bluuebunny/crossref_metadata_2025 huggingface dataset:
BACILLARY LAYER DETACHMENT AND ASSOCIATED ABNORMALITIES IN RHEGMATOGENOUS RETINAL DETACHMENT
Authors: Martins Melo Isabela , Bansal Aditya , Lee Wei Wei , Oquendo Paola Lourdes , Hamli Hesham , Muni Rajeev H.
Published: December 2022

Purpose:

To describe bacillary layer detachment and related abnormalities of the foveal bouquet in rhegmatogenous retinal detachment and assess their impact on photoreceptor recovery and full-thickness macular hole formation, using optical coherence tomography.

Methods:

Prospective cohort of 93 consecutive patients with fovea-off rhegmatogenous retinal detachment presenting to St. Michael's Hospital from January 2020 to April 2022, with gradable preoperative foveal optical coherence tomography.

Results:

23.7% (22/93) of patients had evidence of bacillary layer detachment and associated abnormalities. The mean fovea-off duration was 6.4 days (±5.6 SD). 86.4% (19/22) had foveal bacillary layer detachment, 15.8% (3/19) of which had cleavage planes extending from the outer nuclear layer into the myoid zone, and 14% (3/22) had an inner lamellar hole with a residual bridge of photoreceptor remnants (all of which progressed to full-thickness macular hole). Among patients with gradable optical coherence tomography at 3 months post-operatively, 80% (12/15) had ellipsoid zone discontinuity, which persisted in 41% (5/12) at 1 year.

Conclusion:

Bacillary layer detachment was described for the first time in the setting of rhegmatogenous retinal detachment. This is hypothesized to occur from horizontal traction secondary to hydration/lateral expansion of the outer retina in the presence of the Müller cell cone scaffold. Bacillary layer detachment may render the fovea susceptible to further injury, possibly representing a pathophysiological basis for full-thickness macular hole formation in rhegmatogenous retinal detachment.
Indocyanine green angiography guided photocoagulation of large microvascular abnormalities (“TelCaps”) in a patient with persistent macula oedema in the context of radiation retinopathy
Authors: Perrin Elise L , Porter Rowan GB
Published: December 2022

Purpose:

The purpose of this report is to describe a patient with radiation retinopathy who responded to ICGA-guided photocoagulation as treatment for persistent macula oedema secondary to TelCaps, a newly defined type of large microvascular abnormality1,2.

Methods:

Retrospective case report.

Results: A 40-year-old man with a history of bilateral retinoblastoma and right enucleation presented with decreased vision in the left eye secondary to macula oedema. Examination revealed radiation retinopathy with a cluster of ICGA-avid large microaneurysms temporal to the macula. The patient did not respond to treatment with intravitreal bevacizumab or triamciolone. Complete resolution of macula oedema was demonstrated following two rounds of ICGA-guided focal photocoagulation to the aforementioned microaneurysm cluster. No subsequent or adjunctive intravitreal injections of anti-VEGF were required, and there was no recurrence of the TelCaps lesions at follow up to eight years.

Conclusion:

TelCaps are large microvascular abnormalities with high affinity for ICG1,2. These lesions may not have been recognized due to difficulties in their detection on routine examination and with investigations including OCT angiogram and fluorescein angiogram2. Early evidence supports their role in macula oedema that is not responsive to intravitreal injections of anti-VEGF3. ICGA-guided photocoagulation of TelCaps lesions can result in resolution of macula oedema3,4. To our knowledge, this is the first reported case of TelCaps secondary to radiation retinopathy.
Arachnoid Granulation Causing Unilateral Pulsatile Tinnitus Treated With Dural Venous Sinus Stenting
Authors: Gadot Ron , Hoang Alex N. , Raper Daniel M.S. , Sweeney Alexander D. , Juliano Mario , Lustrin Elizabeth , Tanweer Omar
Published: December 2022

Background

Large arachnoid granulations that protrude into dural venous sinuses and partially obstruct outflow are an underappreciated etiology of pulsatile tinnitus (PT). Endovascular dural venous sinus stenting is thought to diminish turbulent venous outflow and may relieve obstruction caused by arachnoid granulations.

Methods

Four patients at two institutions were evaluated for unilateral PT. Magnetic resonance imaging and digital subtraction angiography revealed moderate-to-severe stenoses from large arachnoid granulations within the implicated transverse sinus. All patients underwent venous manometry and endovascular sinus stenting.

Results

All patients experienced immediate and complete remission of their PT. Stenoses were relieved by a mean of 93% by Warfarin-Aspirin Symptomatic Intracranial Disease criteria. There were no procedural or periprocedural complications. All patients continued to report complete symptom resolution at a mean of 8-month follow-up.

Conclusions

PT from arachnoid granulations are an underappreciated pathomechanism. Endovascular dural venous sinus stenting is an effective intervention for treating unilateral PT secondary to large arachnoid granulation.
Disease-Modifying Antirheumatic Drugs in the Treatment of Autoimmune Inner Ear Disease: A Systematic Review and Meta-Analysis of Auditory and Vestibular Outcomes
Authors: Gordis Tamar M. , Shah Sunny R. , Ward Celine , Rizk Habib G.
Published: December 2022

Objective

To answer the following question: In patients with primary autoimmune inner ear disease (AIED), (population) what impact do disease-modifying antirheumatic agents (DMARDs) (intervention) when compared with no treatment or corticosteroids (comparison) have on auditory and vestibular outcomes (outcome)?

