bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcanal Endoscopic Ear Surgery for Advanced External Auditory Canal Cholesteatoma in Naim Stage III and IV
Authors: Li Yang , Sheng Ying , Xia Cui , Yan Jing , Guo Li , Ren XiaoYong , Wu BaoJun
Published: November 2021

Objective:

To report the clinical characteristics and treatment outcomes, as well as endoscopic-assisted ear surgery techniques used in patients with advanced external auditory canal cholesteatoma (EACC).

Study Design:

Retrospective case series.

Setting:

University hospital.

Methods:

From October 2014 to September 2017, adult patients (age > 18) with advanced EACC (Naim's classification: stage III or IV) who underwent transcanal endoscopic ear surgery (TEES) were enrolled. The presenting features, extent of the lesion, and reconstruction techniques used were assessed. The healing time which was defined as the time required to develop a dry, re-epithelialized, and self-cleaning external auditory canal, was compared between stage III and IV.

Results:

Twenty-three patients were included. EACC was categorized as stage III in 11 ears and stage IV in 12 ears. Cholesteatoma involved the mastoid (30%), middle ear (26%), chorda tympani (22%), temporomandibular joint, antrum, and facial nerve (17% for each). In 96% of patients, a dry and self-cleaning external auditory canal (EAC) was maintained after a mean follow-up of 15 months. The median healing time was 8 weeks in stage III, which was significantly shorter than the 12 weeks required for stage IV (p < 0.05). There was no significant difference in the median healing time between TEES and the canal wall up mastoidectomy for stage IV EACC (14 weeks) performed by the same surgeon over the same period (p > 0.05).

Conclusions:

TEES is a feasible and safe technique for the exposure and eradication of advanced EACC. Some critical endoscopic techniques for resecting disease and reconstructing the defect in the EAC and middle ear should be mastered before performing this operation.
Electroconvulsive Therapy in a Patient With a Liver Transplant
Authors: Gunther Steven R. , Chatham Peggy E. , Stewart Jonathan T.
Published: November 2021

Depression is common in patients after liver transplantation and, when severe, can threaten both viability of the graft and the patient’s life. Electroconvulsive therapy (ECT) is a safe and highly effective therapy for severe depression, but there have been very few reports of its use in liver transplant recipients. We describe a patient who had undergone a successful orthotopic liver transplant 26 years previously, who developed severe major depression. The patient tolerated an index course of ECT well and responded robustly. There were no complications pertinent to the graft or otherwise. Liver transplantation is not a contraindication to ECT, and clinicians should not hesitate to proceed when necessary.
Assessing Self-reported Recovery in a Community Psychiatry Setting
Authors: Rodriguez Katrina M. , Von Mach Tara , Spivak Stanislav , Mojtabai Ramin , Cullen Bernadette A.
Published: November 2021

Objective:

This study examined demographic and diagnostic characteristics associated with self-reported recovery in patients with serious mental illness.

Methods:

Patient demographics and diagnoses were obtained from a retrospective review of charts from 981 patients attending a community psychiatry outpatient program between January 2015 and December 2016. All patients completed the Recovery Assessment Scale-Revised (RAS-R), a self-report recovery questionnaire consisting of 5 subscales, approximately every 6 months. Generalized estimating equation models were used to assess change in RAS-R scores over time and to test for associations with demographic characteristics, clinical diagnoses, and appointment adherence.

Results:

RAS-R scores increased among all demographic and diagnostic groups during the study period. A primary diagnosis of a psychotic disorder (including schizophrenia) was associated with higher 2-year average RAS-R total scores and scores on the Personal Confidence and Hope, Goal and Success Orientation, and Not Dominated by Symptoms subscales. African American race was associated with higher 2-year average scores on the Personal Confidence and Hope subscale. Increasing age was associated with higher total RAS-R scores and multiple subscale scores. No significant associations were found between sex or appointment adherence and RAS-R total scores or any of the subscale scores.

Conclusions:

While certain demographic and diagnostic groups were associated with higher RAS-R scores, study results suggest that time in treatment is itself associated with higher self-reported recovery among all demographic groups. Age, race, and diagnosis were all associated with higher scores on the Personal Confidence and Hope subscale, highlighting the need for individualized treatment that takes multiple patient characteristics into account.
A Case Series of Very Late-onset Schizophrenia-like Psychosis: Is It a Dimension of Dementia?
Authors: Zazaian Danielle , Gifford Lindsey , Rath Swapnil
Published: November 2021

Background:

Emerging research has shown that there may be a subset of patients who develop a first-break psychosis later in life when they are over 60 years of age. Very late-onset schizophrenia-like psychosis (VLOSLP) differs from early-onset schizophrenia in a few very important ways that lead us to believe that there may be a distinct pathologic process involved.

Methods:

We present 4 cases of females with psychotic symptoms that first appeared after the patients were 60 years of age. We conducted a literature review and found that our older adult psychiatric unit is not alone in struggling with diagnoses for these individuals.

Results:

Some of these patients have a disease that will progress to a neurocognitive disorder, but a large group of others will remain cognitively intact. Fortunately, the treatment for both processes is very similar, but studies have shown that patients with VLOSLP will need significantly lower doses of antipsychotics compared with those with early-onset schizophrenia.

