bluuebunny/crossref_metadata_2025 huggingface dataset:
Troubles in Prague Escalate
Authors: Akkerman Nadine
Published: December 2021

Although the Bohemian princes had rallied behind their new king, those of the Empire as a whole, Protestant and Catholic alike, agreed that Frederick should abdicate. Frederick refused on matters of law, but the Emperor saw only recalcitrance, and four armies were raised against Frederick. Elizabeth asked her father for help but even though he sent Sir Andrew Gray with soldiers to aid her, he stopped short of the unequivocal support she demanded – and Elizabeth blamed the Spanish faction at his court. James continued to make diplomatic overtures, but a miscalculation on his part allowed the Spanish to attack the Palatinate with impunity while the Protestant Union was effectively neutralised. In September of 1620, Elizabeth found herself alone in Prague as the situation became increasingly desperate, and she sent her eldest son, Frederick Henry, away for his own safety. Frederick pleaded with her to leave Prague as well but she refused to abandon her subjects. In November 1620, Fredrick’s armies were crushed at the Battle of White Mountain and he and Elizabeth were forced to flee, leaving many of their possessions behind when the wagon train carrying them was attacked by rogue members of their own forces. Elizabeth fled cradling one son, Rupert, in her arms while pregnant with another, Maurice, to whom she gave birth while on the run. As support for the deposed King and Queen of Bohemia melted away, they made for Rotterdam in the United Provinces and home of Frederick’s cousin, Maurice, Prince of Orange.
A Widow’s Weeds
Authors: Akkerman Nadine
Published: December 2021

Frederick V’s unexpected death was accompanied by fear that Elizabeth’s grief would overcome her, and that the Palatinate would never be recovered from the Swedes. Charles I sent for her, but she refused the invitation, citing familial obligations. Now a widow, Elizabeth needed to fight for her children to save the Palatinate alone, and asserted her position through art and diplomacy, but she had a rival – Amalia von Solms, once her lady-in-waiting, now Princess of Orange. The two courts struggled for dominance. Elizabeth created a cult of widowhood, dressing in black for the rest of her life, and from this moment would fight her battles via her secretaries, also absorbing Frederick's secretariat into her own, doubling its size. The Swedes demanded 6,000 Imperial dollars for her dower Frankenthal as compensation for war expenses. Sir Francis Nethersole, her secretary for foreign affairs, attempted to raise a voluntary contribution in England for this purpose. Charles, troubled that this contribution was not kept more low-key and afraid public knowledge would put pressure upon him to recall parliament, attacked Nethersole. Nethersole was first pardoned, but thereafter incarcerated when Elizabeth again tried to raise money to buy back the Palatinate in order to avoid embracing the French protection. She was forced to dismiss Nethersole to obtain his release. Her supporters such as Sir Thomas Roe felt threatened and her other secretaries became pariahs at the Stuart court. By incapacitating her secretaries, Charles drew the sting from her party's implicit challenge to his authority.
Undesirable Matches, Unfortunate Endings
Authors: Akkerman Nadine
Published: December 2021

Elizabeth’s son Edward married Anne de Gonzaga, a French-Italian noblewoman he met while at the French court, to great scandal, not least because, in the process, he converted to Catholicism. In The Hague, the conflict between Elizabeth and Amalia continued apace, as both sought to win the hand of Frederick William, Elector of Brandenburg for their respective daughters Louise Hollandine and Louise Henriette – Amalia won this round. The House of Commons agreed to renew Elizabeth’s allowance if she dismiss Johnson (Laud had recently lost his head) and replace him with a chaplain of their choosing, William Cooper. Elizabeth did so willingly, but secretly engaged another, George Morley. Charles I was taken prisoner by Parliament, and Rupert and Maurice both fled the country. In The Hague, Elizabeth’s son Philip attracted outrage and his mother’s ire by murdering her court favourite, Count L’Espinay. Descartes and Elisabeth discuss the nature of the passions, and whether an individual can be held responsible for their actions when in their grip. Elizabeth cannot forgive Philip, however, and his sister’s attempts to mediate for him lead to the two women falling out – Elisabeth is sent to German relatives. The Prince of Orange, Frederick Henry, carries out his final military movements before his death in March 1647. The new Prince, William II, opposed his mother Amalia over the Peace of Westphalia. Elizabeth’s nephew Charles Stuart arrived in The Hague and the king her brother is executed by Parliament.
AKEBIA THERAPEUTICS INC v FIBROGEN, INC
Authors:   Patents Court
Published: December 2021

H1 Patents – European patents – Pharmaceuticals – Treatment of anaemia – Revocation – Infringement – Construction – Obviousness – Obvious to try – Reasonable expectation of success – Hindsight – Expert evidence – Sequential unmasking – Insufficiency – Excessive claim breadth – Uncertainty – Identification of technical contribution – Principles of general application – Plausibility – Undue burden – AgrEvo obviousness – Equivalence – File prosecution history – Process limited product claims – Indirect infringement – Means relating to an essential element of the invention – Whether suitable for putting and intended to put invention into effect – “Off-label” use – State of mind of defendants – Intentions of prescribing clinicians – Quia timet claims – Whether stay of infringement claim appropriate
The association of acculturative stress with self-reported sleep disturbance and sleep duration among Asian Americans
Authors: Lee Sunmin , Ryu Soomin , Lee Grace E , Kawachi Ichiro , Morey Brittany N , Slopen Natalie
Published: December 2021

Study Objectives

This study aims to examine associations between acculturative stress—defined as the psychological impact, or stress reaction, of adapting to a new cultural context—and self-reported sleep outcomes among Chinese and Korean immigrants in the United States.