Study Design

Systematic review and meta-analysis.

Data Sources

According to PRISMA guidelines, PubMed, Scopus, CINAHL, and Cochrane Library databases were searched from inception to March 10, 2022.

Study Selection

Studies of patients receiving DMARDs for the treatment of AIED were selected for review. Case reports, phase I/II trials, studies of patients with secondary AIED, and studies of AIED patients receiving solely corticosteroids were excluded.

Data Extraction

Primary outcomes were pure-tone audiometry and speech discrimination scores at baseline and after DMARD treatment. Secondary outcomes were rates of subjective audiovestibular complaints and rates of adverse reactions. No objective vestibular outcomes underwent meta-analysis.

Data Synthesis

Mean differences were calculated using RevMan 5.4. Heterogeneity was assessed with the Q test and I2 statistic. Pooled prevalence rates of audiovestibular symptoms were expressed as a percentage with 95% confidence intervals.

Results

Ten studies with a total of 187 patients were included. Treatments included methotrexate, etanercept, azathioprine, anakinra, cyclophosphamide, rituximab, and infliximab. Mean treatment duration was 10.8 ± 22.2 months and mean follow-up was 13.7 ± 8.1 months. The pure-tone audiometry and speech discrimination scores mean differences between baseline and post-DMARD were −2.1 [−4.1, −0.1] dB and 13.9 [8.5, 19.4] %, respectively. Seven studies reported 38 adverse events, four of which were classified as serious.

Conclusion

DMARDs showed statistically significant improvement in auditory outcomes, as well as subjective symptoms, with relatively low rates of adverse events. They warrant further exploration to better compare with corticosteroids.
Social Media Depictions of Cochlear Implants: An Instagram and TikTok Analysis
Authors: Rossi Nicholas A. , Devarajan Karthik , Chokshi Shivan N. , Ochoa Vanesa J. , Benavidez Mia , Malaya Lauren T. , Ohlstein Jason F. , Young Dayton L. , McKinnon Brian J.
Published: December 2022

Objective

To identify populations of authors who post about cochlear implants (CIs) on Instagram and TikTok, to illustrate the content of these posts, and to elucidate factors that might help surgeons better educate CI patients.

Study Design

Qualitative study.

Setting

Instagram and TikTok social media platforms.

Patients

All public social media posts identified with the search terms below. Posts were excluded if unrelated to CIs or if written in a non-English language.

Intervention

Instagram and TikTok were searched for posts from March 2021 through September 2021 with the search terms #cochlearimplant, #cochlearimplants, #cochlearimplantkids, #cochlearkids, and #cochlearfamily.

Main Outcome Measures

Posts were subclassified and analyzed for content including topics of posts, authorship, timeframe of posts, depiction of CIs, and popularity.

Results

Of 1,942 posts included in the final analysis, 1,400 were found on Instagram and 542 on TikTok. Authors were mostly patients (n = 771, 39.7%), companies (n = 568, 29.2%), and patients’ family members (n = 482, 24.8%). Only 21 posts were made by physicians (1.1%). Out of 379 total educational posts examined, patients themselves were the most common authors (n = 219, 57.8%) followed by patients’ family members (n = 139, 36.7%). Physicians authored only a small fraction of all educational posts (n = 19, 5.0%).

Conclusions

This study showed minimal physician involvement in the CI social media spheres of Instagram and TikTok. In addition, there were few educational posts on either platform, revealing ample opportunity for physicians to become more involved with CI social media.
A Steadier Hand: The First Human Clinical Trial of a Single-Use Robotic-Assisted Surgical Device for Cochlear Implant Electrode Array Insertion
Authors: Gantz Jay A. , Gantz Bruce J. , Kaufmann Christopher R. , Henslee Allan M. , Dunn Camille C. , Hua Xiaoyang , Hansen Marlan R.
Published: December 2022

Objective

To evaluate the safety and utility of an investigational robotic-assisted cochlear implant insertion system.

Study Design

Prospective, single-arm, open-label study under abbreviated Investigational Device Exemption requirements.

Setting

All procedures were performed, and all data were collected, at a single tertiary referral center.

Patients

Twenty-one postlingually deafened adult subjects that met Food and Drug Administration indication criteria for cochlear implantation.

Intervention

All patients underwent standard-of-care surgery for unilateral cochlear implantation with the addition of a single-use robotic-assisted insertion device during cochlear electrode insertion.

Main Outcome Measures

Successful insertion of cochlear implant electrode array, electrode array insertion time, postoperative implant function.

Results

Successful robotic-assisted insertion of lateral wall cochlear implant electrode arrays was achieved in 20 (95.2%) of 21 patients. One insertion was unable to be achieved by either robotic-assisted or manual insertion methods, and the patient was retrospectively found to have a preexisting cochlear fracture. Mean intracochlear electrode array insertion time was 3 minutes 15 seconds. All implants with successful robotic-assisted electrode array insertion (n = 20) had normal impedance and neural response telemetry measures for up to 6 months after surgery.