Conclusions:

It remains unclear if VLOSLP is a unique disorder, a prodrome to dementia, or a different condition that is not yet understood. Further research is needed to develop comprehensive treatment for patients with VLOSLP.
Transgenerational impact of aberrant inflammation in rat pregnancy
Authors: Ushida Takafumi , Cotechini Tiziana , Protopappas Nicole , Atallah Aline , Collyer Charlotte , Macdonald-Goodfellow Shannyn K. , Tse M. Yat , Winn Louise M. , Pang Stephen C. , Adams Michael A. , Othman Maha , Kotani Tomomi , Kajiyama Hiroaki , Graham Charles H.
Published: November 2021

Children of women with pre-eclampsia have increased risk of cardiovascular (CV) and metabolic disease in adult life. Furthermore, the risk of pregnancy complications is higher in daughters born to women affected by pre-eclampsia than in daughters born after uncomplicated pregnancies. While aberrant inflammation contributes to the pathophysiology of pregnancy complications, including pre-eclampsia, the contribution of maternal inflammation to subsequent risk of CV and metabolic disease as well as pregnancy complications in the offspring remains unclear. Here we demonstrate that 24-week-old female rats (F1) born to dams (F0) exposed to lipopolysaccharide (LPS) during pregnancy (to induce inflammation) exhibited mild systolic dysfunction, increased cardiac growth-related gene expression, abnormal glucose tolerance and coagulopathy; whereas male F1 offspring exhibited abnormal glucose tolerance and increased visceral fat accumulation compared with F1 sex-matched offspring born to saline-treated dams. Both male and female F1 offspring born to LPS-treated dams had evidence of anemia. Fetuses (F2) from F1 females born to LPS-treated dams were growth restricted, and this reduction in fetal growth was associated with increased CD68 positivity and decreased expression of glucose transporter-1 in their utero-placental units. These results indicate that abnormal maternal inflammation can contribute to increased risk of CV and metabolic disease in offspring, and that the effects of inflammation may be transgenerational. This study provides evidence in support of early screening for CV and metabolic disease, as well as pregnancy complications in offspring affected by pre-eclampsia or other pregnancy complications associated with aberrant inflammation.
Computation of transcranial magnetic stimulation electric fields using self-supervised deep learning
Authors: Li Hongming , Deng Zhi-De , Oathes Desmond , Fan Yong
Published: November 2021

Electric fields (E-fields) induced by transcranial magnetic stimulation (TMS) can be modeled using partial differential equations (PDEs). Using state-of-the-art finite-element methods (FEM), it often takes tens of seconds to solve the PDEs for computing a high-resolution E-field, hampering the wide application of the E-field modeling in practice and research. To improve the E-field modeling’s computational efficiency, we developed a self-supervised deep learning (DL) method to compute precise TMS E-fields. Given a head model and the primary E-field generated by TMS coils, a DL model was built to generate a E-field by minimizing a loss function that measures how well the generated E-field fits the governing PDE. The DL model was trained in a self-supervised manner, which does not require any external supervision. We evaluated the DL model using both a simulated sphere head model and realistic head models of 125 individuals and compared the accuracy and computational speed of the DL model with a state-of-the-art FEM. In realistic head models, the DL model obtained accurate E-fields that were significantly correlated with the FEM solutions. The DL model could obtain precise E-fields within seconds for whole head models at a high spatial resolution, faster than the FEM. The DL model built for the simulated sphere head model also obtained an accurate E-field whose average difference from the analytical E-fields was 0.0054, comparable to the FEM solution. These results demonstrated that the self-supervised DL method could obtain precise E-fields comparable to the FEM solutions with improved computational speed.
Notch-dependent DNA cis-regulatory elements and their dose-dependent control of C. elegans stem cell self-renewal
Authors: Lynch Tina R , Xue Mingyu , Czerniak Cazza W. , Lee ChangHwan , Kimble Judith
Published: November 2021

A long-standing biological question is how DNA cis-regulatory elements shape transcriptional patterns during metazoan development. The use of reporter constructs, cell culture and computational modeling has made enormous contributions to understanding this fundamental question, but analysis of regulatory elements in their natural developmental context is an essential but rarely used complement. Here, we edited Notch-dependent cis-regulatory elements in the endogenous C. elegans sygl-1 gene, which encodes a key stem cell regulator. We then analyzed the in vivo consequences of those mutations – on both gene expression (nascent transcripts, mRNA, protein) and stem cell maintenance. Mutation of a single element in a three-element homotypic cluster reduced expression as well as stem cell pool size by about half, while mutation of two elements essentially abolished them. We find that LBS number and LBS neighborhood are both important to activity: elements on separate chromosomes function additively, while elements in the same cluster act synergistically. Our approach of precise CRISPR/Cas9 gene editing coupled with quantitation of both molecular and biological readouts establishes a powerful model for in vivo functional analyses of DNA cis-regulatory elements.

