development of KRASG12C inhibitors has not impacted treatment of lung cancers bearing the KRASG12C mutation to the degree that tyrosine kinase inhibitors have changed the treatment outcomes for patients bearing oncogenic mutations in receptor tyrosine kinases. Thus, the field is now exploring combination strategies with KRASG12C inhibitors that may enhance their clinical benefit. Moreover, published findings indicate that host immunity contributes to efficacy of oncogene-directed inhibitors including KRASG12C inhibitors. Thus, these novel murine KRASG12C-driven lung cancer cell lines will provide valuable models for preclinical evaluation of novel drug combinations in immune competent hosts.
Resolving deleterious and near-neutral effects requires different pooled fitness assay designs
Authors: Limdi Anurag , Baym Michael
Published: August 2022

Pooled sequencing-based fitness assays are a powerful and widely used approach to quantifying fitness of thousands of genetic variants in parallel. Despite the throughput of such assays, they are prone to biases in fitness estimates, and errors in measurements are typically larger for deleterious fitness effects, relative to neutral effects. In practice, designing pooled fitness assays involves tradeoffs between the number of timepoints, the sequencing depth, and other parameters to gain as much information as possible within a feasible experiment. Here, we combined theory, simulations, and reanalysis of an existing experimental dataset to explore how assay parameters impact measurements of near-neutral and deleterious fitness effects. We found that sequencing multiple timepoints at relatively modest depth improved estimates of near-neutral fitness effects, but systematically biased measurements of deleterious effects. We identified a theoretical lower bound for estimates from bulk fitness assays, and showed that increasing sequencing depth, and reducing number of timepoints improved resolution of deleterious fitness effects. Our results highlight a tradeoff between measurement of deleterious and near-neutral effect sizes for a fixed amount of data and suggest that fitness assay design should be tuned for fitness effects that are relevant to the specific biological question.
Meiotic gene transcription programs are mediated by A-MYB and BRDT-dependent RNA polymerase II pause release during mammalian prophase I
Authors: Alexander Adriana K. , Rice Edward J. , Barshad Gilad , Zhu Lina , Cohen Paula E , Danko Charles G.
Published: August 2022

During meiotic prophase I, germ cells must balance transcriptional activation with meiotic recombination and chromosome synapsis, biological processes requiring extensive changes to chromatin state and structure. Here we explored the interplay between chromatin accessibility and transcription across a detailed time-course of murine male meiosis by measuring genome-wide patterns of chromatin accessibility, nascent transcription, and processed mRNA. To understand the relationship between these parameters of gene regulation and recombination, we integrated these data with maps of double-strand break formation. Maps of nascent transcription show that Pol II is loaded on chromatin and maintained in a paused state early during prophase I. In later stages of prophase I, paused Pol II is released in a coordinated transcriptional burst resulting in ∼3-fold increase in transcription. Release from pause is mediated by the transcription factor A-MYB and the testis-specific bromodomain protein, BRDT. The burst of transcriptional activity is both temporally and spatially segregated from key steps of meiotic recombination: double strand breaks show evidence of chromatin accessibility earlier during prophase I and at distinct loci from those undergoing transcriptional activation, despite shared chromatin marks. Our findings reveal the mechanism underlying chromatin specialization in either transcription or recombination in meiotic cells.
Biochemically validated structural model of the 15-subunit IFT-B complex
Authors: Petriman Narcis A. , Loureiro-López Marta , Taschner Michael , Zacharia Nevin K. , Georgieva Magdalena M. , Boegholm Niels , Mourão André , Russell Robert B. , Andersen Jens S. , Lorentzen Esben
Published: August 2022

Cilia are ubiquitous eukaryotic organelles important to cellular motility, signalling and sensory reception. Cilium formation requires intraflagellar transport for trafficking of structural and signalling components. The large MDa IFT-B complex constitutes the backbone of polymeric IFT trains that carry ciliary cargo between the cilium and the cell body. Currently, high-resolution structures are only available for smaller IFT-B sub-complexes leaving >50% of the IFT-B complex structurally uncharacterized. We have used recent advances in protein structure prediction as implemented in Alphafold to assemble a structural model for the 15-subunit IFT-B complex. The model was validated using crosslinking/MS data on reconstituted IFT-B complexes, X-ray scattering in solution and diffraction from crystals as well as site-directed mutagenesis and protein binding assays. The IFT-B structural model reveals an elongated and highly flexible complex consistent with cryo-electron tomographic reconstructions of IFT trains. The >400Å long IFT-B complex can roughly be divided into IFT-B1 and IFT-B2 parts with binding sites for ciliary cargo and the inactive IFT dynein motor, respectively. Interestingly, our structural modelling and crosslinking/MS results are consistent with two different binding sites for IFT81/74 on IFT88/70/52/46 suggesting the possibility of two different structural architectures for the IFT-B1 complex. Our data present a structural framework to understand IFT-B complex assembly, function, and ciliopathy variants.
Single-cell profiling reveals the sustained immune infiltration, surveillance, and tumor heterogeneity of infiltrative BCC
Authors: Huang Lingjuan , Wang Xianggui , Pei Shiyao , Li Xin , Dong Liang , Bian Xiaohui , Sun Hongyin , Jin Liping , Hou Huihui , Shi Wensheng , Zhang Xiyuan , Zhang Lining , Zhao Shuang , Chen Xiang , Yin Mingzhu
Published: August 2022