Conclusions

Here we report the first human trial of a single-use robotic-assisted surgical device for cochlear implant electrode array insertion. This device successfully and safely inserted lateral wall cochlear implant electrode arrays from the three device manufacturers with devices approved but he Food and Drug Administration.
Facial Nerve Preservation With Inferior Long-Axis Dissection of Large Vestibular Schwannomas
Authors: Totten Douglas J. , Connell Nathan T. , Howser Lauren A. , Colomb Elaine , Sandelski Morgan M. , Rabbani Cyrus C. , Savage Jesse J. , Shah Mitesh V. , Nelson Rick F.
Published: December 2022

Objective

To describe a tumor resection using the inferior long-axis (ILA) technique for cisternal facial nerve dissection in large vestibular schwannomas (VS).

Study Design

Retrospective case series from 2018 to 2021.

Setting

Tertiary academic medical center.

Patients

Patients who underwent surgical resection with ILA facial nerve dissection of VS (>2.0 cm measured parallel to the petrous ridge) and had at least 3-month follow-up.

Interventions

Cisternal facial nerve dissection during retrosigmoid or translabyrinthine approach using standardized ILA technique developed by author R.N.

Main Outcome Measures

Immediate postoperative and last follow-up facial nerve function with House-Brackmann scores of I to II defined as “good” facial nerve function and House-Brackmann scores III to VI defined as “poor” function. Extent of resection was also assessed.

Results

A total of 48 patients underwent large VS resection with ILA dissection of tumor off of the facial nerve from 2018 to 2021. Mean (standard deviation) tumor size was 3.11 (0.76) cm. Mean (standard deviation) follow-up was 9.2 (9.0) months. Gross-total resection or near-total resection were achieved in 75% (radiographic estimate) to 83% (surgeon estimate) of cases. End-of-case facial nerve stimulation at 0.05 mAmp with a response of at least 240 mV was achieved in 80.4% of patients. Good facial nerve function was observed in 72% immediately postoperatively, 70% 1-month postoperatively, and 82% of patients at last follow-up.

Conclusions

The ILA technique is now the method of choice of the senior surgeon (R.N.) when performing microsurgical dissection of the cisternal facial nerve, with which he has achieved high rates of total or near-total resection with excellent facial nerve preservation.
Recurrent IDH2 Mutations in Salivary Gland Striated Duct Adenoma Define an Expanded Histologic Spectrum Distinct From Canalicular Adenoma
Authors: Rooper Lisa M. , Agaimy Abbas , Assaad Adel , Bal Munita , Eugene Henrietta , Gagan Jeffrey , Nonogaki Hiro , Palsgrove Doreen N. , Shah Akeesha , Stelow Edward , Stoehr Robert , Thompson Lester D.R. , Weinreb Ilan , Bishop Justin A.
Published: December 2022

Striated duct adenoma (SDA) is a rare salivary gland neoplasm defined by histologic similarity to normal striated ducts. However, doubt persists about whether SDA represents a genuine entity distinct from canalicular adenoma and if a malignant counterpart exists. This study aims to evaluate the molecular underpinnings of SDA to clarify its pathogenesis and classification. We identified 10 SDA and 2 tumors called low-grade adenocarcinoma not otherwise specified that were retrospectively recognized to resemble SDA. All cases showed recurrent histologic features including (1) discrete monophasic tubules, (2) tall columnar eosinophilic cells, (3) monotonous oval nuclei, and (4) scant fibrous stroma, and most were positive for S100 protein (91%), SOX10 (80%), and CK7 (80%). Although 1 case was previously called adenocarcinoma based on interdigitation with normal acini, this pattern was also seen in some SDA, and likely does not indicate malignancy; the significance of growth surrounding nerve in 1 other case is less clear. Targeted sequencing identifiedIDH2R172X mutations in all 8 cases with sufficient tissue, with positivity for IDH1/2 mutation-specific immunohistochemistry in 9 cases stained. In contrast, 5 canalicular adenomas lackedIDH2mutations or other oncogenic alterations. Overall,IDH2R172X mutations are a defining feature of SDA that, in combination with its recognizable pathologic profile, confirm it is a unique entity separate from canalicular adenoma. IDH1/2 mutation-specific immunohistochemistry may provide a convenient tool to facilitate diagnosis. Both morphology andIDH2mutations raise parallels between SDA and breast tall cell carcinoma with reverse polarity.
Is the Centralization of Complex Surgical Procedures an Unintended Spillover Effect of Global Capitation? – Insights from the Maryland Global Budget Revenue Program
Authors: Offodile Anaeze C. , Lin Yu-Li , Shah Shivani A. , Swisher Stephen G. , Jain Amit , Butler Charles E. , Aliu Oluseyi
Published: December 2022

Objective:

To determine if global budget revenue (GBR) models incent the centralization of complex surgical care.

Summary Background:

In 2014, Maryland initiated a statewide GBR model. While prior research has shown improvements in cost and outcomes for surgical care post-GBR implementation, the mechanism remains unclear.

Methods:

Utilizing state inpatient databases, we compared the proportion of adults undergoing elective complex surgeries (gastrectomy, pneumonectomy/lobectomy, proctectomies, and hip/knee revision) at high-concentration hospitals (HCHs) in Maryland and control states. Annual concentration, per procedure, was defined as hospital volume divided by state volume. HCHs were defined as hospitals with a concentration at least at the 75th percentile in 2010. We estimated the difference-in-differences (DiD) of the probability of patients undergoing surgery at HCHs before and after GBR implementation.