Summary statement

Notch-dependent DNA cis-regulatory elements work together in their developmental context to shape a transcriptional gradient, control stem cell pool size, and govern differentiation onset.
Effective cell membrane tension is independent of polyacrylamide substrate stiffness
Authors: Kreysing Eva , Mc Hugh Jeffrey , Foster Sarah K. , Andresen Kurt , Greenhalgh Ryan D. , Pillai Eva K. , Dimitracopoulos Andrea , Keyser Ulrich F. , Franze Kristian
Published: November 2021

Most animal cells are surrounded by a cell membrane and an underlying actomyosin cortex. Both structures are linked, and they are under tension. In-plane membrane tension and cortical tension both influence many cellular processes, including cell migration, division, and endocytosis. However, while actomyosin tension is regulated by substrate stiffness, how membrane tension responds to mechanical substrate properties is currently poorly understood. Here, we probed the effective membrane tension of neurons and fibroblasts cultured on glass and polyacrylamide substrates of varying stiffness using optical tweezers. In contrast to actomyosin-based traction forces, both peak forces and steady state tether forces of cells cultured on hydrogels were independent of substrate stiffness and did not change after blocking myosin II activity using blebbistatin, indicating that tether and traction forces are not directly linked. Peak forces in fibroblasts on hydrogels were about twice as high as those in neurons, indicating stronger membrane-cortex adhesion in fibroblasts. Steady state tether forces were generally higher in cells cultured on hydrogels than on glass, which we explain by a mechanical model. Our results provide new insights into the complex regulation of effective membrane tension and pave the way for a deeper understanding of the biological processes it instructs.
International impact of large multi-centre surgical trials of arthroscopic subacromial decompression
Authors: Smith James A. , Kostka Kristin , Beard David J. , Carr Andrew J. , Rees Jonathan L. , Prieto-Alhambra Daniel
Published: November 2021

Objectives

To examine temporal trends in incidence of arthroscopic subacromial decompression (ASAD) surgery internationally during conduct and after publication of placebo controlled trials finding no evidence of meaningful benefit of ASAD for shoulder impingement.

Design

Observational study of incidence rates.

Setting

Large routinely collected datasets were used: outpatient data from Belgium and UK, and insurance claims and outpatient data from US. UK data were from Clinical Practice Research Datalink and Belgium and US data were from IQVIA. US and UK data spanned 2005 – 2019 and Belgium data 2011 – 2019.

Participants

Patients were eligible for inclusion in the study if they had at least one visit recorded in the database in a given year and cases were defined as patients undergoing ASAD for the first time in their records in a given year.

Outcome measures

We calculated incidence of ASAD over time, overall and stratified by age and sex. Characteristics of patients undergoing ASAD were also assessed over time.

Results

UK incidence has fallen since a peak of 4.7 per 10,000 person years in 2011 (when the CSAW trial began) to 1.8 in 2019. US incidence shows no clear pattern and remains consistently higher than the UK, at 11.5 per 100,000 person years in 2019. Changes in incidence patterns were similar across different age groups and sexes. The number of cases in Belgium was too small for meaningful conclusions.

Conclusions

We found ASAD rates have fallen in the UK during conduct and after publication of two large surgical RCTs from the UK and Finland that questioned the effectiveness of ASAD for shoulder impingement. A similar impact on clinical practice has not been seen in US. Further work to understand the barriers or concerns preventing international uptake of high quality evidence into clinical practice is needed.

Strengths and limitations of this study

This is the most comprehensive study of ASAD incidence we are aware of. Routinely collected datasets were used to assess proportions of the patients undergoing this procedure in several countries

Standardised case definitions were used across databases to increase comparability of findings

Temporal changes in database coverage and quality of reporting can influence findings. The observed variation in ASAD incidence may not be entirely attributable to changes in ASAD surgery rates.
Base editing in bovine embryos reveals a species-specific role of SOX2 in regulation of pluripotency
Authors: Luo Lei , Shi Yan , Wang Huanan , Wang Zizengchen , Dang Yanna , Li Shuang , Wang Shaohua , Zhang Kun
Published: November 2021

The emergence of the first three lineages during development are orchestrated by a network of transcription factors, which are best characterized in mice. However, the role and regulation of these factors are not completely conserved in other mammals, including human and cattle. Here, we establish a gene inactivation system by introducing premature codon with cytosine base editor in bovine embryos with a robust efficiency. Of interest, SOX2 is universally localized in early blastocysts but gradually restricted into the inner cell mass in cattle. SOX2 knockout results in a failure of the establishment of pluripotency. Indeed, OCT4 level is significantly reduced and NANOG was barely detectable. Furthermore, the formation of primitive endoderm is compromised with few SOX17 positive cells. Single embryo RNA-seq reveals a dysregulation of 2074 genes, among which 90% are up-regulated in SOX2-null blastocysts. Intriguingly, more than a dozen lineage-specific genes, including OCT4 and NANOG, are down-regulated. Moreover, SOX2 expression is sustained in the trophectoderm in absence of CDX2 in bovine late blastocysts. Overall, we propose that SOX2 is dispensable for OCT4 and NANOG expression and disappearance of SOX2 in the trophectoderm depends on CDX2 in cattle, which are all in sharp contrast with results in mice.

Significance

The first and second cell fate decisions of a new life are important for subsequent embryonic and plancental development. These events are finely controlled by a network of transcriptional factors, which are extensively characterized in mice. Species-specific roles of these proteins are emerging in mammals. Here, we develop a gene loss-of-function system by using cytosine base editors in bovine embryos. We find that expression pattern, functional roles, and regulation of SOX2 are all different between mouse and bovine embryos. Remarkbly, SOX2 is required for OCT4 and NANOG, two well established pluripoteny genes. Furthermore, CDX2 is required to shut down SOX2 in the trophectoderm. Given similar expression pattern of SOX2 between human and bovine blastocysts, bovine embryos represents a putative model to investigate human pluripotency regulation in vivo.
A synthetic distributed genetic multi-bit counter
Authors: Chen Tianchi , Al-Radhawi M. Ali , Voigt Christopher A. , Sontag Eduardo D.
Published: November 2021

A design for genetically-encoded counters is proposed via repressor-based circuits. An N -bit counter reads sequences of input pulses and displays the total number of pulses, modulo 2N .

