bluuebunny/crossref_metadata_2025 huggingface dataset:
Synopsis of Osmunda (royal ferns; Osmundaceae): towards reconciliation of genetic and biogeographic patterns with morphologic variation
Authors: Lehnert Marcus , Monjau Tilo , Rosche Christoph
Published: December 2023

We present an overview of the morphology, biogeography, and ecology of the fern genus Osmunda (i.e. without previously included taxa of Claytosmunda, Osmundastrum, and Plenasium), with a focus on the American O. spectabilis Willd. and Old World O. regalis L. While genetic data supports the separation of these taxa, commonly used morphologic characters to distinguish between O. regalis and O. spectabilis (maximum frond size; pinnae sessile vs. stalked; pinnules opposite vs. alternate; general pinnule proportions) are not infallible. We recorded morphometric differences among and between O. regalis and O. spectabilis and correlated these with spatio-environmental gradients. Our work provides an updated taxonomic overview with full synonymy and diagnostic key of Osmunda. We preliminarily recognize six informal subtaxa in O. regalis (‘regalis’, ‘abyssinica’, ‘huegeliana’, ‘longifolia’, ‘transvaalensis’, ‘obtusifolia’) and three in O. spectabilis (‘spectabilis’, ‘palustris’, ‘piresii’) that separate in a morphological traits-based principal component analysis. The morphotaxa appeared geographically structured and their distribution showed significant correlations with elevation, mean annual precipitation, annual mean temperature, and temperature seasonality. The taxonomic rank and validity of the proposed subtaxa has to be tested through a large-scale sampling, e.g. with comparative cp/nr genomic and cytogenetic analyses. Such future analyses may help to ascertain whether the observed morphologic peculiarities are conditioned solely by abiotic factors (which would allow addressing them as forms) or are manifested in the genome.
fMRI evidence of movement familiarization effects on recognition memory in professional dancers
Authors: Wang Yingying , Zhao Qi , Ji Qingchun , Jin Xinhong , Zhou Chenglin , Lu Yingzhi
Published: December 2023

Dual-process theories propose that recognition memory involves recollection and familiarity; however, the impact of motor expertise on memory recognition, especially the interplay between familiarity and recollection, is relatively unexplored. This functional magnetic resonance imaging study used videos of a dancer performing International Latin Dance Styles as stimuli to investigate memory recognition in professional dancers and matched controls. Participants observed and then reported whether they recognized dance actions, recording the level of confidence in their recollections, whereas blood-oxygen-level-dependent signals measured encoding and recognition processes. Professional dancers showed higher accuracy and hit rates for high-confidence judgments, whereas matched controls exhibited the opposite trend for low-confidence judgments. The right putamen and precentral gyrus showed group-based moderation effects, especially for high-confidence (vs. low-confidence) action recognition in professional dancers. During action recognition, the right superior temporal gyrus and insula showed increased activation for accurate recognition and high-confidence retrieval, particularly in matched controls. These findings highlighting enhanced action memory of professional dancers—evident in their heightened recognition confidence—not only supports the dual-processing model but also underscores the crucial role of expertise-driven familiarity in bolstering successful recollection. Additionally, they emphasize the involvement of the action observation network and frontal brain regions in facilitating detailed encoding linked to intention processing.
Sphingosine-1-phosphate receptor 3 regulates the transendothelial transport of high-density lipoproteins and low-density lipoproteins in opposite ways
Authors: Velagapudi Srividya , Wang Dongdong , Poti Francesco , Feuerborn Renata , Robert Jerome , Schlumpf Eveline , Yalcinkaya Mustafa , Panteloglou Grigorios , Potapenko Anton , Simoni Manuela , Rohrer Lucia , Nofer Jerzy-Roch , von Eckardstein Arnold
Published: December 2023

Aims

The entry of lipoproteins from blood into the arterial wall is a rate-limiting step in atherosclerosis. It is controversial whether this happens by filtration or regulated transendothelial transport.