Findings:

Our sample included 122,882 surgeries. Following GBR implementation, all procedures were increasingly performed at HCHs in Maryland. States satisfied the parallel trends assumption for the centralization of gastrectomy and pneumonectomy/lobectomy. Post-GBR, patients were more likely to undergo gastrectomy (DiD: 5.5 p.p., 95% CI [2.2, 8.8]) and pneumonectomy/lobectomy (DiD: 12.4 p.p., 95% CI [10.0, 14.8]) at an HCH in Maryland compared with control states. For our hip/knee revision analyses, we assumed persistent counterfactuals and noted a positive DiD post-GBR implementation (DiD: 4.8 p.p., 95% CI [1.3, 8.2]). No conclusion could be drawn for proctectomy due to different pre-GBR trends.

Conclusions:

GBR implementation is associated with increased centralization for certain complex surgeries. Future research is needed to explore the impact of centralization on patient experience and access.
Real-world demographic patterns of users of a digital primary prevention service for diabetes
Authors: Balakrishnan Preetha , Jacyshyn-Owen Elizabeth , Eberl Markus , Friedrich Benjamin , Etter Tobias
Published: December 2022

Background

Rapid urbanization has led to an exponential increase in lifestyle-associated metabolic disorders presenting a huge socioeconomic burden. Waya is a digital prevention program that guides overweight and obese individuals to maintain a healthy lifestyle through exercise, diet, and educational videos.

Objectives and aims

We aimed to study the demographic patterns of the Waya cohort and examine the prevalence of diabetes (the most common lifestyle-associated metabolic disorder) and its risk factors in comparison to the GEDA 2014/2015-European Health Interview Survey population.

Methods

Waya participants who registered by 1 October 2020 and who answered at least one health survey question were included in this study. Factors such as obesity, hypertension, and diabetes between the two populations were compared using Chi-square test.

Results

Of the 837 participants, 86.1% were women. The proportion of obese participants was higher in Waya than in the German Health Update (GEDA) cohort (women: 39.4% vs. 18%, P < 0.05; men: 37.1% vs. 18.3%, P < 0.05), whereas the proportion of participants with hypertension (women: 12.1% vs. 30.9% in GEDA, P < 0.05; men: 22.4% vs. 32.8% in GEDA, P < 0.05) was lower. The proportion of women with diabetes was low in our cohort (3.9% vs. 7% in GEDA, P < 0.05); however, the proportion of men with diabetes remained the same between the two groups. We observed significant differences between the GEDA and Waya cohorts due to changes in the prevalence pattern over time or target bias of the digital program.

Conclusion

These findings showcase the usability of Waya in collecting real-world insights, which will be beneficial in monitoring the prevalence of chronic metabolic disorders and associated risk factors over time.
New Approaches to 3D Vision
Authors: Linton Paul , Morgan Michael J. , Read Jenny C. A. , Vishwanath Dhanraj , Creem-Regehr Sarah H. , Domini Fulvio
Published: December 2022

New approaches to 3D vision are enabling new advances in artificial intelligence and autonomous vehicles, a better understanding of how animals navigate the 3D world, and new insights into human perception in virtual and augmented reality. Whilst traditional approaches to 3D vision in computer vision (SLAM: simultaneous localization and mapping), animal navigation (cognitive maps), and human vision (optimal cue integration) start from the assumption that the aim of 3D vision is to provide an accurate 3D model of the world, the new approaches to 3D vision explored in this issue challenge this assumption. Instead, they investigate the possibility that computer vision, animal navigation, and human vision can rely on partial or distorted models or no model at all. This issue also highlights the implications for artificial intelligence, autonomous vehicles, human perception in virtual and augmented reality, and the treatment of visual disorders, all of which are explored by individual articles.

This article is part of a discussion meeting issue ‘New approaches to 3D vision’.
Symmetries and asymmetries in the neural encoding of 3D space
Authors: Jeffery Kate J.
Published: December 2022

The neural coding of space centres on three foundational cell types: place cells, head direction cells and grid cells. One notable characteristic of these neurons is the symmetry properties of their spatial firing patterns. In symmetric environments, firing patterns are often also symmetric: for example, place cells show translational symmetry in aligned sub-compartments of a multi-compartment environment. A single head direction cell has a mirror-symmetric firing pattern, while a sub-class of head direction cells can show multi-fold rotational symmetries in multi-compartment environments, matching the symmetry of the recently experienced environment. The entorhinal grid cells are notable for the symmetry of their firing patterns in both rotational and translational domains. However, these symmetries are broken in a variety of situations. These symmetry-making and -breaking observations shed light on the underlying computations that generate these firing patterns, and also invite speculation as to whether they may have a functional role. This article outlines these findings and speculates on the consequences of the resultant firing symmetries and asymmetries for spatial coding and cognition.