Background

Infiltrative basal cell carcinoma (iBCC) is a particularly aggressive subtype of BCC that tends to recur after surgery, and its progression and malignancy are closely related to its interaction with the local tumor microenvironment (TME).

Methods

Here, we performed single-cell RNA sequencing (scRNA-seq) from 5 patients to determine the dynamic changes of TME between iBCC and adjacent normal skin (ANS).

Results

We found active immune collaborations among CXCL13+ follicular helper-like T cells (Tfh-like cells), SPP1+CXCL9/10high Macro1, and plasma cells, which were enriched in iBCC. Specifically, SPP1+CXCL9/10high Macro1 could activate plasma cells by BAFF signaling, and Tfh-like cells potentially recruited B/Plasma cells through CXCL13. The proinflammatory SPP1+CXCL9/10high Macro1 and angiogenesis-related SPP1+CCL2high Macro1 were characterized, revealing their heterogeneous phenotype within the TME. We also discovered a novel iBCC-enriched ANGPT2+ lymphatic endothelial cell (LEC) subtype with strong abilities to promote leukocyte migration and activation. Interestingly, we found upregulation of MHC-I molecules in fibroblasts in iBCC compared to those in ANS. However, we found that MDK signals derived from malignant basal cells (MBCs) were markedly increased, and their expression was an independent factor in predicting the infiltration depth of iBCC, emphasizing its role in driving malignancy and remodeling the TME. Additionally, we identified differentiation-associated SOSTDC1+IGFBP5+CTSV+ MB1 and epithelial mesenchyme transition (EMT)-associated TNC+SFRP1+CHGA+ MB2. The components of the two heterogeneous subpopulations in the TME might be effective predictors of the malignancy and prognosis of iBCC.

Conclusions

Altogether, our study is beneficial for understanding the cellular heterogeneity involved in the pathogenesis of iBCC and provides potential therapeutic targets for clinical research.
Changes in consumer purchasing patterns at New York City chain restaurants following adoption of the sodium warning icon rule, 2015-2017
Authors: Prasad Divya , Jasek John P. , Anekwe Amaka V. , Dominianni Christine , Mezzacca Tamar Adjoian , Sisti Julia S. , Farley Shannon M. , Kessler Kimberly
Published: August 2022

In 2016, New York City (NYC) began enforcing a sodium warning regulation at chain restaurants, requiring placement of an icon next to any menu item containing ≥2,300 mg sodium. As shifts in consumer purchases are a potential outcome of menu labeling, we investigated whether high-sodium purchases from NYC chains changed following policy implementation. Consumer purchases, using receipts for verification, were assessed at 2 full-service (FSR) and 2 quick-service (QSR) chain restaurants in NYC and Yonkers, NY, which did not have sodium menu labeling, in 2015 (baseline) and 2017 (follow-up). Difference-in-difference regression models, adjusted for demographic and location co-variates, tested whether the proportion of NYC respondents purchasing high-sodium item(s) (containing ≥2,300 mg sodium) or whether mean sodium content of purchases changed, in FSR or QSR. Relative to Yonkers, the proportion of NYC respondents purchasing 1 or more high-sodium items did not significantly differ from baseline to follow-up at FSR (difference-in-difference: -4.6%, p=0.364) or QSR (difference-in-difference: -8.9%, p=0.196). Among NYC FSR respondents, mean sodium purchased significantly declined compared to Yonkers (difference-in-difference: -524 mg, p=0.012); no changes in mean sodium were observed among QSR participants (difference-in-difference: 258 mg, p=0.185). While the reduction in mean sodium purchased among NYC FSR patrons after the sodium warning implementation is encouraging, there was not a corresponding reduction in the proportion of respondents purchasing high-sodium items. Further research that evaluates longer-term changes in the restaurant environment, including menu offerings and consumer purchases, following such policies is warranted.
A cross-sectional study to assess beta cell function in individuals with recently diagnosed young onset type 2 diabetes mellitus and its complications
Authors: Nagaratnam Shamharini , Rajoo Subashini , Long Bidin Mohamed Badrulnizam , Che Rahim Nur Shafini , Tharmathurai Sangeetha , Arip Masita , Ching Yee Ming , Foo Siew Hui
Published: August 2022