Methods

In this cross-sectional study, acculturative stress was assessed using a 9-item scale, and sleep disturbance was measured using the 8-item scale. Sleep duration was self-reported. Poisson and linear regression analyses were conducted to examine the associations between acculturative stress, sleep disturbance, and sleep duration.

Results

Our sample consists of 400 participants (females: 52%, Chinese: 50%, Koreans: 50%, the mean of age = 58.4). 81.8% of them were classified as having no sleep disturbance, whereas 18.2% were classified as having sleep disturbance. Poisson models revealed that greater acculturative stress was associated with a higher prevalence of sleep disturbance (Prevalence Ratio (PR): 1.18, 95% confidence interval (CI): 1.06% to 1.31%). In linear models, a one-unit increase in acculturative stress was associated with 0.08 hr less sleep (p < .05). Interaction tests indicated effect modification for sleep disturbance by sex and ethnic identity: only women had a significant association between acculturative stress and sleep disturbance (PR: 1.30; 95% CI: 1.13 to 1.49), while the association was significant for individuals identifying as “very Asian” (PR: 1.21; 95% CI: 1.08 to 1.35), but not for those identifying as “mostly Asian” or “bicultural/western”.

Conclusions

If findings are replicated, we suggest developing intervention programs for Asian immigrants to minimize acculturative stress and bolster protective factors that decrease the risk for poor sleep outcomes.

Information on Clinical Trial:

Name: Screening To Prevent ColoRectal Cancer (STOP CRC) among At-Risk Asian American Primary Care Patients

NCT Number: NCT03481296

URL: https://clinicaltrials.gov/ct2/show/NCT03481296?term=Sunmin+Lee&draw=2&rank=1
Effects of shear force reduction during mechanical testing and day-to-day variation on stiffness of commercial prosthetic feet: a technical note
Authors: Halsne Elizabeth G. , Turner Anne T. , Curran Carl S. , Hansen Andrew H. , Hafner Brian J. , Caputo Joshua M. , Morgenroth David C.
Published: December 2021

Background:

Mechanical testing is the principal method used to quantify properties of commercial prosthetic feet in a controlled and standardized manner. To test feet in a mechanical testing machine without overconstraining the system, tangential shear forces must be minimized. However, there is scant published information comparing techniques for reducing shear forces during mechanical testing. Furthermore, there are no data on variability in linear stiffness across testing sessions.

Objectives:

To compare techniques for reducing shear forces during mechanical testing of prosthetic feet and to evaluate variation in linear stiffness across testing sessions.

Study design:

Repeated measures.

Technique:

Force–displacement data were collected at two pylon progression angles, one for the forefoot and one for the heel, and compared across three conditions: roller plate (RoPl), low-friction interface on the shoe (SB), and no method for reducing shear forces (NoSB). Data were collected for a range of commercial prosthetic foot models and sizes. Select data were collected over multiple days to assess variation over test sessions.

Results:

Differences in stiffness between RoPl and SB test conditions ranged from −0.9% to +2.6% across foot models. By contrast, differences between RoPl and no method for reducing shear conditions ranged from −2.9% to +14.6%. Differences in linear stiffness between test sessions ranged from −2.2% to +3.6%.

Conclusions:

Methods for reducing shear force in this study demonstrated roughly equivalent effects. Thus, a low-friction interface may be used as a less expensive and less complex method for reducing shear force in prosthetic foot testing. In addition, mechanical testing results were relatively consistent across multiple test sessions, lending confidence to test consistency.
Synaptosome microRNAs regulate synapse functions in Alzheimer’s disease
Authors: Kumar Subodh , Orlov Erika , Gowda Prashanth , Bose Chhanda , Swerdlow Russell H. , Lahiri Debomoy K. , Reddy P. Hemachandra
Published: December 2021

MicroRNAs (miRNAs) are found in nerve terminals, synaptic vesicles, and synaptosomes, but it is unclear whether synaptic and cytosolic miRNA populations differ in Alzheimer’s disease (AD) or if synaptosomal miRNAs affect AD synapse activity. To address these questions, we generated synaptosomes and cytosolic fractions from postmortem brains of AD and unaffected control (UC) samples and analyzed them using a global Affymetrix miRNAs microarray platform. A group of miRNAs significantly differed (p<0.0001) with high fold changes variance (+/- >200-fold) in their expressions in different comparisons- 1) UC synaptosome vs UC cytosol, 2) AD synaptosomes vs AD cytosol, 3) AD cytosol vs UC cytosol, and 4) AD synaptosomes vs UC synaptosomes. MiRNAs data analysis revealed that some potential miRNAs were consistently different across sample groups. These differentially expressed miRNAs were further validated using AD postmortem brains, brains of APP transgenic (Tg2576), Tau transgenic (P301L), and wild type mice. The miR-501-3p, miR-502-3p and miR-877-5p were identified as potential synaptosomal miRNAs upregulated with disease progression based on AD Braak stages. Gene Ontology Enrichment and Ingenuity Pathway Analysis of synaptosomal miRNAs showed the involvement of miRNAs in nervous system development, cell junction organization, synapse assembly formation, and function of GABAergic synapse. This is the first description of synaptic versus cytosolic miRNAs in AD and their significance in synapse function.
The grape MYB24 mediates the coordination of light-induced terpene and flavonol accumulation in response to berry anthocyanin sunscreen depletion
Authors: Chen Zhang , Zhanwu Dai , Thilia Ferrier , Luis Orduña , Antonio Santiago , Arnau Peris , Darren Wong , Christian Kappel , Stefania Savoi , Rodrigo Loyola , Alessandra Amato , Bartosz Kozak , Miaomiao Li , David Carrasco , Carlos Meyer , Carmen Espinoza , Ghislaine Hilbert , Rosa Figueroa-Balderas , Dario Cantu , Rosa Arroyo , Patricio Arce-Johnson , Patricia Claudel , Eric Duchêne , Carol Huang Shao-shan , Diego Castellarin Simone , Battista Tornielli Giovanni , Francois Barrieu , Tomás Matus J.
Published: December 2021