This article is part of a discussion meeting issue ‘New approaches to 3D vision’.
Enhanced efficiency in visually guided online motor control for actions redirected towards the body midline
Authors: Maselli Antonella , Ofek Eyal , Cohn Brian , Hinckley Ken , Gonzalez-Franco Mar
Published: December 2022

Reaching objects in a dynamic environment requires fast online corrections that compensate for sudden object shifts or postural changes. Previous studies revealed the key role of visually monitoring the hand-to-target distance throughout action execution. In the current study, we investigate how sensorimotor asymmetries associated with space perception, brain lateralization and biomechanical constraints, affect the efficiency of online corrections. Participants performed reaching actions in virtual reality, where the virtual hand was progressively displaced from the real hand to trigger online corrections, for which it was possible to control the total amount of the redirection and the region of space in which the action unfolded. The efficiency of online corrections and the degree of awareness of the ensuing motor corrections were taken as assessment variables. Results revealed more efficient visuo-motor corrections for actions redirected towards, rather than away from the body midline. The effect is independent on the reaching hand and the hemispace of action, making explanations associated with laterality effects and biomechanical constraints improbable. The result cannot either be accounted for by the visual processing advantage in the straight-ahead region. An explanation may be found in the finer sensorimotor representations characterizing the frontal space proximal to body, where a preference for visual processing has been documented, and where high-value functional actions, like fine manipulative skills, typically take place.

This article is part of a discussion meeting issue ‘New approaches to 3D vision’.
From pictures to reality: modelling the phenomenology and psychophysics of 3D perception
Authors: Vishwanath Dhanraj
Published: December 2022

The dominant inferential approach to human 3D perception assumes a model of spatial encoding based on a physical description of objects and space. Prevailing models based on this physicalist approach assume that the visual system infers an objective, unitary and mostly veridical representation of the external world. However, careful consideration of the phenomenology of 3D perception challenges these assumptions. I review important aspects of phenomenology, psychophysics and neurophysiology which suggest that human visual perception of 3D  objects and space is underwritten by distinct and dissociated spatial encodings that are optimized for specific regions of space. Specifically, I argue that 3D perception is underwritten by at least three distinct encodings for (1) egocentric distance perception at the ambulatory scale, (2) exocentric distance (scaled depth) perception optimized for near space, and (3) perception of object shape and layout (unscaled depth). This tripartite division can more satisfactorily account for the phenomenology, psychophysics and adaptive logic of human 3D perception.

This article is part of a discussion meeting issue ‘New approaches to 3D vision’.
Perceiving distance in virtual reality: theoretical insights from contemporary technologies
Authors: Creem-Regehr Sarah H. , Stefanucci Jeanine K. , Bodenheimer Bobby
Published: December 2022

Decades of research have shown that absolute egocentric distance is underestimated in virtual environments (VEs) when compared with the real world. This finding has implications on the use of VEs for applications that require an accurate sense of absolute scale. Fortunately, this underperception of scale can be attenuated by several factors, making perception more similar to (but still not the same as) that of the real world. Here, we examine these factors as two categories: (i) experience inherent to the observer, and (ii) characteristics inherent to the display technology. We analyse how these factors influence the sources of information for absolute distance perception with the goal of understanding how the scale of virtual spaces is calibrated. We identify six types of cues that change with these approaches, contributing both to a theoretical understanding of depth perception in VEs and a call for future research that can benefit from changing technologies. This article is part of the theme issue ‘New approaches to 3D vision’.
Stereopsis for rapidly moving targets
Authors: Morgan Michael
Published: December 2022

Stereoscopic depth perception is possible with luminance-defined target velocities at least as high as 600° s
−1
, up to the limit of 30 Hz imposed by the high-temporal frequency cut-off of the eye. The limitation for perceiving depth from stereo disparity of moving targets is not their velocity but the temporal frequency bandwidth of the eye, which is affected by adaption state. Stereoacuity for a depth shift in a horizontally moving grating depends not on spatial disparity between corresponding luminance points in spatial units of arc min, but on the spatial shift as a fixed proportion of the period of the grating, in other words, on the phase angle difference between the two eyes, as is also the case for obliquely orientated, stationary gratings. Phase differences explain not only the classic Pulfrich stereophenomenon but its equivalent with dynamic visual noise, and a new effect in which depth results from interocular phase differences in luminance modulation.

This article is part of a discussion meeting issue ‘New approaches to 3D vision’.
Prosthetic valve endocarditis due to Candida parapsilosis- a rare case report

Authors: Sharma Shivang , Samantaray Subhashree , Kumar Deepak , Meena Durga Shankar , Chaudhary Rahul , Jain Vidhi , Bohra Gopal Krishana , Garg Mahendra Kumar
Published: December 2022

Fungal endocarditis is a rare and fatal condition ,  most frequently caused by   the  Candida  and  Aspergillus  species. Fever and changing heart murmur are the most common clinical manifestations. The diagnosis of fungal endocarditis is challenging, especially that of prosthetic valve endocarditis is extremely difficult. The optimal management of the condition still remains debatable.  We hereby present a case of prosthetic valve endocarditis caused by  Candida parapsilosis , managed empirically with liposomal amphotericin B and later on was shifted to combination therapy with high dose echinocandin and fluconazole, but had a fatal outcome because he could not undergo timely surgical intervention.  Treating  Candida parapsilosis  endocarditis cases are difficult because of their ability of biofilm production on native and prosthetic heart valves. A combined approach consisting of high index of clinical suspicion, early diagnosis by using serological markers followed by culture or PCR and prompt initiation of appropriate antifungals may aid in improving the outcome.
Campylobacter majalis sp. nov. and Campylobacter suis sp. nov., novel Campylobacter species isolated from porcine gastrointestinal mucosa
Authors: Lynch Caoimhe , Peeters Charlotte , Walsh Niamh , McCarthy Conor , Coffey Aidan , Lucey Brigid , Vandamme Peter
Published: December 2022