Because sphingosine-1-phosphate (S1P) preserves the endothelial barrier, we investigated in vivo and in vitro, whether S1P and its cognate S1P-receptor 3 (S1P3) regulate the transendothelial transport of lipoproteins.

Methods and results

Compared to apoE-haploinsufficient mice (CTRL), apoE-haploinsufficient mice with additional endothelium-specific knock-in of S1P3 (S1P3-iECKI) showed decreased transport of LDL and Evan’s Blue but increased transport of HDL from blood into the peritoneal cave. After 30 weeks of high-fat diet feeding, S1P3-iECKI mice had lower levels of non-HDL-cholesterol and less atherosclerosis than CTRL mice. In vitro stimulation with an S1P3 agonist increased the transport of 125I-HDL but decreased the transport of 125I-LDL through human aortic endothelial cells (HAECs). Conversely, inhibition or knock-down of S1P3 decreased the transport of 125I-HDL but increased the transport of 125I-LDL. Silencing of SCARB1 encoding scavenger receptor B1 (SR-BI) abrogated the stimulation of 125I-HDL transport by the S1P3 agonist. The transendothelial transport of 125I-LDL was decreased by silencing of SCARB1 or ACVLR1 encoding activin-like kinase 1 but not by interference with LDLR. None of the three knock-downs prevented the stimulatory effect of S1P3 inhibition on transendothelial 125I-LDL transport.

Conclusion

S1P3 regulates the transendothelial transport of HDL and LDL oppositely by SR-BI-dependent and SR-BI-independent mechanisms, respectively. This divergence supports a contention that lipoproteins pass the endothelial barrier by specifically regulated mechanisms rather than passive filtration.
Churros: a Docker-based pipeline for large-scale epigenomic analysis
Authors: Wang Jiankang , Nakato Ryuichiro
Published: December 2023

The epigenome, which reflects the modifications on chromatin or DNA sequences, provides crucial insight into gene expression regulation and cellular activity. With the continuous accumulation of epigenomic datasets such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) data, there is a great demand for a streamlined pipeline to consistently process them, especially for large-dataset comparisons involving hundreds of samples. Here, we present Churros, an end-to-end epigenomic analysis pipeline that is environmentally independent and optimized for handling large-scale data. We successfully demonstrated the effectiveness of Churros by analyzing large-scale ChIP-seq datasets with the hg38 or Telomere-to-Telomere (T2T) human reference genome. We found that applying T2T to the typical analysis workflow has important impacts on read mapping, quality checks, and peak calling. We also introduced a useful feature to study context-specific epigenomic landscapes. Churros will contribute a comprehensive and unified resource for analyzing large-scale epigenomic data.
The Impact of Dietary Interventions on the Microbiota in Inflammatory Bowel Disease: A Systematic Review
Authors: Nieva Cheenie , Pryor Jennifer , Williams Georgina M , Hoedt Emily C , Burns Grace L , Eslick Guy D , Talley Nicholas J , Duncanson Kerith , Keely Simon
Published: December 2023

Background and Aims

Diet plays an integral role in the modulation of the intestinal environment, with the potential to be modified for management of individuals with inflammatory bowel disease [IBD]. It has been hypothesised that poor ‘Western-style’ dietary patterns select for a microbiota that drives IBD inflammation and, that through dietary intervention, a healthy microbiota may be restored. This study aimed to systematically review the literature and assess current available evidence regarding the influence of diet on the intestinal microbiota composition in IBD patients, and how this may affect disease activity.

Methods

MEDLINE, EMBASE, Scopus, Web of Science, and Cochrane Library were searched from January 2013 to June 2023, to identify studies investigating diet and microbiota in IBD.