The primary objective of this study was to assess beta cell function of recently diagnosed young onset type 2 diabetes mellitus (T2DM) individuals. The secondary objective examined the association between C-peptide with metabolic factors and diabetes complications. A cross-sectional study was conducted for young onset T2DM individuals aged 18-35 years with disease duration not more than 5 years. Plasma basal and stimulated C-peptide was measured before and after intravenous glucagon injection. Demographic data, medical history and complications were obtained from medical records and clinical assessment. A total of 113 participants with young onset T2DM with mean age of 29 years and median disease duration of 24 months were included in this study. The median (interquartile range) basal and stimulated C-peptide was 619 (655) pmol/L and 1231(1024) pmol/L. Adequate beta cell function was present in 78-86% of the participants based on the basal and stimulated C-peptide levels. Obesity and hypertension were independently associated with higher basal and stimulated C-peptide while diabetic kidney disease was independently associated with higher basal C-peptide. We found most recently diagnosed young onset T2DM have adequate beta cell function. Elevated C-peptide levels associated with obesity, hypertension and diabetic kidney disease suggests insulin resistance as the key driving factor for complications.
scraps: an end-to-end pipeline for measuring alternative polyadenylation at high resolution using single-cell RNA-seq
Authors: Fu Rui , Riemondy Kent A. , Sheridan Ryan M. , Hesselberth Jay R. , Jordan Craig T. , Gillen Austin E.
Published: August 2022

Alternative cleavage and polyadenylation (APA) contributes to the diversity of mRNA 3′ ends, affecting post-transcriptional regulation by including or excluding cis-regulatory elements in mRNAs, altering their stability and translational efficiency. While APA analysis has been applied broadly in mixed populations of cells, the heterogeneity of APA among single cells has only recently begun to be explored. We developed an approach we termed scraps (Single Cell RNAPolyA Site Discovery), implemented as a user-friendly, scalable, and reproducible end-to-end workflow, to identify polyadenylation sites at near-nucleotide resolution in single cells using 10X Genomics and other TVN-primed single-cell RNA-seq (scRNA-seq) libraries. Our approach, which performs best with long (>100bp) read 1 sequencing and paired alignment to the genome, is both unbiased relative to existing methods that utilize only read 2 and recovers more sites at higher resolution, despite the reduction in read quality observed on most modern DNA sequencers following homopolymer stretches. For libraries sequenced without long read 1, we implement a fallback approach using read 2-only alignments that performs similarly to our optimal approach, but recovers far fewer polyadenylation sites per experiment. scraps also enables assessment of internal priming capture events, which we demonstrate occur commonly but at higher frequency during apoptotic 3′ RNA decay. We also provide an R package, scrapR, that integrates the results of the scaps pipeline with the popular Seruat single-cell analysis package. Refinement and expanded application of these approaches will further clarify the role of APA in single cells, as well as the effects of internal priming on expression measurements in scRNA-seq libraries.
Interactive webtool for analyzing drug sensitivity and resistance associated with genetic signatures of cancer cell lines
Authors: Boeschen Myriam , Le Duc Diana , Stiller Mathias , von Laffert Maximilian , Schöneberg Torsten , Horn Susanne
Published: August 2022

A wide therapeutic repertoire has become available to oncologists including radio- and chemotherapy, small molecules and monoclonal antibodies. However, drug efficacy can be limited by genetic changes that allow cancer cells to escape therapy. Here, we designed a webtool that facilitates the data analysis of the Genomics of Drug Sensitivity in Cancer (GDSC) database on 265 approved compounds in association with a plethora of genetic changes documented for 1001 cell lines in the Cancer Cell Line Encyclopedia (CCLE, cBioPortal). The webtool computes odds ratios of drug resistance for a queried set of genetic alterations. It provides results on the efficacy of single or groups of compounds assigned to cellular signaling pathways. Using this webtool we replicated known genetic drivers and identified new candidate genes, germline variants, co-mutation, and pharmacogenomic modifiers of both cancer drug resistance and drug repurposing. Webtool availability: https://tools.hornlab.org/GDSC/.

Author Summary

Tumors develop through uncontrolled cell growth enabled by various alterations that create tumor heterogeneity. Changes of the genome and thus cancer cells cause every patient to react differently to drugs and can lead to drug resistance in cancer therapies. To overcome drug resistance, researchers focus on developing personalized therapies. Here, we provide a straightforward tool to test public in vitro drug sensitivity data on a range of drugs for custom analyses of genetic changes. This may inform the identification of potential drug candidates and improve our understanding of signaling pathways as we can test drug response with custom sets of genetic changes according to specific research questions. The tool and underlying code can be adapted to larger drug response datasets and other data types, e.g. metabolic data, to help structure and accommodate the increasingly large biomedical knowledge base.