The presence of naturally-occurring color mutants in plants has permitted the identification of many regulatory genes implicated in the synthesis of discrete metabolic compounds, mostly anthocyanins and carotenoids. Conversely, transcription factors that coordinate more than one specialized metabolic pathway seem challenging to screen from a forward genetics’ perspective. We explored the relationship between different branches of the phenylpropanoid and isoprenoid pathways while examining an infrequent berry skin color variegation in grapevine. Red and white berry skin sections were compared at the genetic, transcriptomic and metabolomic levels showing that, as in most cultivated white grape varieties, the uncolored skin section convened the non-functional alleles of the anthocyanin regulators MYBA1 and MYBA2, explaining the lack of pigments. In contrast, light-responsive flavonols and monoterpenes increased in anthocyanin-depleted areas. We disclosed an enrichment of the flavonol, terpene and carotenoid pathways among up-regulated genes from white-skin sections, accompanied by increased expressions of flavonol regulators and the still uncharacterized MYB24 gene. We used DAP-seq to examine the in vitro binding of affinity-purified MYB24 protein to genomic DNA and demonstrated its binding in the promoter regions of terpene (22) and carotenoid (6) genes, in addition to more than 30 photosynthesis and light-response genes, including the flavonol-regulator HY5 homologue (HYH). We confirmed the activation of TPS35 and HYH promoter:luciferase reporters in the presence of MYB24 and the grape bHLH MYC2, all of which correlate in their higher expression in white skin variegated sections. The integration of several datasets allowed to define a list of high confidence targets, suggesting MYB24 as a modulator of light responses including the synthesis of flavonoids (flavonols) and isoprenoids (terpenes, and putatively carotenoids). The correspondence between MYB24 and monoterpenes in all conditions surveyed implies that this regulatory network is broadly triggered towards berry ripening, and that the absence of anthocyanin sunscreens accelerates its activation most likely in a dose-dependent manner due to increased radiation exposure.
Diverse and rapidly evolving viral strategies modulate arthropod vector gene expression
Authors: Eliash Nurit , Suenaga Miyuki , Mikheyev Alexander S.
Published: December 2021

Vector-borne viral diseases threaten human and wildlife worldwide. Vectors are often viewed as a passive syringe injecting the virus, however to survive, replicate and spread, viruses must manipulate vector biology. While most vector-borne viral research focuses on vectors transmitting a single virus, in reality vectors often carry diverse viruses. Yet how viruses affect the vectors remains poorly understood. Here we focused on the varroa mite, an emergent parasite that vectors over 20 honey bee viruses, and has been responsible for colony collapses worldwide, as well as changes in global viral populations. Co-evolution of the varroa and the viral community makes it possible to investigate whether viruses affect vector gene expression, and whether these interactions affect viral epidemiology. Using a large set of available varroa transcriptomes we identified how abundances of individual viruses affect the vector’s transcriptional network. Perhaps surprisingly, we found no evidence of competition between viruses, but rather that some virus abundances are positively correlated. Furthermore, we found a strong correlation between the extent to which a virus interacts with the vector’s gene expression and co-occurrence with other viruses, suggesting that interactions with the vector affect epidemiology. We experimentally validated this observation by silencing candidate genes using RNAi and found that reduction in varroa gene expression was accompanied by a change in viral load. Combined, the meta-transcriptomic analysis and experimental results shed light on the mechanism by which viruses interact with each other and with their vector to shape the disease course.
Effects of ozone on sickness and depressive-like behavioral and biochemical phenotypes and their relations to serum amyloid A and kynurenine in blood
Authors: Baumann Kristen K. , Liang W. Sandy , Quaranta Daniel V. , Wilson Miranda L. , Asrat Helina S. , Thysell Jarl A. , Sarchi Angelo V. , Banks William A. , Erickson Michelle A.
Published: December 2021

