bluuebunny/crossref_metadata_2025 huggingface dataset:
Macular Hole with an Intact Bacillary Layer
Authors: Fu Yu-Teng , Yang Chung-May , Lai Tso-Ting , Ho Tzyy-Chang , Yang Chang-Hao , Hsieh Yi-Ting
Published: December 2024

Purpose:

To describe the clinical characteristics of macular holes (MH) with an intact bacillary layer.

Methods:

This retrospective study analyzed the characteristics and surgical results of 23 eyes with MH and an intact bacillary layer, with or without rhegmatogenous retinal detachment (RRD).

Results:

Among the 23 eyes, 11 had only MH, and 12 had concurrent fovea-off RRD. Ten eyes (43.5%) were highly myopic. In the MH-only group, no bacillary layer detachment (BALAD) was observed before MH formation. Ten eyes underwent vitrectomy with internal limiting membrane (ILM) peeling and intravitreal injection of C3F8, and the other one received an intravitreal C3F8 only. The MH closure rate was 90.9% after one operation and 100% after two. In the RRD group, 66.7% had BALAD. ILM peeling was performed in 8 eyes (66.7%). The MH closure rate was 91.7% after one operation and 100% after two. Both groups showed significant visual improvement after surgery (P < 0.05).

Conclusions:

An intact bacillary layer can be observed in MH with or without concurrent fovea-off RRD. Surgical outcomes are similar to typical MH cases, and the intact bacillary layer may not facilitate MH sealing like the ILM. An ILM flap should be considered for large MHs or highly myopic eyes.
Orbital Apex Venous Malformation: Case Report on an Unusual Clinical and Radiological Presentation
Authors: Sung Jeffrey , Tong Jessica Y. , Patel Sandy , Slattery James , Jukes Alistair , Selva Dinesh
Published: December 2024

The authors present a case of an orbital apex venous malformation that presented with an intermittent oculomotor nerve palsy over a 15-year period. Radiologically, the lesion presented as a well-circumscribed orbital mass with T2 hyperintensity and enhancement that could only be demonstrated on 2-hour delayed phase imaging. The venous malformation was initially steroid-responsive but eventually became refractory to medical treatment alone. This necessitated a medial apical decompression, followed by a deep lateral orbitotomy 18 months later.
Longitudinal Study of Epibulbar Dermolipomas Over Five-Year Follow-Up: Growth Analysis, Refractive Errors, and Surgical Outcomes
Authors: Anklesaria Vidhi , Basu Sayan , Singh Swati
Published: December 2024

Purpose:

To evaluate the growth, management, and outcomes of epibulbar dermolipomas over a 5-year follow-up period.

Methods:

This was a retrospective chart review of epibulbar dermolipoma patients with a minimum follow-up of 5 years, which analyzed the changes in size, refractive errors (spherical equivalent), best-corrected visual acuity, histology, and surgical outcomes.

Results:

A total of 61 eyes of 53 patients (32 females) with an average presenting age of 4.4 years were included. Eight patients had bilateral involvement, and 22 (41.5%) had Goldenhar syndrome. Forty-one eyes had corneal and conjunctival involvement, and 12 had only conjunctival involvement. Forty-five eyes (73.7%) had refractive errors, and 39 (63.9%) were amblyopic. The average lesion size was 8.3 ± 6.1 by 7.4 ±4.9 mm and 7.1 ± 5 by 7.5 ±5.4 mm in operated and unoperated eyes, respectively. Of 61 eyes, 30 underwent simple surgical excision with conjunctival autograft (3), amniotic membrane graft (7), partial thickness corneal transplant (18), and amniotic membrane graft plus limbal epithelial transplant (2). Fifty-five (90%) of operated eyes had better cosmesis and a significant change in refractive error (p = 0.003). The best-corrected visual acuity improved in operated eyes by 0.4 logMAR units (p = 0.05). A mean size increase of 0.4 ± 0.8 by 0.4 ± 0.9 mm occurred in 31 eyes managed conservatively, with improved best-corrected visual acuity but no change in refractive errors. Amblyopic eyes showed improvement in best-corrected visual acuity of 0.7 (p = 0.007) after occlusion therapy in 13 unoperated and 26 operated eyes.

Conclusion:

Epibulbar dermolipomas often have associated refractive errors and amblyopia. Timely surgical excision improves cosmesis and refractive errors. Occlusion therapy for amblyopic eyes should be offered to help improve vision.
Complex causal relationships between genetic predictions of 731 immune cell phenotypes and novel coronavirus: A two-sample mendelian randomization analysis
Authors: Niu Ze-Su , Liu Ru-Xin , Hu Yi , Meng Xiao-Rui , Liu Li-Hong , Yang Li-Ting , Bai Xue , Chen Meng-Fei , Pan Dong-Feng
Published: December 2024

Background:

COVID-19, caused by SARS-CoV-2, has had a significant impact on global health. While the virus primarily affects the respiratory system, the intricate interplay between immune cells and the virus remains poorly understood. This study investigates the causal relationship between 731 immune cell phenotypes and COVID-19 using Mendelian randomization analysis.

Methods:

A bidirectional two-sample Mendelian randomization (MR) analysis was conducted using genetic variants strongly associated with immune cell phenotypes as instrumental variables. Data for 731 immune cell phenotypes were sourced from the GWAS Catalog, while data for COVID-19 susceptibility were obtained from the OPEN GWAS database. Five MR methods (IVW, MR-Egger, weighted median, simple mode, and weighted mode) were employed to estimate causal effects, with IVW as the primary analysis method.