Results

Thirteen primary studies met the inclusion criteria and were selected for narrative synthesis. Reported associations between diet and microbiota in IBD were conflicting due to the considerable degree of heterogeneity between studies. Nine intervention studies trialled specific diets and did not demonstrate significant shifts in the diversity and abundance of intestinal microbial communities or improvement in disease outcomes. The remaining four cross-sectional studies did not find a specific microbial signature associated with habitual dietary patterns in IBD patients.

Conclusions

Diet modulates the gut microbiota, and this may have implications for IBD; however, the body of evidence does not currently support clear dietary patterns or food constituents that are associated with a specific microbiota profile or disease marker in IBD patients. Further research is required with a focus on robust and consistent methodology to achieve improved identification of associations.
Arthropod predator community associated with soybean gall midge,Resseliella maxima(Diptera: Cecidomyiidae), in Minnesotan soybean fields
Authors: Melotto Gloria , Potter Bruce D , Lindsey Amelia R I , Koch Robert L
Published: December 2023

The soybean gall midge, Resseliella maxima Gagné (Diptera: Cecidomyiidae), is a pest that injures soybeans in the Midwest United States. Little is known about the natural enemies of R. maxima or the potential for biological control. Therefore, we performed a 2-yr survey in Minnesota to examine the predator community associated with R. maxima infestations. We found that Orius insidiosus (Say) (Heteroptera: Anthocoridae) and Pterostichus melanarius (Illiger) (Coleoptera: Carabidae) were the most common foliar- and ground-foraging predators, respectively. Some of the commonly encountered predator species were tested in laboratory predation experiments. Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae) and O. insidiosus represented the foliar-foraging predators tested, and H. axyridis consumed significantly more R. maxima larvae than O. insidiosus. Among the ground-foraging predators, 4 carabids were tested. Poecilus lucublandus (Say) (Coleoptera: Carabidae) and Pt. melanarius consumed significantly more R. maxima larvae than Poecilus chalcites (Say) (Coleoptera: Carabidae) and Bembidion quadrimaculatum oppositum (Say) (Coleoptera: Carabidae). We conclude that Pt. melanarius should receive further attention as a potential biological control agent of R. maxima, due to its high abundance in the soybean fields in this study, temporal overlap with the pest, and high propensity to feed on the pest.
Cryoballoon ablation of peri-mitral atrial flutter refractory to radiofrequency ablation: a case report
Authors: Takahashi Masao , Kujiraoka Hirofumi , Arai Tomoyuki , Hojo Rintaro , Fukamizu Seiji
Published: December 2023

Background

The radiofrequency catheter ablation of peri-mitral atrial flutter is occasionally difficult, mostly due to epicardial or intramural conduction on the mitral isthmus (MI). However, cryoballoon ablation (CBA) of peri-mitral atrial flutter refractory to radiofrequency ablation has not been reported.

Case summary

We report a case of a 66-year-old male patient who experienced a recurrence of atypical atrial flutter and underwent the sixth catheter ablation. The activation and entrainment maps showed that this atypical atrial flutter (AFL) was peri-mitral AFL via pathways other than endocardial conduction in the MI. Previous radiofrequency catheter ablation attempts on the MI line, including endocardial, coronary sinus, and epicardial ablations, failed to achieve a bidirectional block of the MI. In this case, we selected CBA for the MI area and successfully achieved a bidirectional block of the MI.

Discussion

Although using CBA in the MI is off-label, it could be safely implemented using CARTOUNIVU™. We attributed the success of the bidirectional block of the MI in this case to the crimping of the northern hemisphere of the CBA to the mitral isthmus area, which resulted in the formation of a broad, uniform, and deep ablation lesion site.
England’s Mercantilism: Trading Companies, Employment and the Politics of Trade in Global History, 1688–1704
Authors: Bromley Hugo
Published: December 2023