Ozone (O3) is an air pollutant which primarily damages the lungs, but growing evidence supports that O3exposure can also affect the brain. Serum amyloid A (SAA) and kynurenine have been identified as circulating factors that are upregulated by O3, and both can contribute to depressive-like behaviors in mice. However, little is known about the relations of O3exposure to sickness and depressive-like behaviors in experimental settings. In this study, we evaluated O3dose-, time- and sex-dependent changes in circulating SAA in context of pulmonary inflammation and damage, sickness and depressive-like behavioral changes, and systemic changes in kynurenine and indoleamine 2,3-dioxygenase (IDO), an enzyme that regulates kynurenine production and contributes to inflammation-induced depressive-like behaviors. Our results in Balb/c and CD-1 mice showed that 3ppm O3, but not 2 or 1ppm O3, caused elevations in serum SAA and pulmonary neutrophils, and these responses resolved by 48 hours. Sickness and depressive-like behaviors were observed at all O3doses (1-3ppm), although the detection of certain behavioral changes varied by dose. We also found thatIdo1mRNA expression was increased in the brain and spleen 24 hours after 3ppm O3, and that kynurenine was increased in blood. Together, these findings indicate that acute O3exposure induces transient symptoms of sickness and depressive-like behaviors which may occur in the presence or absence of overt pulmonary neutrophilia and systemic increases of SAA. We also present evidence that the IDO/kynurenine pathway is upregulated systemically following an acute exposure to O3in mice.
Disrupting ATXN1 Nuclear Localization in a Knock-in SCA1 Mouse Model Improves a Spectrum of SCA1-Like Phenotypes and their Brain Region Associated Transcriptomic Profiles
Authors: Handler Hillary P. , Duvick Lisa , Mitchell Jason , Cvetanovic Marija , Reighard Molly , Soles Alyssa , Rainwater Orion , Serres Shannah , Nichols-Meade Tessa , Coffin Stephanie L. , You Yun , Ruis Brian , O’Callaghan Brennon , Henzler Christine , Zoghbi Huda Y. , Orr Harry T.
Published: December 2021

Spinocerebellar ataxia type 1 (SCA1) is a dominant trinucleotide repeat neurodegenerative disease characterized by motor dysfunction, cognitive impairment, and premature death. Degeneration of cerebellar Purkinje cells is a frequent and prominent pathological feature of SCA1. We previously showed that transport of ATXN1 to Purkinje cell nuclei is required for pathology, where mutant ATXN1 alters transcription. To examine the role of ATXN1 nuclear localization broadly in SCA1-like disease pathogenesis, CRISPR-Cas9 was used to develop a mouse with the amino acid alteration (K772T) in the nuclear localization sequence of the expanded ATXN1 protein.

Characterization of these mice indicates proper nuclear localization of mutant ATXN1 contributes to many disease-like phenotypes including motor dysfunction, cognitive deficits, and premature lethality. RNA sequencing analysis of genes whose expression was corrected to WT levels in Atxn1175QK772T/2Q mice indicates that transcriptomic aspects of SCA1 pathogenesis differ between the cerebellum, brainstem, cerebral cortex, hippocampus, and striatum.
Dopamine and GPCR-mediated modulation of DN1 clock neurons gates the circadian timing of sleep
Authors: Schlichting M. , Richhariya S. , Herndon N. , Ma D. , Xin J. , Lenh W. , Abruzzi K. , Rosbash M.
Published: December 2021

The metronome-like circadian regulation of sleep timing must still adapt to an uncertain environment. Recent studies in Drosophila indicate that neuromodulation not only plays a key role in clock neuron synchronization but also affects interactions between the clock network and brain sleep centers. We show here that the targets of neuromodulators, G-Protein Coupled Receptors (GPCRs), are highly enriched in the fly brain circadian clock network. Single cell sequencing indicates that they are not only differentially expressed but also define clock neuron identity. We generated a comprehensive guide library to mutagenize individual GPCRs in specific neurons and verified the strategy with a targeted sequencing approach. Combined with a behavioral screen, the mutagenesis strategy revealed a novel role of dopamine in sleep regulation by identifying two dopamine receptors and a clock neuron subpopulation that gate the timing of sleep.
Conditions for maintaining and eroding pseudo-overdominance and its contribution to inbreeding depression
Authors: Awad Diala Abu , Waller Donald
Published: December 2021

Classical models that ignore linkage predict that deleterious recessive mutations should purge or fix within inbred populations, yet inbred populations often retain moderate to high segregating load. True overdominance could generate balancing selection strong enough to sustain inbreeding depression even within inbred populations, but this is considered rare. However, arrays of deleterious recessives linked in repulsion could generate appreciable pseudo-overdominance that would also sustain segregating load. We used simulations to explore how long pseudo-overdominant (POD) zones persist once created (e.g., by hybridization between populations fixed for alternative mildly deleterious mutations). Balanced haplotype loads, tight linkage, and moderate to strong cumulative selective effects all serve to maintain POD zones. Tight linkage is key, suggesting that such regions are most likely to arise and persist in low recombination regions (like inversions). Selection and drift unbalance the load, eventually eliminating POD zones, but this process is quite slow under strong pseudo-overdominance. Background selection accelerates the loss of weak POD zones but reinforces strong ones in inbred populations by disfavoring homozygotes. Models and empirical studies of POD dynamics within populations help us understand how POD zones may allow the load to persist, greatly affecting load dynamics and mating systems evolution.
Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones
Authors: Koppes Erik A. , Johnson Marie A. , Moresco James J. , Luppi Patrizia , Lewis Dale W. , Stolz Donna B. , Diedrich Jolene K. , Yates John R. , Wek Ronald C. , Watkins Simon C. , Gollin Susanne M. , Park Hyun J. , Drain Peter , Nicholls Robert D.
Published: December 2021