Strains LMG 7974T and LMG 8286T represent single, novel

Campylobacter

lineages with

Campylobacter pinnipediorum

and

Campylobacter mucosalis

as nearest phylogenomic neighbours, respectively. The results of average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) analyses of LMG 7974T, LMG 8286T and type strains of species of the genus

Campylobacter

confirmed that these strains represent novel species of the genus

Campylobacter

. The 16S rRNA gene sequences of both strains showed highest identity towards

C. mucosalis

(97.84 and 98.74 %, respectively). Strains LMG 7974T and LMG 8286T shared 72.5 and 73.7% ANI, respectively, with their nearest phylogenomic neighbours and less than 21 % dDDH. The draft genome sizes of LMG 7974T and LMG 8286T are 1 945429 bp and 1 708214 bp in length with percentage DNA G+C contents of 33.8 and 37.2 %, respectively. Anomalous biochemical characteristics and low MALDI-TOF mass spectrometry log scores supported their designation as representing novel species of the genus Campylobacte. We therefore propose to classify strain LMG 7974T (=CCUG 20705T) as the type strain of the novel species Campylobacter majalis sp. nov. and strain LMG 8286T (=CCUG 24193T, NCTC 11879T) as the type strain of the novel species Campylobacter suis sp. nov.
Streptomyces coriariae sp. nov., a novel streptomycete isolated from actinorhizal nodules of Coriaria intermedia
Authors: Berckx Fede , Bandong Cyndi Mae , Wibberg Daniel , Kalinowski Jörn , Willemse Joost , Brachmann Andreas , Simbahan Jessica , Pawlowski Katharina
Published: December 2022

An actinobacterial strain, CMB-FB, was isolated from surface-sterilized root nodules of a Coriaria intermedia plant growing along Halsema Highway in the province of Benguet (Luzon, Philippines). The 16S rRNA gene sequence of CMB-FB showed high sequence similarity to those of the type strains of

Streptomyces rishiriensis

(99.4 %),

Streptomyces humidus

(99.1 %),

Streptomyces cacaoi

subsp.

asoensis

(99.0 %), and

Streptomyces phaeofaciens

(98.6 %). The major menaquinones of CMB-FB were composed of MK-9(H4), MK-9(H6) and MK-9(H8), and there was a minor contribution of MK-9(H10). The polar lipid profile consisted of phosphatidylethanolamine, unidentified aminolipids and phospholipids, a glycophospholipid and four unidentified lipids. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The results of physiological analysis indicated that CMB-FB was mesophilic. The results of phylogenetic, genome-genome distance calculation and average nucleotide identity analysis indicated that the isolated strain represents the type strain of a novel species. On the basis of these results, strain CMB-FB (=DSM 112754T=LMG 32457T) is proposed as the type strain of the novel species Streptomyces coriariae sp. nov.
Ralstonia wenshanensis sp. nov., a novel bacterium isolated from a tobacco field in Yunnan, China
Authors: Lu Can-Hua , Chen Wei , Yin Hong-Hui , Lin Zhong-Long , Li Jun-Ying , Ma Jun-Hong , Gai Xiao-Tong , Jiang Ning , Cao Zheng-Hua , Qian Lei , Zhang Li-Qun , Jin Yan , Xia Zhen-Yuan
Published: December 2022

A Gram-negative, aerobic, motile with paired polar flagella and rod-shaped bacterium strain (56D2T) was isolated from tobacco planting soil in Yunnan, PR China. Major fatty acids were C16  :  1
ω7c (summed feature 3), C16  :  0 and C18  :  1 ω7c (summed feature 8). The polar lipid profile of strain 56D2T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid and one unidentified glycolipid. Moreover, strain 56D2T contained ubiquinone Q-8 as the sole respiratory quinone. 16S rRNA gene sequence analysis showed that strain 56D2T was closely related to members of the genus

Ralstonia

and the two type strains with the highest sequence identities were

R. mannitolilytica

LMG 6866T (98.36 %) and

R. pickettii

K-288T (98.22 %). The 16S rRNA gene sequence identities between strain 56D2T and other members of the genus

Ralstonia

were below 98.00 %. Genome sequencing revealed a genome size of 5.87 Mb and a G+C content of 63.7 mol%. The average nucleotide identity values between strain 56D2T and

R. pickettii

K-288T,

R. mannitolilytica

LMG 6866 T and

R. insidiosa

CCUG 46789T were less than 95 %, and the in silico DNA–DNA hybridization values (yielded by formula 2) were less than 70 %. Based on these data, we conclude that strain 56D2T represents a novel species of the genus

Ralstonia

, for which the name Ralstonia wenshanensis sp. nov. is proposed. The type strain of Ralstonia wenshanensis sp. nov. is 56D2T (=CCTCC AB 2021466T=GDMCC 1.2886T=JCM 35178T).
Cholesterol-dependent activity of dapsone against non-replicating persistent mycobacteria
Authors: Gibson Savannah E. R. , Harrison James , Molloy Antonia , Cox Jonathan A. G.
Published: December 2022

One-third of the world’s population is estimated to be latently infected with

Mycobacterium tuberculosis

. This reservoir of bacteria is largely resistant to antimicrobial treatment that often only targets actively replicating mycobacteria, with current treatment for latent infection revolving around inhibiting the resuscitation event rather than preventing or treating latent infection. As a result, antimicrobials that target latent infection often have little to no activity in vivo. Here we report a method of in vitro analysis of physiologically relevant non-replicating persistence (NRP) utilizing cholesterol as the sole carbon source, alongside hypoxia as a driver of