A close study of how the status of trading companies changed after 1688 demonstrates that mercantilist decision-making was a more widespread, more national process than is commonly assumed. English manufacturers and merchants looked to the state to support them in an increasingly global economy. Parliament’s position as the key decision-making institution helped turn London into an ‘open archive’ of pamphlets, petitions and correspondence that became the basis for mercantilist policy. In this chaotic debate between private interests, domestic employment was considered the primary objective of wider English participation in the global economy, and those English producers who could claim to be employing others were valued particularly highly. The role of the wider English nation in shaping the global impact of the state suggests the need for a fuller exploration of the role of mercantilism in early modern global history.
William Byrd’s Come, woeful Orpheus in context: motion as visual and musical affect
Authors: Bank Katie
Published: December 2023

Looking at William Byrd’s consort song Come, woeful Orpheus (1611) and the Orpheus overmantel at Haddon Hall (Derbyshire), this article imagines how music and visual culture provided reciprocal somatic and symbolic cues within the domestic sphere. Using Richard Haydock’s Tracte containing the artes of curious paintinge (1598), it considers how the Orpheus trope, cogitated and embodied through visual and musical media, could be used to produced ‘fellow feeling’ and affect through ‘motion’. ‘Motion’ was not only fundamental to early modern theories of affective communication but was thought to provide the spark of life that aided interpersonal connection.

This research explores the shared language between the theoretical and affective aspects of music and art in early modern England, stemming from classical sources on decorum and persuasive oration, to provide a more nuanced understanding of contemporary experiences of recreational music-making. I argue that the embodied and visual contributions of the performers are crucial to understanding Byrd’s song, as early modern approaches to motion and affect relied upon the body and voice, and were best communicated through sight and sound.
Major in-hospital complications after catheter ablation of cardiac arrhythmias: individual case analysis of 43 031 procedures
Authors: Eckardt Lars , Doldi Florian , Anwar Omar , Gessler Nele , Scherschel Katharina , Kahle Ann-Kathrin , von Falkenhausen Aenne S , Thaler Raffael , Wolfes Julian , Metzner Andreas , Meyer Christian , Willems Stephan , Köbe Julia , Lange Philipp Sebastian , Frommeyer Gerrit , Kuck Karl-Heinz , Kääb Stefan , Steinbeck Gerhard , Sinner Moritz F
Published: December 2023

Aims

In-hospital complications of catheter ablation for atrial fibrillation (AF), atrial flutter (AFL), and ventricular tachycardia (VT) may be overestimated by analyses of administrative data.

Methods and results

We determined the incidences of in-hospital mortality, major bleeding, and stroke around AF, AFL, and VT ablations in four German tertiary centres between 2005 and 2020. All cases were coded by the G-DRG- and OPS-systems. Uniform code search terms were applied defining both the types of ablations for AF, AFL, and VT and the occurrence of major adverse events including femoral vascular complications, iatrogenic tamponade, stroke, and in-hospital death. Importantly, all complications were individually reviewed based on patient-level source records. Overall, 43 031 ablations were analysed (30 361 AF; 9364 AFL; 3306 VT). The number of ablations/year more than doubled from 2005 (n = 1569) to 2020 (n = 3317) with 3 times and 2.5 times more AF and VT ablations in 2020 (n = 2404 and n = 301, respectively) as compared to 2005 (n = 817 and n = 120, respectively), but a rather stable number of AFL ablations (n = 554 vs. n = 612). Major peri-procedural complications occurred in 594 (1.4%) patients. Complication rates were 1.1% (n = 325) for AF, 1.0% (n = 95) for AFL, and 5.3% (n = 175) for VT. With an increase in complex AF/VT procedures, the overall complication rate significantly increased (0.76% in 2005 vs. 1.81% in 2020; P = 0.004); but remained low over time. Following patient-adjudication, all in-hospital cardiac tamponades (0.7%) and strokes (0.2%) were related to ablation. Major femoral vascular complications requiring surgical intervention occurred in 0.4% of all patients. The in-hospital mortality rate adjudicated to be ablation-related was lower than the coded mortality rate: AF: 0.03% vs. 0.04%; AFL: 0.04% vs. 0.14%; VT: 0.42% vs. 1.48%.