The design is based on distributed computation, with specialized cell types allocated to specific tasks. This allows scalability and bypasses constraints on the maximal number of circuit genes per cell due to toxicity or failures due to resource limitations.

The design starts with a single-bit counter. The N -bit counter is then obtained by interconnecting (using diffusible chemicals) a set of N single-bit counters and connector modules.

An optimization framework is used to determine appropriate gate parameters and to compute bounds on admissible pulse widths and relaxation (inter-pulse) times, as well as to guide the construction of novel gates.

This work can be viewed as a step toward obtaining circuits that are capable of finite-automaton computation, in analogy to digital central processing units.

Graphical Abstract
Similarities Between Somatosensory Cortical Responses Induced via Natural Touch and Microstimulation in the Ventral Posterior Lateral Thalamus in Macaques
Authors: Francis Joseph Thachil , Rozenboym Anna , von Kraus Lee , Xu Shaohua , Chhatbar Pratik , Semework Mulugeta , Hawley Emerson , Chapin John
Published: November 2021

Lost sensations, such as touch, could be restored by microstimulation (MiSt) along the sensory neural substrate. Such neuroprosthetic sensory information can be used as feedback from an invasive brain-machine interface (BMI) to control a robotic arm/hand, such that tactile and proprioceptive feedback from the sensorized robotic arm/hand is directly given to the BMI user. Microstimulation in the human somatosensory thalamus (Vc) has been shown to produce somatosensory perceptions. However, until recently, systematic methods for using thalamic stimulation to evoke naturalistic touch perceptions were lacking. We have recently presented rigorous methods for determining a mapping between ventral posterior lateral thalamus (VPL) MiSt, and neural responses in the somatosensory cortex (S1), in a rodent model (Choi et al., 2016; Choi and Francis, 2018). Our technique minimizes the difference between S1 neural responses induced by natural sensory stimuli and those generated via VPL MiSt. Our goal is to develop systems that know what MiSt will produce a given neural response and possibly a more natural “sensation.” To date, our optimization has been conducted in the rodent model and simulations. Here we present data from simple non-optimized thalamic MiSt during peri-operative experiments, where we MiSt in the VPL of macaques with a somatosensory system more like humans. We implanted arrays of microelectrodes across the hand area of the macaque S1 cortex as well as in the VPL thalamus. Multi and single-unit recordings were used to compare cortical responses to natural touch and thalamic MiSt in the anesthetized state. Post stimulus time histograms were highly correlated between the VPL MiSt and natural touch modalities, adding support to the use of VPL MiSt towards producing a somatosensory neuroprosthesis in humans.
Acoustic and postural displays in a miniature and transparent teleost fish, Danionella dracula
Authors: Tatarsky Rose L. , Guo Zilin , Campbell Sarah C. , Kim Helena , Fang Wenxuan , Perelmuter Jonathan T. , Schuppe Eric R. , Reeve Hudson K. , Bass Andrew H.
Published: November 2021

Acoustic communication is widespread across vertebrates, including among fishes. We report robust acoustic displays during aggressive interactions for a laboratory colony of Danionella dracula, a relatively recently discovered miniature and transparent species of teleost fish closely related to zebrafish (Danio rerio). Males produce bursts of pulsatile, click-like sounds and a distinct postural display, extension of a hypertrophied lower jaw, during aggressive but not courtship interactions. Females lack a hypertrophied lower jaw and show no evidence of sound production or jaw extension in such contexts. Novel pairs of size-matched or -mismatched males were combined in resident-intruder assays where sound production and jaw extension could be linked to individuals. Resident males produce significantly more sound pulses and extend their jaw more often than intruders in both dyad contexts, and relatively larger males are significantly more sonic and exhibit more jaw extensions in size-mismatched pairs. The majority of highest sound producers in both contexts also show increased jaw extension during periods of heightened sonic activity. These studies firmly establish D. dracula as a sound-producing species that modulates both acoustic and postural displays during aggressive interactions based on either residency or body size, providing a foundation for further investigating the role of multimodal displays in a new model clade for neurogenomic studies of aggression, courtship, and other social interactions.
Real-time motion monitoring improves functional MRI data quality in infants
Authors: D’Andrea Carolina Badke , Kenley Jeanette K. , Montez David F. , Mirro Amy E. , Miller Ryland L. , Earl Eric A. , Koller Jonathan M. , Sung Sooyeon , Yacoub Essa , Elison Jed T. , Fair Damien A. , Dosenbach Nico U.F. , Rogers Cynthia , Smyser Christopher D. , Greene Deanna J.
Published: November 2021