Mycobacterium bovis

BCG into the NRP state. Using the minimal cholesterol media NRP assay, we observed an increased state of in vitro resistance to front-line anti-tubercular compounds. However, following a phenotypic screen of an approved-drug library, we identified dapsone as a bactericidal active molecule against cholesterol-dependent NRP

M. bovis

BCG. Through an overexpression trial of probable antimicrobial target enzymes, we further identified FolP2, a non-functional dihydropteroate synthase homologue, as the likely target of dapsone under cholesterol-NRP due to a significant increase in bacterial resistance when overexpressed. These results highlight the possible reason for little in vivo activity seen for current front-line anti-NRP drugs, and we introduce a new methodology for future drug screening as well as a potential role for dapsone inclusion within the current treatment regime.
Stability of spectral results in cardiac dual-source photon-counting CT
Authors: Liu Leening P. , Shapira Nadav , Sahbaee Pooyan , Gang Grace J. , Knollman Friedrich D. , Chen Marcus Y. , Litt Harold I. , Noël Peter B.
Published: December 2022

Objective

Evaluate stability of spectral results at different heart rates, acquisition modes, and cardiac phases in first-generation clinical dual-source photon-counting CT (PCCT).

Materials and Methods

A cardiac motion simulator with a coronary stenosis mimicking a 50% eccentric calcium plaque was scanned with a first-generation dual-source PCCT at five different heart rates (0, 60, 70, 80, 100 bpm). Scans were performed at 120 kVp with the three available cardiac scan modes (high pitch prospectively ECG-triggered spiral, prospectively ECG-triggered axial, retrospectively ECG-gated spiral). Subsequently, virtual monoenergetic images at 50, 70, and 150 keV and iodine density maps were reconstructed at both diastole and systole to investigate the effect of the cardiac phase. Full width half max (FWHM) of the stenosis, Dice score (DSC) for the stenosed region, and eccentricity of the non-stenosed region were analyzed.

Results

FWHM exhibited average differences from the static FWHM across cardiac phase and heart rates of -0.20, -0.28, and -0.15 mm at VMI 150 keV for high pitch prospectively ECG-triggered spiral, prospectively ECG-triggered axial, and retrospectively ECG-gated spiral scans, respectively. DSC demonstrated similarity among parameters with standard deviations of 0.08, 0.09, 0.11, and 0.08 for VMI 50, 70, and 150 keV, and iodine density maps, respectively, with larger differences present at systole and with high pitch scans. Similarly, eccentricity illustrated small differences across heart rate and acquisition mode for each spectral result.

Conclusions

Consistency of spectral results at different heart rates and acquisition modes for different cardiac phase demonstrates the added benefit of spectral results from PCCT to dual-source CT to further increase confidence in quantification and advance cardiovascular diagnostics.
Vehicle safety tests, rankings, curb weight, and fatal crash rates: automatic emergency brakes associated with increased death rates
Authors: Robertson Leon S.
Published: December 2022

The European New Car Assessment Programme (Euro NCAP), the Insurance Institute for Highway Safety (IIHS), and the U.S. National Highway Traffic Safety Administration (NHTSA) each publish safety ratings of new passenger vehicles based on crash test results and crash avoidance technology soon after they are introduced into the market. IIHS alone singles out vehicles for “Top Safety Pick”. The Institute also periodically lists driver death rates of vehicles during their first few years of use, accompanied by assertions that larger, heavier passenger vehicles are safer. Median death rates by vehicle size in the Institute’s data do not support the assertion. This study examines the association of vehicle weight to the risk of all deaths in fatal crashes where specific makes and models were involved, controlling statistically for the Institute’s vehicle safety ratings as well as NHTSA ratings of full-frontal crash tests and rollover propensity, lane retention warnings, adaptive cruise control, and automatic braking. Increased weight is slightly related to a lower fatal risk in the 2014-2017 models but not the 2018-2019 models. Lane retention warnings and IIHS’s higher ratings of crashworthiness are related to reduced death risk. Adaptive cruise control is not associated with fatal crash risk. Automatic emergency braking (AEB) technology rated “superior” is a criterion for an IIHS “Top Safety Pick” but it is correlated to higher fatal crash involvement of vehicles that have the technology as optional or standard equipment. IIHS tests of AEB systems are conducted only at low speeds. The statistical results are not definitive but suggest that a rating system based on modeling death risk prediction from more detailed data from various tests such as Euro NCAP tests of AEB systems could better inform consumer choice of vehicles.
SAINT-Angle: self-attention augmented inception-inside-inception network and transfer learning improve protein backbone torsion angle prediction
Authors: Hasan A.K.M. Mehedi , Ahmed Ajmain Yasar , Mahbub Sazan , Rahman M. Saifur , Bayzid Md. Shamsuzzoha
Published: December 2022

Motivation

Protein structure provides insight into how proteins interact with one another as well as their functions in living organisms. Protein backbone torsion angles (ϕandψ) prediction is a key sub-problem in predicting protein structures. However, reliable determination of backbone torsion angles using conventional experimental methods is slow and expensive. Therefore, considerable effort is being put into developing computational methods for predicting backbone angles.