Conclusion

Major adverse events are low and comparable after catheter ablation for AFL and AF (∼1.0%), whereas they are five times higher for VT ablations. In the presence of an increase in complex ablation procedures, a moderate but significant increase in overall complications from 2005–20 was observed. Individual case analysis demonstrated a lower than coded ablation-related in-hospital mortality. This highlights the importance of individual case adjudication when analysing administrative data.
Male harm suppresses female fitness, affecting the dynamics of adaptation and evolutionary rescue
Authors: Gómez-Llano Miguel , Faria Gonçalo S , García-Roa Roberto , Noble Daniel W A , Carazo Pau
Published: December 2023

One of the most pressing questions we face as biologists is to understand how climate change will affect the evolutionary dynamics of natural populations and how these dynamics will in turn affect population recovery. Increasing evidence shows that sexual selection favors population viability and local adaptation. However, sexual selection can also foster sexual conflict and drive the evolution of male harm to females. Male harm is extraordinarily widespread and has the potential to suppress female fitness and compromise population growth, yet we currently ignore its net effects across taxa or its influence on local adaptation and evolutionary rescue. We conducted a comparative meta-analysis to quantify the impact of male harm on female fitness and found an overall negative effect of male harm on female fitness. Negative effects seem to depend on proxies of sexual selection, increasing inversely to the female relative size and in species with strong sperm competition. We then developed theoretical models to explore how male harm affects adaptation and evolutionary rescue. We show that, when sexual conflict depends on local adaptation, population decline is reduced, but at the cost of slowing down genetic adaptation. This trade-off suggests that eco-evolutionary feedback on sexual conflict can act like a double-edged sword, reducing extinction risk by buffering the demographic costs of climate change, but delaying genetic adaptation. However, variation in the mating system and male harm type can mitigate this trade-off. Our work shows that male harm has widespread negative effects on female fitness and productivity, identifies potential mechanistic factors underlying variability in such costs across taxa, and underscores how acknowledging the condition-dependence of male harm may be important to understand the demographic and evolutionary processes that impact how species adapt to environmental change.
Estimating the potential impact of a health tax on the demand for unhealthy food and beverages and on tax revenue in India
Authors: Varghese Beena , Panicker Rajashree , Mukhopadhyay Dripto , Backholer Kathryn , Sethi Vani , de Wagt Arjan , Murira Zivai , Bhatia Neena , Arora Monika
Published: December 2023

Foods high in fat, sugar or salt are important contributors to the rising burden of non-communicable diseases globally and in India. Health taxes (HTs) have been used by over 70 countries as an effective tool for reducing consumption of sugar sweetened beverages (SSBs). However, the potential impacts of HTs on consumption and on revenues have not been estimated in India. This paper aims to estimate the potential impact of health taxes on the demand for sugar, SSBs and foods high in fat, sugar or salt (HFSS) in India while exploring its impact on tax revenues. PE of sugar was estimated using Private Final Consumption Expenditure and Consumer Price Index data while price elasticities for SSBs and HFSS were obtained from literature. The reduction in demand was estimated for an additional 10–30% HT added to the current goods and services tax, for varying levels of price elasticities. The results show that for manufacturers of sweets and confectionaries who buy sugar in bulk and assuming a higher price elasticity of −0.70, 20% additional HT (total tax 48%) would result in 13–18% decrease in the demand for sugar used for confectionaries and sweets. For SSBs, HT of 10–30% would result in 7–30% decline in the demand of SSBs. For HFSS food products, 10–30% HT would result in 5–24% decline in the demand for HFSS products. These additional taxes would increase tax revenues for the government by 12–200% across different scenarios. Taxing unhealthy foods is likely to reduce demand, while increasing government revenues for reinvestment back into public health programmes and policies that may reduce obesity and the incidence of non-communicable diseases in India.
Factors Associated With Extraintestinal Manifestations of Inflammatory Bowel Disease in SPARC-IBD
Authors: Alizadeh Madeline , Motwani Kiran , Siaton Bernadette C , Abutaleb Ameer , Ravel Jacques , Cross Raymond K ,   SPARC-IBD Investigators, Russ Kirk , Bewtra Meena , Lewis James , Cross Raymond , Wong Uni , Snapper Scott , Korzenik Josh , Bishu Shrinivas , Duerr Rick , Saha Sumona , Caldera Freddy , Raffals Laura , Shukla Richa , Dassopoulos Themistocles , Bohm Matthew , Beniwal-Patel Poonam , Hudesman David , Brook Lauren , Pekow Joel , Scoville Elizabeth , Ciorba Matthew , Deepak Parakkal
Published: December 2023