Results:

The study identified 57 immune cell phenotypes causally associated with COVID-19 risk across two independent GWAS datasets. Five immune cell phenotypes were consistently associated with COVID-19 risk across both datasets: CD3-lymphocyte %lymphocyte (protective), CD27 on CD20- (protective), CD20 on IgD+ CD38- unsw mem (increased risk), CD27 on IgD- CD38- (increased risk), and CD19 on B cell (increased risk). Sensitivity analyses confirmed the robustness of the findings.

Conclusion:

This study provides compelling evidence for a causal relationship between specific immune cell phenotypes and COVID-19 risk. These findings highlight the potential for targeting these immune cell phenotypes as novel therapeutic targets for COVID-19 treatment and prevention.
2024 Charles F. Prentice Medal award lecture: Moments of inspiration
Authors: Efron Nathan
Published: December 2024

In this Prentice Medal Award lecture, I shall recount my career in vision science in the context of three types of inspiration—“being inspired,” “personal inspiration,” and “inspiring others.”

My research has derived inspiration from a variety of sources, such as contemporary and historical research doyens in the ophthalmic field and beyond, artists, Greek philosophers, and abstract constructs such as principles and adages. A given moment of inspiration can range from being a profound experience to a subtle realization during a quiet moment of reflection. Here I shall recount the primary research domains of vision science that have defined my academic career in the context of the three types of inspiration defined above. These research domains are ophthalmic markers of diabetic neuropathy, ocular response to contact lens wear, contact lens–induced parainflammation, contact lens–associated microbial keratitis, grading scales for contact lens complications, contact lens prescribing surveys, material properties of contact lenses, contact lens compliance, history of contact lenses, ocular thermography, and ophthalmic bibliometrics. The notions of “being inspired” and “personal inspiration” are necessarily subjective, although I have endeavored to present them here in a scientific context. Conversely, the notion of “inspiring others” can be objectively gauged, at least in part, by counting article citations or the number of times articles are read online or downloaded from a journal website. In conclusion, my research in the vision sciences has been inspired by others, derived from personal ideas, and perhaps in turn has inspired others.
Choosing the road less traveled: reflections on the past and prospects of the International Psycho-Oncology Society (IPOS)
Authors: Baider Lea , Goldzweig Gil
Published: December 2024

As the International Psycho-Oncology Society (IPOS) marks its 40th anniversary, this commentary reflects on the profound impact and evolution of the organization. IPOS has blazed a trail in improving psychosocial oncology care, evolving into a significant global entity that influences oncology care by addressing the complex emotional needs of patients with cancer, caregivers, and health care providers. While great strides have been made, many challenges remain. As disparities in health care persist and global crises, demographic shifts, and aging affect cancer care, IPOS role becomes ever more crucial in advocating for comprehensive, culturally sensitive, and accessible psychosocial support. This commentary urges a commitment to the fundamental IPOS principles, promoting deeper engagement with patients' experiences and needs, fostering global collaboration, and driving innovative, meaningful research to enhance the quality of life for all affected by cancer. IPOS must remain open, flexible, and loyal to its humanistic, democratic principles as the field explores new frontiers.
Preadmission VACS Index as a Predictor of Hospital Acute Kidney Injury in People with HIV
Authors: Fisher Molly C. , Hanna David B. , Fazzari Melissa , Felsen Uriel R. , Wyatt Christina M. , Abramowitz Matthew K. , Ross Michael J.
Published: December 2024

Background:

The Veterans Aging Cohort Study (VACS) Index is a summary measure of routinely obtained clinical variables that predicts numerous health outcomes. Since there are currently no tools to predict acute kidney injury (AKI) in persons with HIV (PWH), we investigated the association of preadmission VACS Index with hospital AKI in PWH.

Methods:

We conducted an observational study of PWH hospitalized in a New York City health system between 2010-2019. The VACS Index, calculated using outpatient laboratory values within 8-365 days of admission, was examined continuously and in quartiles. Multivariable Cox proportional hazards models, adjusting for sociodemographic factors, comorbidities, and ICU admission, determined the association of the VACS Index with AKI.

Results:

Among 1,186 PWH, median age was 53, 43.5% were women, 86.2% were Hispanic or Black, 23.1% were coinfected with hepatitis C, and 65% were virally suppressed (<200 copies/mL). Overall AKI incidence was 20.9%. The proportion with AKI was higher by increasing VACS index quartile: 10.7%, 18.6%, 28.1% and 60.7% in quartiles 1-4, respectively. There was a graded, independent association of VACS Index quartile with AKI. Compared to those in the lowest quartile, the adjusted relative hazard of AKI was 1.55, 1.92, and 3.07 times higher in quartiles 2-4, respectively (P for trend <0.001).

Conclusion:

Preadmission VACS Index is associated with hospital AKI. Use of the VACS Index may allow for early identification of PWH at risk for AKI and initiation of preventative strategies. These findings should be externally validated in other health systems, including its predictive performance in specific hospital settings.
Poorer longitudinal growth among HIV exposed compared to unexposed infants in Kenya
Authors: Glass Delaney J. , Kinge Maureen , Njuguna Irene , McGrath Christine J. , Lawley Kendall , Moraa Hellen , Onyango Alvin , Wamalwa Dalton , Shattuck Eric , Enquobahrie Daniel A. , John-Stewart Grace
Published: December 2024

Background:

Most infants born to women living with HIV (WLH) are HIV-exposed but uninfected exposed infants have poorer growth than HIV-unexposed uninfected children. Few large studies have compared children who are exposed (CHEU) and unexposed (CHUU) in the era of dolutegravir (DTG)-based antiretroviral treatment (ART).