Results

We present SAINT-Angle, a highly accurate method for predicting protein backbone torsion angles using a self-attention based deep learning network called SAINT, which was previously developed for the protein secondary structure prediction. We extended and improved the existing SAINT architecture as well as used transfer learning to predict backbone angles. We compared the performance of SAINT-Angle with the state-of-the-art methods through an extensive evaluation study on a collection of benchmark datasets, namely, TEST2016, TEST2018, CAMEO, and CASP. The experimental results suggest that our proposed self-attention based network, together with transfer learning, has achieved notable improvements over the best alternate methods.

Availability and implementation

SAINT-Angle is freely available as an open-source project athttps://github.com/bayzidlab/SAINT-Angle.

Contact

shams_bayzid@cse.buet.ac.bd

Supplementary information

Supplementary material SM.pdf.
Indirect genetic effects improve female extra-pair heritability estimates
Authors: Dobson Sarah , Dunning Jamie , Burke Terry , Janet Chik Heung Ying , Schroeder Julia
Published: December 2022

The question of why females engage in extra-pair behaviours is long-standing in evolutionary biology. One suggestion is that these behaviors are maintained through pleiotropic effects on male extra-pair behaviors and lifetime reproductive success (genes controlling extra-pair behaviours are shared between sexes, but only beneficial to one, in this case, males). However, for this to occur extra-pair behaviour must be heritable and positively genetically correlated between sexes. Although previous studies have suggested low heritability with no evidence for between-sex genetic correlations in extra-pair behaviours, indirect genetic effects (those derived from the behaviour of others, IGEs) from the social partner, the influence of the social partner’s genotype on the phenotype of an individual, have not been considered, despite the potential to uncover hidden heritability. Using data from a closed house sparrow population with a genetic pedigree spanning two decades, we tested the influence of IGEs on heritability and genetic correlation estimates of extra-pair behaviour. We found that the inclusion of IGEs improved model fit for both male and female extra-pair heritability. While IGEs did not change between-sex genetic correlations, we found a reduction in uncertainty in our estimates. Future studies should consider the effect of IGEs on the mechanisms of sex specific extra-pair behaviour.
Snakeobjects: an object-oriented workflow management system
Authors: Yamrom Boris , Lee Yoon-ha , Marks Steven , Chorbadjiev Lubomir , Meyer Hannah V , Iossifov Ivan
Published: December 2022

Snakemake is one of the most popular workflow management systems, particularly in biological sciences. Snakemake workflows are highly portable, scalable, and transparent. Moreover, they enable the painless reproduction of published results and adaption to similar data processing and analysis projects. Here we present Snakeobjects, an extension of Snakemake that considerably simplifies the development of workflows and improves their readability and adaptability while preserving all the benefits of Snakemake that ensure the large and growing community of its users.
Learning orientation-invariant representations enables accurate and robust morphologic profiling of cells and organelles
Authors: Burgess James , Nirschl Jeffrey J. , Zanellati Maria-Clara , Cohen Sarah , Yeung Serena
Published: December 2022

Cell and organelle morphology are driven by diverse genetic and environmental factors and thus accurate quantification of cellular phenotypes is essential to experimental cell biology. Representation learning methods for phenotypic profiling map images to feature vectors that form anembedding spaceof morphological variation useful for clustering, dimensionality reduction, outlier detection, and supervised learning problems. Morphology properties do not change with orientation, and thus we argue that representation learning methods should encode this orientation invariance. We show that prior methods are sensitive to orientation, which can lead to suboptimal clustering. To address this issue, we develop O2-VAE, an unsupervised learning method that learns robust, orientation-invariant representations. We use O2-VAE to discover novel morphology subgroups in segmented cells and mitochondria, detect outlier cells, and rapidly characterise cellular shape and texture in large datasets, including in a newly generated synthetic benchmark.
Sensory evaluations of a novel iron and zinc-enriched powder for the potential treatment and prevention of iron deficiency in women of reproductive age
Authors: Miller Clara H , Sheyholislami Hauna , Burns Jessie L , Connor Kristin L
Published: December 2022

Iron deficiency (ID) and iron deficiency with anaemia (IDA) are serious global health problems that disproportionately affect women aged 15-49 years. Although food fortification is one of the most effective and sustainable ways to combat nutritional deficiencies, iron remains one of the most difficult micronutrients to fortify, given its tendency to react strongly with food constituents. Therefore, it is important to assess the sensory properties of foods fortified with iron to determine the acceptability and palatability in target populations. We aimed to determine the palatability and acceptability of a novel iron and zinc enriched powder fortified in tap water by conducting sensory evaluations in 35 women of reproductive age using a 9-point hedonic scale, where participants rated the sensory properties of six samples containing different amounts of the active or placebo. We found significant differences between samples reconstituted at 1g/L, 2g/L, and 3g/L for sensory properties, including overall taste. Participants were found to be more willing to drink the mineral-enriched powder when prepared at the lowest concentration (1g/L) compared to higher concentrations. Our results provide important insight on sensory qualities of a novel formulation of an iron and zinc -enriched powder for at-home fortification, and indicate consumer acceptability in reproductive aged women, a key group at risk for ID/IDA. If found to improve iron status, novel treatments like this product will contribute to global efforts to develop safe, acceptable and sustainable interventions for ID and IDA.