Background

Extraintestinal manifestations (EIMs) of inflammatory bowel diseases (IBDs) are a common and debilitating feature of disease, occurring in up to 40% of patients with IBD, yet predicting who may develop them is difficult. The goal of our study was to better characterize which patients may be at highest risk of developing not only 1 EIM, but also multiple EIMs, across both diseases.

Methods

A retrospective study of participants enrolled in the SPARC IBD (Study of Prospective Adult Research Cohort with IBD) registry was performed, and demographic and clinical data were analyzed. A total of 1211 patients with data available on EIMs were included, and differences among variables with vs without EIMs were assessed.

Results

A total of 329 participants with at least 1 EIM were identified, compared with 882 participants without any EIMs. Crohn’s disease patients and women were more likely to have 2 or more EIMs (P = .005 and P ≤ .001, respectively). Participants with ocular manifestations were likeliest to have at least 2 EIMs (P ≤ .001). Even when diagnosis was controlled for, involvement of the right colon (P = .021) was predictive of IBD-associated arthritis across both diseases in a multivariate generalized linear model.

Conclusions

This is the first comprehensive large-cohort assessment of how EIMs relate to one another at the individual vs systems levels. Further, our analysis is the first to recognize specific locations of colon involvement associated with EIMs of IBD, regardless of IBD type. These results are important in identifying patients at risk of developing future EIMs and may help with risk stratification when choosing treatments.
Fungal Microbiota Composition in Inflammatory Bowel Disease Patients: Characterization in Different Phenotypes and Correlation With Clinical Activity and Disease Course
Authors: Catalán-Serra Ignacio , Thorsvik Silje , Beisvag Vidar , Bruland Torunn , Underhill David , Sandvik Arne Kristian , Granlund Atle van Beelen
Published: December 2023

Background

There is growing evidence of the role of the mycobiome in inflammatory bowel disease (IBD). Variations within phenotypes and activity and with prognosis have been poorly studied.

Methods

A total of 111 individuals were prospectively enrolled: 89 IBD patients (52 ulcerative colitis and 37 Crohn’s disease [CD]) and 22 healthy individuals. Disease characteristics were collected and a fecal calprotectin >100 μg/mg was considered indicative of activity. A subset of patients was followed for 6 ± 2 years. Disease course was designated as either complicated or uncomplicated based on the need of intensified medication and/or surgery. ITS sequencing was performed targeting the ITS1 region.

Results

We found lower Ascomycota/Basidiomycota ratio in IBD. Patients showed a marked increase in Candida dublinensis and Ca albicans and were depleted of Aspergillus rubrobrunneus and Penicillium brevicompactum (P ≤ .001) Saccharomyces was predominant in total colitis and Penicillium in proctitis. Several Penicillium species were depleted in total colitis vs proctitis. Ileal CD patients were enriched in Debaromyces hansenii and depleted of Ca tropicalis (P ≤ .001). Ca albicans was overrepresented in inflammatory (B1) vs fibrostenosing (B2) CD. Ca dublinensis was more abundant in active patients and correlated positively with fecal calprotectin and neutrophil gelatinase-associated lipocalin, while S pastorianus correlated inversely with activity. Ca sake was associated with complicated disease and increased abundance of Cryptococcus carnescens with the need for surgery in CD.