Setting:

Longitudinal study of mother-infant CHEU and CHUU pairs in Nairobi and Western Kenya.

Methods:

Mother-infant pairs were enrolled at 6 weeks postpartum with 6-monthly growth assessments. We compared longitudinal growth between CHEU and CHUU infants during the first year and assessed biological and social factors affecting growth (length and weight-for-age z-scores [LAZ, WAZ] and weight for length z-scores [WLZ]) and stunting (LAZ<-2), underweight (WAZ<-2), and wasting (WLZ<-2) from birth to 1 year.

Results:

Among 2000 infants (1000 CHEU and 1000 CHUU), CHEU infants had significantly lower LAZ at 6 months (-0.165 (95% CI: -0.274, -0.056), p-value = 0.003) and 12 months (-0.195, 95% CI:-0.294, -0.095, p-value = 0.0001; n = 1616). CHEU infants had a higher prevalence of stunting at 6 months compared to CHUU infants (Prevalence Ratio: 1.45, 95% CI: 1.14, 1.85). Among all children, greater maternal BMI, education, and caregiver-perceived social support were positively associated with growth. Higher maternal and infant comorbidities were associated with growth deficits for CHEU infants. Among CHEU, ART timing (before versus during pregnancy) and ART regimen (dolutegravir(DTG)-based, efavirenz-based, and protease inhibitor/other) did not affect growth.

Conclusion:

Growth deficits among CHEU persist, despite DTG-based ART. Addressing comorbidities, amplifying social support, and education may improve growth outcomes.
Ultra High-Frequency Ultrasound of Median Nerve Fascicles at the Wrist in Amyotrophic Lateral Sclerosis: An Exploratory Study
Authors: Meiling James B. , Caress James B. , Cartwright Michael S.
Published: December 2024

Purpose:

High-frequency ultrasound (HFUS) of muscle and nerve has the potential to be a reliable, responsive, and informative biomarker of disease progression for individuals with amyotrophic lateral sclerosis (ALS). High-frequency ultrasound is not able to visualize median nerve fascicles to the same extent as ultra-high-frequency ultrasound (UHFUS). Evaluating the number and size of fascicles within a nerve may facilitate a better understanding of nerve diseases. This exploratory study aims to image median nerve fascicles at the wrist in individuals with ALS using UHFUS and compare these findings with those from previously observed controls.

Methods:

Fifteen individuals with ALS underwent sonographic examination of the median nerves on each upper limb using UHFUS with a 48-MHz linear array transducer. Fascicle count and density in each examined nerve were determined by a single rater. Demographic and sonographic data from 20 previously studied controls were compared.

Results:

In individuals with ALS, the average fascicle number was 22.4 (SD 5.2) and average fascicle density 1.7 (SD 0.5). There was no significant difference in fascicle counts between individuals with ALS and controls.

Conclusions:

Fascicular quantification using UHFUS is possible in individuals with ALS. Given the lack of appreciable difference between fascicle counts in individuals with ALS and controls, UHFUS of the median nerve at the wrist may not be a responsive biomarker for ALS disease progression.
Structure-guided engineering of α-ketoisocaproate dioxygenase increases isobutene production inSynechocystissp. PCC 6803
Authors: Schumann Conrad , Kugler Amit , Shah Bhavik , Berggren Gustav , Land Henrik , Blikstad Cecilia , Stensjö Karin
Published: December 2024

Isobutene is a promising precursor for jet fuel due to its high energy density and favorable combustion properties. Light-driven bioproduction of isobutene has recently been investigated as an alternative strategy to crude oil refinement or fermentation-based manufacturing processes by harnessing the unicellular cyanobacteriumSynechocystissp. PCC 6803 and the α-ketoisocaproate dioxygenase (RnKICD) fromRattus norvegicus. However, the obtained production level was not sufficient, partially due the promiscuous activity ofRnKICD. The enzyme catalyzes both the reaction with ρ-hydroxyphenylpyruvate (HPP) for homogentisate formation, as well as the reaction with α-ketoisocaproate (KIC), the precursor for isobutene synthesis. Here, to overcome this bottleneck step in the isobutene biosynthesis, protein engineering was employed to improveRnKICD activity and in vivo isobutene production. PurifiedRnKICD variants were characterized by measuring in vitro KIC and HPP consumption rates, as well as isobutene formation rate. The active site mutations F336V, N363A altered the KIC and HPP consumption rates, while the KIC-to-isobutene conversion ratio was only marginally affected. Besides, theRnKICD variants F336V, N363A and F336V/N363A exhibited a substantially enhanced substrate selectivity for KIC over HPP. Among the examined engineeredSynechocystisstrains, Syn-F336V showed a 4-fold improvement in isobutene production, compared to the base strain (Syn-RnKICD). Our findings reveal that residues F336 and N363 play a crucial role in substrate interactions, as targeted mutations at these sites shifted the substrate selectivity towards KIC and elevated the in vivo isobutene production levels significantly. We conclude that engineering the active site ofRnKICD is a potent tool for improving isobutene bioproduction inSynechocystis.

Highlights

Promiscuous α-ketoisocaproate dioxygenase (KICD) fromRattus norvegicuswas overproduced inSynechocystissp. PCC 6803.

Protein engineering was used to improve substrate selectivity.