Prader-Willi syndrome (PWS) is a multisystem disorder with neurobehavioral, metabolic, and hormonal phenotypes, caused by loss of expression of a paternally-expressed imprinted gene cluster. Prior evidence from a PWS mouse model identified abnormal pancreatic islet development with retention of aged insulin and deficient insulin secretion. To determine the collective roles of PWS genes in β-cell biology, we used genome-editing to generate isogenic, clonal INS-1 insulinoma lines having 3.16 Mb deletions of the silent, maternal (control) or active, paternal PWS-alleles. PWS β-cells demonstrated a significant cell-autonomous reduction in basal and glucose-stimulated insulin secretion. Further, proteomic analyses revealed reduced levels of cellular and secreted hormones, including all insulin peptides and amylin, concomitant with reduction of at least ten endoplasmic reticulum (ER) chaperones, including GRP78 and GRP94. Critically, transcriptomic studies demonstrated that the broad reduction of ER chaperones originated from transcriptional downregulation without corresponding changes for Ins1 and Ins2. In contrast to the dosage compensation previously seen for ER chaperones in Grp78 or Grp94 gene knockouts or knockdown, compensation is precluded by the stress-independent deficiency of ER chaperones in PWS β-cells. Consistent with reduced ER chaperones levels, PWS INS-1 β-cells are more sensitive to ER stress, leading to earlier activation of all three arms of the unfolded protein response. These findings suggest that a chronic shortage of ER chaperones in PWS β-cells leads to a deficiency of protein folding and/or delay in ER transit of insulin and other cargo. In summary, our results illuminate the pathophysiological basis of pancreatic β-cell hormone deficits in PWS, with evolutionary implications for the multigenic PWS-domain, and indicate that PWS-imprinted genes coordinate concerted regulation of ER chaperone biosynthesis and β-cell secretory pathway function.
Superinfection Exclusion of Alphaherpesviruses Interferes with Virion Trafficking
Authors: Cwick James P. , Owen Jonathan I. , Kochetkova Irina , Van Horssen Nick , Taylor Matthew P.
Published: December 2021

Superinfection exclusion (SIE) is a phenomenon in which a primary viral infection interferes with secondary viral infections within that same cell. Although SIE has been observed across many viruses, it has remained relatively understudied. A recently characterized glycoprotein D (gD) -independent SIE of alphaherpesviruses presents a novel mechanism of co-infection restriction for Herpes Simplex Virus Type 1 (HSV-1) and Pseudorabies virus (PRV). In this study, we evaluated the role of multiplicity of infection (MOI), receptor expression, and trafficking of virions to gain greater insight into potential mechanisms of alphaherpesvirus SIE.

We observed that high MOI secondary viral infections were able to overcome SIE in a manner that was independent of receptor availability. Utilizing recombinant viruses expressing fluorescent protein fusions, we assessed virion localization during SIE through live fluorescent microscopy of dual-labeled virions and localization of capsid assemblies. Analysis of these assemblies confirmed changes in the distribution of capsids during SIE. These results indicate that SIE during PRV infection inhibits viral entry or fusion while HSV-1 SIE inhibits infection through a post-entry mechanism. Although the timing and phenotype of SIE is similar between alphaherpesviruses, the related viruses implement different mechanisms to restrict coinfection.

IMPORTANCE

Most viruses utilize a form of superinfection exclusion to conserve resources and control population dynamics. gD-dependent superinfection exclusion in alphaherpesviruses is well-documented. However, the under-characterized gD-independent SIE provides new insight into how alphaherpesviruses limit sequential infection. The observations described here demonstrate that gD-independent SIE differs between PRV and HSV-1. Comparing these differences provide new insights into the underlying mechanisms of SIE implemented by two related viruses.
eXNVerify: coverage analysis for long and short-read sequencing data in clinical context
Authors: Porebski Sebastian , Stokowy Tomasz
Published: December 2021

Accurate identification of genetic variants to a large extent is based on type of experimental technology, quality of the material and coverage of obtained sequencing data. Our motivation was to create a tool that will evaluate genome coverage and accelerate the introduction of long-read sequencing to medical diagnostics and clinical practice. Here we present eXNVerify: a tool for inspection of clinical data in the context of pathogenic variants. The tool calculates Clinical Depth Coverage – a measure of coverage which we introduce to evaluate loci with pathogenic germline and somatic variants reported in ClinVar. The tool additionally provides visualization options for user-defined genes of interest. Finally, we present an examples of BRCA1, TP53, CFTR application and results of a test conducted in the Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development. eXNVerify is available at https://github.com/porebskis/eXNVerify and can be directly pulled from the DockerHub repository: docker pull porebskis/exnverify:1.0.
Structural, functional and computational studies of membrane recognition by Plasmodium Perforin-Like Proteins 1 and 2
Authors: Williams Sophie I. , Yu Xiulian , Ni Tao , Gilbert Robert J. C. , Stansfeld Phillip J.
Published: December 2021