Imaging the infant brain with MRI has improved our understanding of early stages of neurodevelopment. However, head motion during MRI acquisition is detrimental to both functional and structural MRI scan quality. Though infants are commonly scanned while asleep, they commonly exhibit motion during scanning, causing data loss. Our group has shown that providing MRI technicians with real-time motion estimates via Framewise Integrated Real-Time MRI Monitoring (FIRMM) software helps obtain high-quality, low motion fMRI data. By estimating head motion in real time and displaying motion metrics to the MR technician during an fMRI scan, FIRMM can improve scanning efficiency. Hence, we compared average framewise displacement (FD), a proxy for head motion, and the amount of usable fMRI data (FD ≤ 0.2mm) in infants scanned with (n = 407) and without FIRMM (n = 295). Using a mixed-effects model, we found that the addition of FIRMM to current state-of-the-art infant scanning protocols significantly increased the amount of usable fMRI data acquired per infant, demonstrating its value for research and clinical infant neuroimaging.
Deep learning methods for designing proteins scaffolding functional sites
Authors: Wang Jue , Lisanza Sidney , Juergens David , Tischer Doug , Anishchenko Ivan , Baek Minkyung , Watson Joseph L. , Chun Jung Ho , Milles Lukas F. , Dauparas Justas , Expòsit Marc , Yang Wei , Saragovi Amijai , Ovchinnikov Sergey , Baker David
Published: November 2021

Current approaches to de novo design of proteins harboring a desired binding or catalytic motif require pre-specification of an overall fold or secondary structure composition, and hence considerable trial and error can be required to identify protein structures capable of scaffolding an arbitrary functional site. Here we describe two complementary approaches to the general functional site design problem that employ the RosettaFold and AlphaFold neural networks which map input sequences to predicted structures. In the first “constrained hallucination” approach, we carry out gradient descent in sequence space to optimize a loss function which simultaneously rewards recapitulation of the desired functional site and the ideality of the surrounding scaffold, supplemented with problem-specific interaction terms, to design candidate immunogens presenting epitopes recognized by neutralizing antibodies, receptor traps for escape-resistant viral inhibition, metalloproteins and enzymes, and target binding proteins with designed interfaces expanding around known binding motifs. In the second “missing information recovery” approach, we start from the desired functional site and jointly fill in the missing sequence and structure information needed to complete the protein in a single forward pass through an updated RoseTTAFold trained to recover sequence from structure in addition to structure from sequence. We show that the two approaches have considerable synergy, and AlphaFold2 structure prediction calculations suggest that the approaches can accurately generate proteins containing a very wide array of functional sites.
Individual exploration and selective social learning: Balancing exploration-exploitation trade-offs in collective foraging
Authors: Garg Ketika , Kello Christopher T. , Smaldino Paul E.
Published: November 2021

Search requires balancing exploring for more options and exploiting the ones previously found. Individuals foraging in a group face another trade-off: whether to engage in social learning to exploit the solutions found by others or to solitarily search for unexplored solutions. Social learning can better exploit learned information and decrease the costs of finding new resources, but excessive social learning can lead to over-exploitation and too little exploration for new solutions. We study how these two trade-offs interact to influence search efficiency in a model of collective foraging under conditions of varying resource abundance, resource density, and group size. We modeled individual search strategies as Lévy walks, where a power-law exponent (µ) controlled the trade-off between exploitative and explorative movements in individual search. We modulated the trade-off between individual search and social learning using a selectivity parameter that determined how agents responded to social cues in terms of distance and likely opportunity costs. Our results show that social learning is favored in rich and clustered environments, but also that the benefits of exploiting social information are maximized by engaging in high levels of individual exploration. We show that selective use of social information can modulate the disadvantages of excessive social learning, especially in larger groups and when individual exploration is limited. Finally, we found that the optimal combination of individual exploration and social learning gave rise to trajectories withµ ≈2 and provide support for the general optimality of such patterns in search. Our work sheds light on the interplay between individual search and social learning, and has broader implications for collective search and problem-solving.
Epigenetic regulation of translation repression in ferroptosis, and a role of Alternative splicing and tRNA methylation
Authors: Rashad Sherif , Saigusa Daisuke , Zhou Yuan , Zhang Liyin , Tominaga Teiji , Niizuma Kuniyasu
Published: November 2021

Ferroptosis is a non-apoptotic cell death mechanism characterized by the production of lipid peroxides. Ferroptosis plays important roles in many diseases such as cancer and neurodegenerative diseases. While many effectors in the ferroptosis pathway have been mapped, its epigenetic and epitranscriptional regulatory processes are not yet fully understood. Ferroptosis can be induced via system xCT inhibition (Class I) or GPX4 inhibition (Class II). Previous works have revealed important differences in cellular response to Class I and Class II ferroptosis inducers. Importantly, blocking mRNA transcription or translation appears to protect cells against Class I ferroptosis inducing agents but not Class II. Understanding these subtle differences is important in understanding ferroptosis as well as in developing therapeutics based on ferroptosis for various diseases. In this work, we examined the impact of blocking transcription (via Actinomycin D) or translation (via Cycloheximide) on Erastin (Class I) or RSL3 (Class II) induced ferroptosis. Blocking transcription or translation protected cells against Erastin but was detrimental against RSL3. Cycloheximide led to increased levels of GSH alone or when co-treated with Erastin and the activation of the reverse transsulfuration pathway. RNA sequencing analysis revealed an important and unexplored role of Alternative splicing (AS) in regulating ferroptosis stress response and mRNA translation repression. Our results indicated that translation repression is protective against Erastin but detrimental against RSL3. We tested this theory in Alkbh1 overexpressing glioma cells. Alkbh1 demethylates tRNA and represses translation and is associated with worse outcome in glioma patients. Our results showed that Alkbh1 overexpression protected glioma cells against Erastin but was detrimental against RSL3.
Ensemble cryo-electron microscopy reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex
Authors: Chen James , Wang Qi , Malone Brandon , Llewellyn Eliza , Pechersky Yakov , Maruthi Kashyap , Eng Ed T. , Perry Jason K. , Campbell Elizabeth A. , Shaw David E. , Darst Seth A.
Published: November 2021