The generated F336V variant led to a 4-fold increase in isobutene productionin vivo.
Hemin-binding DNA structures on the surface of bacteria promote extracellular electron transfer
Authors: Ajunwa Obinna M. , Minero Gabriel Antonio S. , Jensen Sissel D. , Meyer Rikke L.
Published: December 2024

Recent research has shown that bacteria in anoxic layers ofPseudomonas aeruginosabiofilms can respire by transferring electrons to oxygen via extracellular DNA (eDNA) and DNA- binding redox mediators that are unique to this species1. In this study, we propose a similar but generic mechanism by which bacteria can transfer electrons via DNA in biofilms, using hemin as a redox-mediator and hemin-binding G-quadruplex (G4) DNA structures in the extracellular matrix.

UsingStaphylococcus epidermidisas a model organism, voltammetry showed that eDNA and hemin were needed for extracellular electron transfer (EET). Surface-associated G4-DNA formed a complex with hemin, which transferred electrons from the bacteria to an electrode under anoxic conditions. Addition of G4-DNA and hemin to growing biofilms promoted EET which was stable for days. G4-DNA/hemin is also a peroxidase-like DNAzyme, capable of transferring electrons from bacteria to H2O2.

G4-DNA were only recently discovered to be abundant in the extracellular matrix of biofilms2,3. We now show that hemin turns these structures into conduits for EET. The study opens the door to new and generic mechanisms for bacterial energy conservation under oxygen- limiting conditions, and for tackling H2O2, a common host defense mechanism against bacterial infections.
Chronic Obstructive Pulmonary Disease Prediction Using Deep Convolutional Network
Authors: Alve Shahran Rahman , Mahmud Muhammad Zawad , Islam Samiha , Khan Mohammad Monirujjaman
Published: December 2024

AI and deep learning are two recent innovations that have made a big difference in helping to solve problems in the clinical space. Using clinical imaging and sound examination, they also work on improving their vision so that they can spot diseases early and correctly. Because there aren’t enough trained HR, clinical professionals are asking for help with innovation because it helps them adapt to more patients. Aside from serious health problems like cancer and diabetes, the effects of respiratory infections are also slowly getting worse and becoming dangerous for society. Respiratory diseases need to be found early and treated quickly, so listening to the sounds of the lungs is proving to be a very helpful tool along with chest X-rays. The presented research hopes to use deep learning ideas based on Convolutional Brain Organization to help clinical specialists by giving a detailed and thorough analysis of clinical respiratory sound data for Ongoing Obstructive Pneumonic identification. We used MFCC, Mel-Spectrogram, Chroma, Chroma (Steady Q), and Chroma CENS from the Librosa AI library in the tests we ran. The new system could also figure out how serious the infection was, whether it was mild, moderate, or severe. The test results agree with the outcome of the deep learning approach that was proposed. The accuracy of the framework arrangement has been raised to a score of 96% on the ICBHI. Also, in the led tests, we used K-Crisp Cross-Approval with ten parts to make the presentation of the new deep learning approach easier to understand. With a 96 percent accuracy rate, the suggested network is better than the rest. If you don’t use cross-validation, the model is 90% accurate.
Do-it-yourselfde novoantibody sequencing workflow that achieves complete accuracy of the variable regions
Authors: He Meng-Ting , Li Ning , Wang Jian-Hua , Wei Zhi-Zhong , Feng Jie , Li Wen-Ting , Sui Jian-Hua , Huang Niu , Dong Meng-Qiu
Published: December 2024

Antibodies are widely used as research tools or therapeutic agents. Knowing the sequences of the variable regions of an antibody—both the heavy chain and the light chain—is a prerequisite for the production of recombinant antibodies. Mass spectrometry-basedde novosequencing is a frequently used, and sometimes the only approach to gaining this information. Here, we describe a workflow that enables accurate sequence determination of monoclonal antibodies based on mass spectrometry data and freely available software tools. This workflow, which we developed using a homemade anti-FLAG monoclonal antibody as a reference sample, achieved 100% accuracy of the variable regions with clear distinction between leucine (L) and isoleucine (I). Using this workflow, we successfully decoded a monoclonal anti-HA antibody, for which we had no prior knowledge of its sequence. Based on thede novosequencing result, we generated a recombinant anti-HA antibody, and demonstrated that it has the same specificity, sensitivity, and affinity as the commercial antibody.

Abstract Figure
mRNA-1273 vaccines adapted to JN.1 or KP.2 elicit cross-neutralizing responses against the JN.1 sublineages of SARS-CoV-2 in mice
Authors: Lee Diana Wing , Nasir Arshan , Elbashir Sayda , Jani Hardik , Speidel Tessa , Gorrie Amy , Montes Berrueta Daniela , Martin Philippa , Tan Swan , Hou Yixuan Jacob , Hardcastle Kath , Edwards Darin , Wu Kai , Carfi Andrea , Budigi Yadunanda
Published: December 2024