Perforin-like proteins (PLPs) play key roles in the mechanisms associated with parasitic disease caused by apicomplexans such as Plasmodium (malaria) and Toxoplasma. The T. gondii PLP1 (TgPLP1) mediates tachyzoite egress from cells, while the five Plasmodium PLPs carry out various roles in the life cycle of the parasite and with respect to the molecular basis of disease. Here we focus on Plasmodium vivax PLP1 and PLP2 (PvPLP1 and PvPLP2) compared to TgPLP1; PvPLP1 is important for invasion of mammalian hosts by the parasite and establishment of a chronic infection, PvPLP2 is important during the symptomatic blood stage of the parasite life cycle. Determination of the crystal structure of the membrane-binding APCβ domain of PvPLP1 reveals notable differences with that of TgPLP1, which are reflected in its inability to bind lipid bilayers in the way that TgPLP1 and PvPLP2 can be shown to. Molecular dynamics simulations combined with site-directed mutagenesis and functional assays allow a dissection of the binding interactions of TgPLP1 and PvPLP2 on lipid bilayers, and reveal a similar tropism for lipids found enriched in the inner leaflet of the mammalian plasma membrane. In addition to this shared mode of membrane binding PvPLP2 displays a secondary synergistic interaction side-on from its principal bilayer interface. This study underlines the substantial differences between the biophysical properties of the APCβ domains of Apicomplexan PLPs, which reflect their significant sequence diversity. Such differences will be important factors in determining the cell targeting and membrane-binding activity of the different proteins, in their different developmental roles within parasite life cycles.
False-positive detection of Group B Streptococcus (GBS) in chromogenic media due to presence of Enterococcus faecalis in High Vaginal Swabs
Authors: Singh Abhishek , Husein Atahar , Singh Salomi , Ghattargi Vikas , Dhotre Dhiraj , Shouche Yogesh S. , Colaco Stacy , Abhyankar Vivek , Patekar Suyash , Chhabria Karisma , Kumar Sushil , Urhekar A.D. , Modi Deepak
Published: December 2021

Vaginal colonization of Group B Streptococcus (GBS) is associated with preterm births and neonatal sepsis. Thus, routine screening of GBS in prenatal care is recommended. Chromogenic media are useful in rapid and sensitive screening for GBS. herein, we evaluated the performance of Carrot broth for the detection of GBS in vaginal swabs of pregnant women. In all 20/201 (9.9%) vaginal swab samples were positive in the carrot broth. 17/20 (85%) and 19/20 (95%) samples yielded colonies on Blood agar and Crome agar respectively. However, 16s rRNA sequencing revealed that none of the carrot broth positive cultures had sequence similarities to the Enterococcus faecalis and not GBS. Furthermore, Enterococcus faecalis was detected by PCR in DNA isolated from the corresponding uncultured vaginal swabs samples, while GBS could be detected by PCR only in 4 samples. Thus carrot broth-based culture can lead to false-positive detection due to the presence of Enterococcus faecalis.
Reduced sensitivity of SARS-CoV-2 Omicron variant to booster-enhanced neutralization
Authors: Yu Xiaoqi , Wei Dong , Xu Wenxin , Li Yulong , Li Xinxin , Zhang Xinxin , Qu Jieming , Yang Zhitao , Chen Erzhen
Published: December 2021

The Omicron Variant of Concern (B.1.1.529) has spread internationally and is raising serious concerns about reduced vaccine efficacy and the increased risk of reinfection. We assessed the serum neutralizing activity using a pseudovirus-based neutralization assay in 292 healthcare workers who had received a homologous booster dose of BBIBP-CorV vaccine, 8 to 9 months after completing the priming two-dose vaccination schedule, to investigate whether the newly identified Omicron variant can escape serum antibody neutralization induced by the booster vaccination. The booster dose of BBIBP-CorV rapidly induced a significantly high level of humoral immune response, and the neutralization geometric mean titer (GMT) against the wild-type strain on day 28 after the booster dose was 294.85 (252.99-343.65), 6.1 times higher than the level on day 28 after the second dose. The neutralization against the Omicron variant was also improved by the booster vaccination, although the GMT showed an approximately 20.1-fold reduction to 14.66 (12.30-17.48) when compared with the wild-type strain. This study demonstrated that a booster dose of BBIBP-CorV led to a significant rebound in neutralizing immune response against SARS-CoV-2, while the Omicron variant showed partial resistance to neutralizing antibodies induced by the booster vaccination.
Magnitude, global variation, and temporal development of the COVID-19 infection fatality burden
Authors: Bohk-Ewald Christina , Acosta Enrique , Riffe Tim , Dudel Christian , Myrskylä Mikko
Published: December 2021

How deadly is an infection with SARS-CoV-2 worldwide over time? This information is critical for developing and assessing public health responses on the country and global levels. However, imperfect data have been the most limiting factor for estimating the COVID-19 infection fatality burden during the first year of the pandemic. Here we leverage recently emerged compelling data sources and broadly applicable modeling strategies to estimate the crude infection fatality rate (cIFR) in 77 countries from 28 March 2020 to 31 March 2021, using 2.4 million reported deaths and estimated 435 million infections by age, sex, country, and date. The global average of all cIFR estimates is 1.2% (10th to 90th percentile: 0.2% to 2.4%). The cIFR varies strongly across countries, but little within countries over time, and it is often lower for women than men. Cross-country differences in cIFR are largely driven by the age structures of both the general and the truly infected population. While the broad trends and patterns of the cIFR estimates are more robust, we show that their levels are uncertain and sensitive to input data and modeling choices. In consequence, increased efforts at collecting high-quality data are essential for accurately estimating the cIFR, which is a key indicator for better understanding the health and mortality consequences of this pandemic.
Variation of female pronucleus reveal oocyte or embryo abnormality: An expert experience deep learning of non-dark box analysis
Authors: Yang Jingwei , Wang Yikang , Li Chong , Han Wei , Liu Weiwei , Xiong Shun , Zhang Qi , Tong Keya , Huang Guoning , Zhang Xiaodong
Published: December 2021

Background

Pronuclear assessment appears to have the ability to distinguish good and bad embryos in the zygote stage, but paradoxical results were obtained in clinical studies. This situation might be caused by the robust qualitative detection of the development of dynamic pronuclei. Here, we aim to establish a quantitative pronuclear measurement method by applying expert experience deep learning from large annotated datasets.