The SARS-CoV-2 nonstructural proteins coordinate genome replication and gene expression. Structural analyses revealed the basis for coupling of the essential nsp13 helicase with the RNA dependent RNA polymerase (RdRp) where the holo-RdRp and RNA substrate (the replication-transcription complex, or RTC) associated with two copies of nsp13 (nsp132-RTC). One copy of nsp13 interacts with the template RNA in an opposing polarity to the RdRp and is envisaged to drive the RdRp backwards on the RNA template (backtracking), prompting questions as to how the RdRp can efficiently synthesize RNA in the presence of nsp13. Here, we use cryo-electron microscopy and molecular dynamics simulations to analyze the nsp132-RTC, revealing four distinct conformational states of the helicases. The results suggest a mechanism for the nsp132-RTC to turn backtracking on and off, using an allosteric mechanism to switch between RNA synthesis or backtracking in response to stimuli at the RdRp active site.
Serum from COVID-19 patients early in the pandemic shows limited evidence of cross-neutralization against variants of concern
Authors: Griffin Amanda J. , O’Donnell Kyle L. , Shifflett Kyle , Lavik John-Paul , Russell Patrick M. , Zimmerman Michelle K. , Relich Ryan F. , Marzi Andrea
Published: November 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in a variety of clinical symptoms ranging from no or mild to severe disease. Currently, there are multiple postulated mechanisms that may push a moderate to severe disease into a critical state. Human serum contains abundant evidence of the immune status following infection. Cytokines, chemokines, and antibodies can be assayed to determine the extent to which a patient responded to a pathogen. We examined serum and plasma from a cohort of patients infected with SARS-CoV-2 early in the pandemic and compared them to negative-control sera. Cytokine and chemokine concentrations varied depending on the severity of infection, and antibody responses were significantly increased in severe cases compared to mild to moderate infections. Neutralization data revealed that patients with high titers against an early 2020 isolate had detectable but limited neutralizing antibodies against newly circulating SARS-CoV-2 variants of concern. This study highlights the potential of re-infection for recovered COVID-19 patients.
Myocarditis After mRNA-1273 Vaccination: A Population-Based Analysis of 151 Million Vaccine Recipients Worldwide
Authors: Straus Walter , Urdaneta Veronica , Esposito Daina B. , Mansi James A. , Rodriguez Cesar Sanz , Burton Paul , Vega José M.
Published: November 2021

Background

Growing evidence indicates a causal relationship between SARS-CoV-2 infection and myocarditis. Post-authorization safety data have also identified myocarditis as a rare safety event following mRNA COVID-19 vaccination, most notably among younger adult males and after dose 2. To further evaluate the potential risk after vaccination, we queried the Moderna global safety database to assess the occurrence of myocarditis/myopericarditis among mRNA-1273 vaccine recipients worldwide since first international Emergency Use Authorization issuance.

Methods

Reports of myocarditis/myopericarditis entered into the Moderna global safety database from December 18, 2020 to September 30, 2021 were reviewed and classified based on the Brighton Collaboration case definition. The cumulative observed occurrence of myocarditis/myopericarditis was assessed by calculating the reported rate after any known dose of mRNA-1273 according to age and sex. This reporting rate was compared to a population-based incidence rate (US military) to calculate observed-to-expected rate ratios (RR).

Results

Through September 30, 2021, a total of 1,439 cases of myocarditis/myopericarditis among approximately 151.1 million mRNA-1273 vaccine recipients were reported to the Moderna global safety database. The overall reporting rate among all vaccine recipients was 0.95 cases per 100,000 vaccine recipients, which was lower than the expected rate from the reference population (2.12 cases per 100,000 vaccine recipients; RR [95% CI]: 0.45 [0.42–0.48]). When stratified by sex and age, observed rates were highest for males aged ≤39 years, particularly those aged 18–24 years (7.40 cases per 100,000 vaccine recipients), which was higher than expected (RR [95% CI]: 3.49 [2.88–4.22]). For males and females aged <18 years, the rate ratio for myocarditis was 1.05 (95% CI, 0.52–2.13) and 0.21 (95% CI, 0.04–0.94), respectively. When considering only cases occurring within 7 days after vaccination, the observed rate was highest for males aged 18–24 years after dose 2 (4.9 cases per 100,000 doses administered).

Conclusion

Myocarditis/myopericarditis accounted for 0.4% of adverse events reported to the Moderna global safety database after mRNA-1273 vaccination; rates were higher than expected in males aged 18–24 years, with most occurring by 7 days after dose 2, but were not higher than expected for the overall population of vaccine recipients and were lower than that observed in individuals infected with SARS-CoV-2.
The primacy of meeting public university students’ essential needs during the COVID-19 pandemic: a new higher education priority
Authors: Manze Meredith , Lattanzio Anna , Larsen Jenna , Keegan Julia , Freudenberg Nick , Jones Heidi E.
Published: November 2021

Objectives

We investigated the holistic experiences of university students during the pandemic.