The continued diversification of SARS-CoV-2 omicron lineage has given rise to the JN.1 variant and descendant strains (KP.2, KP.3, and XEC) that have prolonged the JN.1 infection wave. JN.1 and KP.2 show decreased susceptibility to neutralization sera in recipients of XBB.1.5 vaccine boosters, supporting the recent authorization of JN.1- and KP.2-matched mRNA vaccines in the United States, Europe, and other regions. We evaluated the immunogenicity of two updated monovalent variant-containing formulations of mRNA-1273 vaccines encoding the spike protein of the omicron subvariants JN.1 (mRNA-1273.167) and KP.2 (mRNA-1273.712) as compared with the monovalent XBB.1.5 vaccine (mRNA-1273.815). The vaccines were administered either as a two-dose primary series in naive mice or as a booster (third) dose in mice previously immunized with two-dose primary series of mRNA-1273 (ancestral strain). The neutralizing antibody response elicited by these vaccines against JN.1 subvariants (KP.3 and LA.2) and the recombinant strain (XEC), which achieved dominance in the United States during late 2024, was evaluated. Primary series immunization with either JN.1- or KP.2-matched vaccine elicited robust neutralizing antibody titers against the matched strains and effectively cross-neutralized KP.3, LA.2, and XEC, but not the antigenically distant XBB.1.5. Similarly, JN.1- and KP.2-matched vaccines administered as a booster (third) dose increased titers against the corresponding strains and JN.1-related subvariants, but not against XBB.1.5. These data suggest these strains are antigenically similar with relatively few spike differences between JN.1 and KP.2/JN.1-related subvariants. Our results demonstrate the potency of JN.1- and KP.2-containing mRNA-1273 vaccines in neutralizing the matched variants and their utility in cross-neutralizing JN.1-related subvariants KP.3, LA.2, and XEC. Taken together, these data suggest that the licensed JN.1 and KP.2 mRNA vaccines are likely to continue to protect against the emerging strains as the JN.1 lineage further evolves.
LPS-induced sepsis disrupts brain activity in a region- and vigilance-state specific manner
Authors: Leemburg Susan , Kala Annu , Nataraj Athira , Karkusova Patricia , Baindur Siddharth , Suresh Amritesh , Blahna Karel , Jezek Karel
Published: December 2024

Sepsis-associated encephalopathy (SAE) is a common complication of sepsis and the systemic inflammatory response syndrome that leads to lasting consequences in survivors. It manifests as early EEG changes, that are region-, time- and state-specific, possibly reflecting distinct mechanisms of injury.

Here, we investigated the effects of 5mg/kg lipopolysaccharide (LPS) on hippocampal and cortical sleep-wake states, oscillatory and non-oscillatory neuronal activity, as well as on within and between state dynamics using state-space analysis.

LPS induced rapid-onset severe temporal and spatial vigilance state fragmentation, which preceded all other spectral changes by ∼90 minutes. Thereafter, LPS led to specific destabilization and increased delta oscillatory activity in wakefulness, but not NREM sleep, although state transitions remained largely normal. Instead, reduced NREM delta power resulted from aperiodic spectrum changes. LPS specifically reduced higher frequency hippocampal gamma oscillations (60-80Hz peak) in wakefulness, but not cortical high gamma or lower frequency gamma oscillations.

These results suggest that disruption of sleep-wake patterns could serve as an early indicator of sepsis and associated encephalopathy, independent of spectral changes. Moreover, treatment aimed at stabilizing vigilance states in early stages of sepsis might prove to be a novel option preventing the development of further pathological neurophysiology, as well as limiting inflammation-related brain damage.
Stress-induced organismal death is genetically regulated by the mTOR-Zeste-Phae1 axis
Authors: Matsumura Takashi , Ryuda Masasuke , Matsumoto Hitoshi , Kamiyama Takumi , Kondo Shu , Nakamura Akira , Hayakawa Yoichi , Niwa Ryusuke
Published: December 2024

All organisms are exposed to various stressors, which can sometimes lead to organismal death, depending on their intensity. While stress-induced organismal death has been observed in many species, the underlying mechanisms remain unclear. In this study, we investigated the molecular mechanisms of stress-induced organismal death in the fruit flyDrosophila melanogaster. We identified a chymotrypsin-like serine proteasePhaedra1(Phae1) as a death mediator inD. melanogasterlarvae.Phae1expression was upregulated by lethal heat stress (40 °C) but not non-lethal heat stress (38 °C or lower). The most prominent induction ofPhae1occurred in the central nervous system (CNS). We found neuro-specific knockdown ofPhae1increased survival and reduced neuronal caspase activity following exposure to lethal heat stress, suggesting that the transcriptional upregulation ofPhae1in the CNS is essential for stress-induced organismal death. We next found via bioinformatic and biochemical analyses that the transcription factor Zeste (Z) bound thePhae1enhancer region and thatzloss-of-function impairedPhae1induction in the CNS, increasing survival following lethal heat stress. In addition, we found via chemical screening that rapamycin, a chemical inhibitor of mechanistic target of rapamycin (mTOR), suppressedPhae1expression. Neuro-specific knockdown ofmTorreduced the protein levels of both Phae1 and Z, leading to an increase in survival following lethal heat stress. Together, these results indicate that heat stress-induced organismal death inD. melanogasterlarvae is regulated by a genetically encoded transcriptional signaling pathway involving the mTOR-Z-Phae1 axis.
A novel newborn screening modality: Non-targeted proteome analysis using low-cost iron powders
Authors: Nakajima Daisuke , Ishikawa Masaki , Konno Ryo , Sasai Hideo , Ohara Osamu , Kawashima Yusuke
Published: December 2024

In this study, we developed a simple protein extraction method for dried blood spots (DBS) that potentially meets the throughput required for newborn screening (NBS) and optimizes non-targeted proteomic analysis in combination with liquid chromatography coupled mass spectrometry in the data-independent-acquisition mode (DIA-LC-MS/MS). The developed pipeline, termedNon-targetedAnalysis ofNon-specificallyDBS-Absorbed proteins (NANDA), successfully addressed the following three challenges: (1) processing of 96 3.2-mm DBS punches in parallel using low-cost iron powders with a robotic system, (2) identifying more than 5,000 proteins using DIA-LC-MS/MS, and (3) improving DIA-LC-MS/MS throughput to 40 samples/day with minimal compromise in protein coverage depth. The results imply that this pipeline can open new venues for conducting NBS using non-targeted quantitative proteome profiling, which has been a currently missing modality in NBS.
Target deconvolution of an insulin hypersecretion-inducer acting through VDAC1 with a distinct transcriptomic signature in beta-cells
Authors: Roy Gitanjali , Ordóñez Andrea , Binns Derk D. , Rodrigues dos Santos Karina , Kwakye Michael B. , King George C. , Mukherjee Noyonika , Templin Andrew T. , Tan Zhiyong , Richardson Timothy I. , Doud Emma H. , Mosley Amber L. , Emfinger Christopher H. , Attie Alan D. , Keller Mark P. , Johnson Travis S. , Kalwat Michael A.
Published: December 2024