Methods

Convinced handle-annotated 2PN images (13419) were used for deep learning then corresponded errors were recorded through handle check for subsequent parameters adjusting. We used 790 embryos with 52479 PN images from 155 patients for analysis the area of pronuclei and the pre-implantation genetic test results. Establishment of the exponential fitting equation and the key coefficient β 1was extracted from the model for quantitative analysis for pronuclear(PN) annotation and automatic recognition.

Findings

Based on the female original PN coefficient β1, the chromosome-normal rate in the blastocyst with biggest PN area is much higher than that of the blastocyst with smallest PN area (58.06% vs. 45.16%, OR=1.68 [1.07–2.64]; P=0.031). After adjusting coefficient β1 by the first three frames which high variance of outlier PN areas was removed, coefficient β1 at 12 hours and at 14 hours post-insemination, similar but stronger evidence was obtained. All these discrepancies resulted from the female propositus in the PGT-SR subgroup and smaller chromosomal errors.

Conclusion(s)

The results suggest that detailed analysis of the images of embryos could improve our understanding of developmental biology.

Funding

None
Mirtazapine treatment in a young female mouse model of Rett syndrome identifies time windows for the rescue of early phenotypes during development
Authors: Gutiérrez Javier Flores , Natali Giulia , Giorgi Jacopo , De Leonibus Elvira , Tongiorgi Enrico
Published: December 2021

Rett Syndrome (RTT) is a rare X-linked neurodevelopmental disorder, mainly caused by mutations in the MECP2 gene. Reduction in monoamine levels in RTT patients and mouse models suggested the possibility to rescue clinical phenotypes through antidepressants. Accordingly, we tested mirtazapine (MTZ), a noradrenergic and specific-serotonergic tetracyclic antidepressant (NaSSA). In previous studies, we showed high tolerability and significant positive effects of MTZ in male Mecp21m1.1Bird-knock-out mice, adult female Mecp2tm1.1Bird-heterozygous (Mecp2+/-) mice, and adult female RTT patients. However, it remained to explore MTZ efficacy in female Mecp2+/- mice at young ages. As RTT-like phenotypes in young Mecp2+/- mice have been less investigated, we carried out a behavioural characterization to analyze Mecp2+/- mice in “early adolescence” (6 weeks) and “late adolescence/young adulthood” (11 weeks) and identified several progressive phenotypes. Then, we evaluated the effects of either a 15- or a 30-day MTZ treatment on body weight and impaired motor behaviours in 11-week-old Mecp2+/- mice. Finally, since defective cortical development is a hallmark of RTT, we performed a histological study on the maturation of perineuronal nets (PNNs) and parvalbuminergic (PV) neurons in the primary motor cortex. The 30-day MTZ treatment was more effective than the shorter 15-day treatment, leading to the significant rescue of body weight, hindlimb clasping and motor learning in the accelerating rotarod test. Behavioral improvement was associated with normalized PV immunoreactivity levels and PNN thickness. These results support the use of MTZ as a new potential treatment for adolescent girls affected by RTT and suggest a possible mechanism of action.
LONG-TERM MONITORING OF THE EUROPEAN ROLLER (CORACIAS GARRULUS) IN UKRAINE: IS CLIMATE BEHIND THE CHANGES?
Authors: Shupova T. , Tytar V.
Published: December 2021

Since the 1980s there has been a long-term decline in numbers and contraction of range in Europe, including Ukraine. Our specific goals were to reconstruct the climatically suitable range of the species in Ukraine before the 1980s, gain better knowledge on its requirements, compare the past and current suitable areas, infer the regional and environmental variables that best explain its occurrence, and quantify the overall range change in the country. For these purposes we created a database consisting of 347 records of the roller made ever in Ukraine. We employed a species distribution modeling (SDM) approach to hindcast changes in the suitable range of the roller during historical times across Ukraine and to derive spatially explicit predictions of climatic suitability for the species under current climate. SDMs were created for three time intervals (before 1980, 1985-2009, 2010-2021) using corresponding climate data extracted from the TerraClim database. SDMs show a decline of suitable for rollers areas in the country from 85 to 46%. Several factors, including land cover and use, human population density and climate, that could have contributed to the decline of the species in Ukraine were considered. We suggest climate change and its speed (velocity) have been responsible for shaping the contemporary home range of the European roller.
Human genetic variants associated with COVID-19 severity are enriched in immune and epithelium regulatory networks
Authors: Feng Zhanying , Ren Xianwen , Duren Zhana , Wang Yong
Published: December 2021