Participants

38 students in a public university system in New York City (NYC) purposively selected from neighborhoods highly affected by the pandemic based on level of self-reported impact

Methods

We conducted virtual in-depth interviews from May to August 2021 and analyzed data using thematic coding and constant comparison techniques informed by grounded theory.

Results

Financial and social support systems, such as governmental and school resources, were critical to addressing essential needs and allowing students to persist. For those whose essential needs were met, faculty members’ flexibility and students’ experience with online learning were central to their academic success.

Conclusions

Institutions of higher education should strengthen financial and social support systems to meet students’ essential needs. Academic policies to bolster online pedagogy and faculty’s flexibility can facilitate student retention and completion.
Abolishing the prelamin A ZMPSTE24 cleavage site leads to progeroid phenotypes with near-normal longevity in mice
Authors: Wang Yuexia , Shiladardi Khurts , Hsu Trunee , Odinammadu Kamsi O. , Maruyama Takamitsu , Wu Wei , Lin Chyuan-Sheng , Damoci Christopher B. , Spear Eric D. , Shin Ji-Yeon , Hsu Wei , Michaelis Susan , Worman Howard J.
Published: November 2021

Prelamin A is a farnesylated precursor of lamin A, a nuclear lamina protein. Accumulation of the farnesylated prelamin A variant progerin, with an internal deletion including its processing site, causes Hutchinson-Gilford progeria syndrome. Loss of function mutations inZMPSTE24, which encodes the prelamin A processing enzyme, lead to accumulation of full-length farnesylated prelamin A and cause related progeroid disorders. Some data suggest that prelamin A also accumulates with physiological aging.Zmpste24-/-mice die young, at ~20 weeks. Because ZMPSTE24 has functions in addition to prelamin A processing, we generated a mouse model to examine effects solely due to the presence of permanently farnesylated prelamin A. These mice have an L648R amino acid substitution in prelamin A that blocks ZMPSTE24-catalyzed processing to lamin A. TheLmnaL648R/L648Rmice express only prelamin and no mature protein. Notably, nearly all survive to 65-70 weeks, with approximately 40% of male and 75% of femaleLmnaL648R/L648Rmice having near-normal lifespans of 90 weeks (almost 2 years). Starting at ~10 weeks of age, LmnaL648R/L648Rmice of both sexes have lower body masses and body fat than controls. By ~20-30 weeks of age, they exhibit detectable cranial, mandibular and dental defects similar to those observed inZmpste24-/-mice, and have decreased vertebral bone density compared to age- and sex-matched controls. Cultured embryonic fibroblasts fromLmnaL648R/L648Rmice have aberrant nuclear morphology that is reversible by treatment with a protein farnesyltransferase inhibitor. These novel mice provide a robust model to study the effects of farnesylated prelamin A during physiological aging.
Regulating peroxisome-ER contacts via the ACBD5-VAPB tether by FFAT motif phosphorylation and GSK3β
Authors: Kors Suzan , Hacker Christian , Bolton Chloe , Maier Renate , Reimann Lena , Kitchener Emily J.A. , Warscheid Bettina , Costello Joseph L. , Schrader Michael
Published: November 2021

Peroxisomes and the endoplasmic reticulum (ER) cooperate in cellular lipid metabolism. They form membrane contacts through interaction of the peroxisomal membrane protein ACBD5 [acyl-coenzyme A-binding domain protein 5] and the ER-resident protein VAPB [vesicle-associated membrane protein-associated protein B]. ACBD5 binds to the major sperm protein domain of VAPB via its FFAT-like [two phenylalanines (FF) in an acidic tract] motif. However, molecular mechanisms, which regulate formation of these membrane contact sites, are unknown. Here, we reveal that peroxisome-ER associations via the ACBD5-VAPB tether are regulated by phosphorylation. We show that ACBD5-VAPB binding is phosphatase-sensitive and identify phosphorylation sites in the flanking regions and core of the FFAT-like motif, which alter interaction with VAPB and thus, peroxisome-ER contact sites differently. Moreover, we demonstrate that GSK3β [glycogen synthase kinase-3 beta] regulates this interaction. Our findings reveal for the first time a molecular mechanism for the regulation of peroxisome-ER contacts in mammalian cells and expand the current model of FFAT motifs and VAP interaction.