Obesity, insulin resistance, and a host of environmental and genetic factors can drive hyperglycemia, causing β-cells to compensate by increasing insulin production and secretion. In type 2 diabetes (T2D), β-cells under these conditions eventually fail. Rare β-cell diseases like congenital hyperinsulinism (HI) also cause inappropriate insulin secretion, and some HI patients develop diabetes. However, the mechanisms of insulin hypersecretion and how it causes β-cell dysfunction are not fully understood. We previously discovered small molecules (e.g. SW016789) that cause insulin hypersecretion and lead to a loss in β-cell function without cell death. Here, we uncover the protein target of SW016789 and provide the first time-course transcriptomic analysis of hypersecretory responses versus thapsigargin-mediated ER stress in β-cells. In mouse MIN6 and human EndoC-βH1 β-cells, we identified and validated VDAC1 as a SW016789 target using photoaffinity proteomics, cellular thermal shift assays, siRNA, and small molecule inhibitors.

SW016789 raises membrane potential to enhance Ca2+influx, potentially through VDAC1. Chronically elevated intracellular Ca2+appears to underpin the negative impacts of hypersecretion, as nifedipine protected against each small molecule hypersecretion inducer we tested. Using time- course RNAseq, we discovered that hypersecretion induced a distinct transcriptional pattern compared to ER stress. Clustering analyses led us to focus on ER-associated degradation (ERAD) as a potential mediator of the adaptive response. SW016789 reduced the abundance of ERAD substrate OS-9 and pharmacological inhibition of ERAD worsened β-cell survival in response to hypersecretory stress. Changes in other ERAD components in MIN6 and EndoC-βH1 at the protein level were minor with either SW016789 or thapsigargin. However, immunostaining for core ERAD components SEL1L, HRD1, and DERL3 in non-diabetic and T2D human pancreas revealed altered distributions of SEL1L/HRD1 and SEL1L/DERL3 rations in β-cells of T2D islets, in alignment with altered ERAD in stressed β-cells. We conclude that hypersecretory stimuli, including SW016789- mediated VDAC1 activation, cause enhanced Ca2+influx and insulin release. Subsequent differential gene expression represents a β-cell hypersecretory response signature that is reflected at the protein level for some, but not all genes. A better understanding of how β-cells induce hypersecretion and the mechanisms of negative feedback on secretory rate may lead to the discovery of novel therapeutic targets for T2D and HI.
Retinal organoids mirror CRISPR/Cas9 gene editing efficiency observed in vivo
Authors: Pulman Juliette , Malki Hugo , Oudin Paul , Aydin Ecem , Tran Sophie , Visticot Laura , Robert Camille , De Cian Anne , As Marie , Goureau Olivier , Concordet Jean-Paul , Dalkara Deniz
Published: December 2024

Human retinal organoids arein vitro3D structures that recapitulate key molecular and structural characteristics of thein vivoretina. They include the presence of all essential retinal cell types including photoreceptors, making them relevant models for preclinical development of gene therapies. A critical knowledge gap exists in understanding their utility for gene editing optimization, particularly for specific genetic disorders. We assessed the potential of retinal organoids for optimizing CRISPR/Cas9-mediated gene editing, focusing on the therapeutically relevantRHOgene implicated in autosomal dominant Retinitis Pigmentosa (adRP). Using retinal organoids,in vitroHEK293T cells, and two humanized mouse models carrying differentRHOmutations, we compared editing efficiencies. We observed that retinal organoids have lower transfection efficiency compared to HEK293T cells. Notably, they exhibited editing efficiencies more closely aligned with those foundin vivo. We also observed similar delivery patterns of CRISPR/Cas9 tools in both retinal organoids and mouse retinas. These delivery patterns and editing efficiencies remained consistent across dual AAV systems and transiently delivered ribonucleoprotein complexes. Our findings demonstrate that retinal organoids achieve editing outcomes comparable to those observedin vivounderscoring their utility as part of a preclinical testing platform for genome editing, with implications for advancing gene therapy research in inherited retinal diseases.

Graphical abstract

eTOC

Retinal organoids can be used to mirrorin vivomouse retina to develop CRISPR therapeutics. Here, Pulman and colleagues show similar ranges of gene editing and delivery dynamics between the organoids andin vivomouse retina, highlighting the organoid’s underexplored potential for evaluating gene editing therapies in retinal diseases.
Ultrastructural membrane dynamics of mouse and human cortical synapses
Authors: Eddings Chelsy R. , Fan Minghua , Imoto Yuuta , Itoh Kie , McDonald Xiomara , Eilers Jens , Anderson William S. , Worley Paul F. , Lippmann Kristina , Nauen David W. , Watanabe Shigeki
Published: December 2024