Human genetic variants can influence the severity of infection with SARS-COV-2. Several genome-wide association studies (GWAS) have been conducted to identify human risk loci that may be involved with COVID-19 severity. However, candidate genes were investigated in the genomic proximity of each locus without considering their functional cellular contexts. Here, we compiled regulatory networks of 77 human contexts to interpret these risk loci by revealing their relevant contexts and associated transcript factors (TF), regulatory elements (REs), and target genes (TGs). 21 human contexts were identified to be associated with COVID-19 severity and grouped into two categories: immune cells and epithelium cells. We further investigated the risk loci in regulatory network of immune cells, epithelium cells and their crosstalk. Two genomic clusters, chemokine receptors cluster and OAS cluster showed the strongest association with COVID-19 severity in the context specific regulatory networks.
M-CSF-stimulated myeloid cells can convert into epithelial cells to participate in re-epithelialization and hair follicle regeneration during skin wound healing
Authors: Li Yunyuan , Nojeidi Hatem , Kilani Ruhangiz T. , Ghahary Aziz
Published: December 2021

Skin wound healing is a complex process which requires the interaction of many cell types and mediators in a highly sophisticated temporal sequence. Myeloid cells compose a significant proportion of the inflammatory cells recruited to a wound site and play important roles in clearance of damaged tissue and microorganisms. Myeloid cells have also been suggested to convert into fibro-blast-like cells and endothelial cells in participation of wound healing process. However, whether myeloid cells in wound skin can convert into epithelial cells and contribute to re-epithelialization and skin appendage regeneration is still unclear. In this study, we performed double immunofluorescent staining with antibodies for hematopoietic cells and keratinocytes as well as cell tracing technique to investigate hematopoietic cell conversion. The result show that during the healing process, some of the CD45-positive hematopoietic cells are overlapped with keratin 14, the markers of keratinocytes. Further, CD11b-positive myeloid cells seem the origin of converted epithelial cells. To confirm these results, we culture CD11b-posiitve myeloid cells from mouse splenocytes in a medium containing macrophage colony-stimulating factor (M-CSF) and dermal injection of these cells into the healthy skin when punch biopsy is created in mouse skin. Tracing injected labeled splenocyte-derived myeloid cells in skin, we confirm that myeloid cells able to convert into keratinocytes in repaired skin. Furthermore, our results fromin vivoexperiments provide new information on contribution of myeloid cells in hair follicle regeneration. In conclusion, this work highlights the myeloid cell contributions in wound repair and hair follicle regeneration in mice through conversion of M-CSF-stimulated CD11b+ myeloid cells into epithelial cells.
Multiscale 3D Genome Reorganization during Skeletal Muscle Stem Cell Lineage Progression and Muscle Aging
Authors: Zhao Yu , Ding Yingzhe , He Liangqiang , Li Yuying , Chen Xiaona , Sun Hao , Wang Huating
Published: December 2021

3D genome rewiring is known to influence spatiotemporal expression of lineage-specific genes and cell fate transition during stem cell differentiation and aging processes. Yet it is unknown how 3D architecture remodels and orchestrates transcriptional changes during skeletal muscle stem cell (also called satellite cell, SC) activation, proliferation and differentiation course. Here, usingin situHi-C we comprehensively map the 3D genome topology reorganization at multiscale levels during mouse SC lineage progression and integrate with transcriptional and chromatin signatures to elucidate how 3D genome rewiring dictates gene expression program. Specifically, rewiring at compartment level is most pronounced when SC becomes activated. Striking loss in TAD border insulation and chromatin looping also occurs during early activation process. Meanwhile, TADs can also form TAD clusters and super-enhancer containing TAD clusters orchestrate stage-specific gene expression during SC early activation. Furthermore, we elucidate 3D chromatin regulation of key transcription factor, PAX7 and identify cis-regulatory elements that are crucial for local chromatin architecture andPax7expression. Lastly, 3D genome remodeling is profiled in SCs isolated from naturally aging mice, unveiling that geriatric SCs display a prominent gain in long-range contacts and loss of TAD border insulation. Genome compartmentalization and chromatin looping are evidently altered in aged SC while geriatric SC display a more prominent loss in strength of TAD borders. Together, our results implicate 3D chromatin extensively reorganizes at multiple architectural levels and underpin the transcriptome remodeling during SC lineage development and SC aging.
Exploring the meteoric rise of online food ordering apps (OFOAs): the moderating role of visibility
Authors: Chakraborty Debarun
Published: December 2021

Purpose

Online food ordering apps (OFOAs) have become increasingly popular, and consumers have widely recognized their benefits, particularly during pandemics or lockdowns. Despite the growing popularity of OFOAs, little is known about technology acceptance theories and their impact on purchase intention. The current study proposes the amalgamation of three theories to bridge this gap, better explaining customer behaviour toward OFOAs.

Design/methodology/approach

To create a model, the researcher applied technology acceptance theories, visibility and purchase intention. To obtain results, the researcher used structural equation modelling (SEM) and moderation analysis on 432 responses obtained through a questionnaire.

Findings

According to the research, all constructs were found to have a favourable and significant impact on the intention to use OFOAs, except compatibility. The moderating effect of visibility on intent to purchase is shown in the study. The study's findings add to the knowledge of consumer behaviour and practice.

Research limitations/implications

This work sheds light on technology acceptance theories that ensure that OFOA platforms are used indefinitely. Furthermore, the significance of visibility as a mediator of purchase intention provides a deep insight into customer behaviour.

Originality/value

This model, which combines technology acceptance theories' original constructs with visibility to moderate purchase intention on OFOA platforms, is the first of its type in the current literature. Furthermore, this theoretical progress paves the way for future research.