Kors et al. reveal that peroxisome-ER associations via the ACBD5-VAPB tether are regulated by phosphorylation and GSK3β in mammalian cells. Phosphorylation sites in the FFAT-like motif of ACBD5 affect the binding to VAPB and thus, peroxisome-ER contact sites, differently.
Looking for Tumor Specific Transcription Factors. Study of Promoters in Silico
Authors: Kashkin K.N.
Published: November 2021

This study supplements earlier received experimental data using modern databases. Previously tumor-specific activity of several human native and chimeric promoters was demonstrated. Here we compared tumor-specific promoters with promoters of housekeeping genes by the presence of recognition profiles for transcription factors in DNA sequences of the promoters. A number of transcription factor recognition profiles have been identified, the presence of which in promoters may indicate the tumor specificity of the promoters. Transcription factors which may directly regulate promoters of genes involved in cell proliferation and carcinogenesis were revealed by pathway analysis. The results of the study may help in studying the peculiarities of gene transcription in tumors and in the search for or the creation of tumor-specific promoters for cancer gene therapy.
Preclinical studies for plant-based oral enzyme replacement therapy (Oral-ERT) in Pompe disease knockout mice with transgenic tobacco seeds expressing human GAA (tobrhGAA)
Authors: Martiniuk Frank , Mack Adra , Martiniuk Justin , Miller Shoreh , Voronin Gregory O. , Reimer David , Rossi Nancy , Bird Leslie Sheppard , Saleh Sussan , Gupta Ruby , Nigro Mariel , Meinke Peter , Schoser Benedikt , Wu Feng , Kambitsis Angelo , Arvanitopoulos John , Arvanitopoulos Elena , Tchou-Wong Kam-Meng
Published: November 2021

Genetic deficiency of acid α-glucosidase (GAA) results in glycogen storage disease type II (GSDII) or Pompe disease (PD) encompassing at least four clinical subtypes of varying severity (infantile; childhood, juvenile and late onset). Our objective is to develop an innovative and affordable approach for enzyme replacement therapy (ERT) via oral administration (Oral-ERT) to maintain a sustained, therapeutic level of enzyme on a daily basis to improve efficacy of treatment and quality of life for people living with Pompe disease. A consensus at a 2019 US Acid Maltase Deficiency (AMDA) conference suggested that a multi-pronged approach including gene therapy, diet, exercise, etc. must be evaluated for a successful treatment of Pompe disease. Tobacco seeds contain the metabolic machinery that is more compatible with mammalian glycosylation-phosphorylation and processing. Previously, we have shown that a lysate from transgenic tobacco seeds expressing human GAA (tobrhGAA) was enzymatically active and can correct enzyme deficiency in cultured PD cells and in adult lymphocytes of Pompe patients and in vivo in disease-relevant tissues in GAA knockout (KO) mice when administered IP.

We have extended these pre-clinical studies in PD knockout (KO) mice with ground tobrhGAA seeds that supports proof-of-concept for Oral-ERT for future clinical trials. Briefly in GAA KO mice, Oral-ERT with ground tobrhGAA seeds showed significant reversal of fore-limb and hind-limb muscle weakness, increased motor coordination/balance/strength and mobility, improved spontaneous learning, increased GAA baseline activity in tissues, reduced glycogen in tissues and negible serum titers to GAA. Pharmacokinetics showed maximum serum GAA concentration (Cs) at 8-10 hr and peak urine excretion at 10-12 hr. The tobrhGAA was taken up in PD fibroblast, lymphoid and myoblast cells. Enzyme kinetics compared favorably or superior to placental hGAA, plus alglucosidase alfa or other rhGAAs for Km, Vmax, pH optima, thermal heat stability and IC50 for inhibitors. The tobrhGAA in seeds was extremely stable stored for 15 years at room temperature. NGS-genome sequencing of the tobrhGAA and wild-type plants and RNA expression profiles was performed and will be posted on our website. Thus, Oral-ERT with ground tobrhGAA seeds is an innovative approach that overcomes some of the challenges of alglucosidase alfa-ERT and provides a more effective, safe and significantly less expensive treatment.
ORP5 AND ORP8 ORCHESTRATE LIPID DROPLET BIOGENESIS AND MAINTENANCE AT ER-MITOCHONDRIA CONTACT SITES
Authors: Guyard Valentin , Monteiro-Cardoso Vera F. , Omrane Mohyeddine , Sauvanet Cécile , Houcine Audrey , Boulogne Claire , Mbarek Kalthoum Ben , Vitale Nicolas , Facklaris Orestis , El Khallouki Naima , Thiam Abdou Rachid , Giordano Francesca
Published: November 2021

Lipid droplets (LDs) are the primary organelles of lipid storage, buffering energy fluctuations of the cell. They store neutral lipids in their core that is surrounded by a protein-decorated phospholipid monolayer. LDs arise from the Endoplasmic Reticulum (ER). The ER-protein seipin, localizing at ER-LD junctions, controls LD nucleation and growth. However, how LD biogenesis is spatially and temporally coordinated remains elusive. Here, we show that the lipid transfer proteins ORP5 and ORP8 control LD biogenesis at Mitochondria-Associated ER Membrane (MAM) subdomains, enriched in phosphatidic acid. We found that ORP5/8 regulate seipin recruitment to these MAM-LD contacts, and their loss impairs LD biogenesis. Importantly, the integrity of ER-mitochondria contact sites is crucial for the ORP5/8 function in regulating seipin-mediated LD biogenesis. Our study uncovers an unprecedented ORP5/8 role in orchestrating LD biogenesis at MAMs and brings novel insights into the metabolic crosstalk between mitochondria, ER, and LDs at membrane contact sites.

HIGHLIGHTS

ORP5 and ORP8 localize at MAM subdomains where LDs originate.

Phosphatidic acid is enriched in MAM subdomains that are the birthplace of LDs.

ORP5 and ORP8 knockdown impairs LD biogenesis.

ORP5 and ORP8 regulate seipin recruitment to MAM-LD contact sites.