Live human brain tissues provide unique opportunities for understanding the physiology and pathophysiology of synaptic transmission. Investigations have been limited to anatomy, electrophysiology, and protein localization—while crucial parameters such as synaptic vesicle dynamics were not visualized. Here we utilize zap-and-freeze time-resolved electron microscopy to overcome this hurdle. First we validate the approach with acute mouse brain slices to demonstrate that axons parallel to the electrical field can be stimulated to produce calcium signaling. Next we show that ultrafast endocytosis is induced and can be captured in both mouse and human brain slices. Crucially, in both species a protein essential for ultrafast endocytosis Dynamin 1xA (Dyn1xA) localizes to the region peripheral to the active zone, the putative endocytic zone, indicating a likely mechanism conservation between mouse and human. This approach has the potential to reveal dynamic, high-resolution information about synaptic membrane trafficking in intact human brain slices.
Aggression experience and observation promote shared behavioral and neural changes
Authors: Iravedra-Garcia Jorge M. , Guthman Eartha Mae , Cuturela Lenca , Ocasio-Arce Edgar J. , Pillow Jonathan W. , Falkner Annegret L.
Published: December 2024

The ability to observe the social behavior of others and use observed information to bias future action is a fundamental building block of social cognition1,2. A foundational question is whether social observation and experience engage common circuit mechanisms that enable behavioral change. While classic studies on social learning have shown that aggressive behaviors can be learned through observation3, it remains unclear whether aggression observation promotes persistent neural changes that generalize to new contexts. Here, to directly compare the effects of aggression experience and observation at brain-wide scale, we develop a strategy to perform large-scale cell-type specific recordings across subcortical networks for social behavior control and learning. We record longitudinally while animals “train” through direct experience or observation, then probe shared differences in behavior and neural activity in a novel “hard” aggression context. Using supervised and unsupervised methods for behavioral quantification, we detect unique signatures of a shared behavioral strategy not present in animals with no training. During observation, we find widespread activation that mimics experience in networks for behavior generation, with critical differences in signals associated with reward and threat learning. After observation, we observe that changes persist into the novel aggression context, with increased similarity in the neural dynamics between experience and observation groups. Network-level modeling reveals persistent shared changes to a core aggression network, with widespread decoupling of inhibition from a key hypothalamic output region. This demonstrates that “experience-like” activity during observation can recruit a shared plasticity mechanism that biases behavior toward adaptive defensive strategies in new contexts.
Disruption of Collective Behavior Correlates with Reduced Interaction Efficiency
Authors: Nguyen Justine B. , Cook Chelsea N.
Published: December 2024

Group-living organisms commonly engage in collective behavior to respond to an ever-changing environment. How individuals utilize local information to produce such large-scale, cohesive behaviors and the factors that impact these dynamics are of high research interest, especially since animals face increasingly challenging environmental conditions due to pollution and climate change. Western honeybees (Apis mellifera) are highly social insects that depend on the tight coordination of many individuals to ensure optimum colony function. We used fanning, a collective thermoregulatory behavior in honeybees that depends on both social and thermal contexts, as a case study for collective behavior. To elucidate the mechanisms behind the coordination of fanning, we used oxytetracycline, an antibiotic historically used in apiculture and known environmental pollutant that impairs bee physiology and behavior. Specifically, we hypothesized that oxytetracycline will interfere social interactions which will lead to a disruption in honeybee fanning behavior. We found that longer exposure to antibiotics decreases fanning in honeybees. Using an automated tracking software, we show that antibiotic treatment lowers the number of interactions bees have despite increasing average movement velocity, thereby impeding the social dynamics within these small bee groups. Our results contribute strong evidence that interactions between individuals may drive the collective thermoregulatory fanning response in honeybees. This work emphasizes the importance of understanding the social mechanisms that underlie critical collective animal coordination and how the effects of a common environmental pollutant on an individual can scale to affect populations.
CDH3-AS1 antisense RNA enhances P-cadherin translation and acts as a tumor suppressor in melanoma
Authors: Chadourne Manon , Griffith Crystal , Xu Xiaonan , Brennan Emily , Vera Olga , Mecozzi Nicol , Wang Kaizhen , Jaeger Alex M. , Karreth Florian A.
Published: December 2024

Thousands of regulatory noncoding RNAs (ncRNAs) have been annotated; however, their functions in gene regulation and contributions to cancer formation remain poorly understood. To gain a better understanding of the influence of ncRNAs on gene regulation during melanoma progression, we mapped the landscape of ncRNAs in melanocytes and melanoma cells. Nearly half of deregulated genes in melanoma are ncRNAs, with antisense RNAs (asRNAs) comprising a large portion of deregulated ncRNAs.CDH3-AS1, the most significantly downregulated asRNA, overlaps theCDH3gene, which encodes P-cadherin, a transmembrane glycoprotein involved in cell adhesion that was also reduced in melanoma. Overexpression ofCDH3-AS1increased cell aggregation and reduced xenograft tumor growth, mimicking the tumor-suppressive effects ofCDH3.CDH3-AS1interacted withCDH3mRNA and enhanced P-cadherin protein levels. Interestingly, secondary structures at theCDH35’ end regulated P-cadherin translation, and ribosome profiling revealed thatCDH3-AS1promotes ribosome occupancy at theCDH3mRNA. Notably, ribosome occupancy was generally increased in mRNAs having cognate asRNA that are complementary to the 5’UTR. Taken together, this study revealed theCDH3-AS1-mediated enhancement of P-cadherin translation, underscoring the broader potential of asRNAs as regulators of protein-coding genes and their role in diseases like melanoma.
The Effect of Visual Field Occlusion on Visually Induced Motion Sickness
Authors: Aihara Takatsugu , Yamada Sachiko , Ban Hiroshi
Published: December 2024

Visually induced motion sickness (VIMS), characterized by symptoms such as dizziness, nausea, and postural instability, presents significant challenges in modern visual and interactive technologies. These symptoms undermine the immersion into and comfort of virtual and augmented reality (VR/AR) systems and reduce the usability of autonomous vehicles, highlighting the urgent need to address VIMS for broader adoption of these technologies. While previous studies have largely focused on the motion characteristics that induce VIMS, the impact of visual field configuration, such as segmentation and occlusion, has been largely unexplored. To bridge this gap, we conducted five human psychophysics experiments systematically investigating how visual field segmentation and masking influence VIMS under controlled three-dimensional optical flow conditions. Participants were exposed to different masking patterns, including variations in the number of divided sections, the masking of the central screen region, and the thickness of the masks. Paired-comparison methods were employed to assess participants’ susceptibility to VIMS under each condition. Our findings showed that visual field segmentation significantly influenced VIMS susceptibility. Specifically, the results revealed three key findings: (1) segmenting the visual field into multiple subsections using visual masks significantly increased VIMS susceptibility, (2) thinner masks exacerbated motion sickness more than thicker ones, and (3) masking the central region of the screen reduced susceptibility. These effects were independent of the presented motion patterns. Our findings offer new insights for optimizing the design of VR/AR systems, graphical user interfaces, and autonomous vehicles by highlighting the importance of visual field configuration in mitigating VIMS for improving user experience.
Maize TIR-only Proteins ZmTIR1 and ZmTIR2, but not ZmTIR3 Confer Auto-active Hypersensitive Response Likely by Forming Condensation
Authors: Kang Zi-Xuan , Ge Qi-Dong , Zhang Man-Lin , Tang Chang-Xiao , Yang Man , Liu Shuqing , Dai Yu-Chen , Zhang Hua , Zang Ke , Li Shengjun , Wang Guan-Feng
Published: December 2024

Nucleotide binding, leucine-rich-repeat (NLR) proteins are the major intracellular receptors for defending against pathogen infection. The recognition between NLRs and pathogen secreted effectors often triggers a localized programmed cell death termed hypersensitive response (HR). Despite significant progresses have been achieved in understanding canonical NLRs with the N-terminal Toll/interleukin-1 receptor (TIR) domains, the molecular mechanisms underlying TIR-only proteins in plant immune responses remain unclear. In this study, we identified six TIR-containing proteins in maize, including three TIR-only proteins. Functional analysis showed that ZmTIR1 and ZmTIR2, but not ZmTIR3, confer autoactive HR when transiently expressed inN. benthamiana. The autoactivity conferred by ZmTIR1 and ZmTIR2 depends on EDS1-PAD4-RNL module and their putative NADase activities. Interestingly, ZmTIR1 and ZmTIR2 predominantly localize in the punctate dots and likely form condensation, while ZmTIR3 mainly localizes in the cytoplasm and the nucleus. Two specific amino acids in the BB-loop region were identified to be required for ZmTIR1- and ZmTIR2-mediated condensation formation and auto-HR. Furthermore,ZmTIRandZmTIR2are induced byCochliobolus heterostrophus, the causal agent of southern leaf blight (SLB) in maize, and knock-down the expression ofZmTIR1orZmTIR2decreased the resistance to SLB in maize. Our study reveals a novel mechanism of monocot TIR-only proteins in maize immune responses.
Best Cochlear Locations for Delivering Interaural Timing Cues in Electric Hearing
Authors: Borjigin Agudemu , Dennison Stephen R. , Thakkar Tanvi , Kan Alan , Litovsky Ruth Y.
Published: December 2024

Growing numbers of children and adults who are deaf are eligible to receive cochlear implants (CI), which provide access to everyday sound. CIs in both ears (bilateral CIs or BiCIs) are becoming standard of care in many countries. However, their effectiveness is limited because they do not adequately restore the acoustic cues essential for sound localization, particularly interaural time differences (ITDs) at low frequencies. The cochlea, the auditory sensory organ, typically transmits ITDs more effectively at the apical region, which is specifically "tuned" to low frequencies. We hypothesized that effective restoration of robust ITD perception through electrical stimulation with BiCIs depends on targeting cochlear locations that transmit information most effectively. Importantly, we show that these locations can occur anywhere along the cochlea, even on the opposite end of the frequency map from where ITD cues are most dominantly encoded in an acoustic hearing system.
A Variational Autoencoder Model for Clustering of Cell Nuclei on Microgroove Substrates: Potential for Disease Diagnosis
Authors: Roellinger Bettina , Thenier Francois , Leclech Claire , Coirault Catherine , Angelini Elsa , Barakat Abdul I.
Published: December 2024

Various diseases including laminopathies and certain types of cancer are associated with abnormal nuclear mechanical properties that influence cellular and nuclear deformations in complex environments. Recently, microgroove substrates designed to mimic the anisotropic topography of the basement membrane have been shown to induce significant 3D nuclear deformations in various adherent cell types. Importantly, these deformations are different in myoblast cells derived from laminopathy patients from those in cells derived from normal individuals. Here we assess the ability of a variational autoencoder (VAE) and a Gaussian Mixture Model (GMM) to cluster patches of nuclei of both wildtype myoblast cells and myoblast cells with laminopathy-associated mutations cultured on microgroove substrates, and we explore the impact of image processing parameters on clustering performance. We show that a standard VAE with GMM is able to cluster nuclei based on their morphologies and degrees of deformations and that these clusters correspond to either wildtype myoblasts or myoblasts with LMNA mutations. The current results suggest that combining deep learning techniques with microgroove substrates enables automatic classification of nuclear deformations and thus provides a promising approach for easy and rapid diagnosis of pathologies that involve abnormalities in nuclear deformation.