Conclusions

This study shows important differences in the mycobiome in IBD and within phenotypes. Selected fungal species were associated with complicated disease and the need of surgery in CD. This work adds to our understanding of the role of fungi in IBD, with potential clinical implications.
AI Regulation and the Protection of Source Code
Authors: Mitchell Andrew D , Let Dominic , Tang Lingxi
Published: December 2023

Artificial intelligence (AI) has been rapidly developing since the mid-20th century. Today, AI is deployed in many aspects of our daily lives and is increasingly ubiquitous. At the same time, concerns about AI, including discrimination, privacy, and security, have prompted calls for greater regulation. To this end, regulators may seek access to AI’s source code (the human-readable program for the software). However, many trade agreements contain provisions prohibiting source code disclosure as a condition for market access in the relevant countries. This article considers the tension between AI regulation and these provisions. In situations where such provisions apply, for AI regulation to remain compliant, we argue that regulators can only require access to source code in exceptional cases where the general exceptions in the General Agreement on Trade in Services apply.
A dynamic overflow triage model in an outpatient queuing system
Authors: Li Junxiang , Lu Yiling
Published: December 2023

Accepted by: M. Zied Babai

In the medical service system, when the number of expert seats is in short supply, it is difficult to make full use of hospital resources by the traditional queuing method. Without changing the existing resources, an overflow model with triage in a Markov queuing system is established by overflowing a part of patients in the expert queue into the general queue under a certain condition to allocate reasonably the capacity of each outpatient. The numerical simulation using ProModel, a simulation software, shows that the average queue length, waiting time and other service indices are better than the traditional models.
Staying positive: challenges and solutions in using pure multiplicative ETS models
Authors: Svetunkov Ivan , Boylan John E
Published: December 2023

Accepted by: Zied Babai

Exponential smoothing in state space form (ETS) is a popular forecasting technique, widely used in research and practice. While the additive error ETS models have been well studied, the multiplicative error ones have received much less attention in forecasting literature. Still, these models can be useful in cases, when one deals with positive data, because they are supposed to work in such situations. Unfortunately, the classical assumption of normality for the error term might break this property and lead to non-positive forecasts on positive data. In order to address this issue, we propose using Log-Normal, Gamma and Inverse Gaussian distributions, which are defined for positive values only. We demonstrate what happens with ETS(M,*,*) models in this case, discuss conditional moments of ETS with these distribution and show that they are more natural for the models than the Normal one. We conduct the simulation experiments in order to study the bias introduced by point forecasts in these models and then compare the models with different distributions. We finish the paper with an example of application, showing how pure multiplicative ETS with a positive distribution works.
Affine Stresses, Inverse Systems, and Reconstruction Problems
Authors: Murai Satoshi , Novik Isabella , Zheng Hailun
Published: December 2023

A conjecture of Kalai asserts that for $d\geq 4$, the affine type of a prime simplicial $d$-polytope $P$ can be reconstructed from the space of affine $2$-stresses of $P$. We prove this conjecture for all $d\geq 5$. We also prove the following generalization: for all pairs $(i,d)$ with $2\leq i\leq \lceil \frac d 2\rceil -1$, the affine type of a simplicial $d$-polytope $P$ that has no missing faces of dimension $\geq d-i+1$ can be reconstructed from the space of affine $i$-stresses of $P$. A consequence of our proofs is a strengthening of the Generalized Lower Bound Theorem: it was proved by Nagel that for any simplicial $(d-1)$-sphere $\Delta $ and $1\leq k\leq \lceil \frac {d}{2}\rceil -1$, $g_{k}(\Delta )$ is at least as large as the number of missing $(d-k)$-faces of $\Delta $; here we show that, for $1\leq k\leq \lfloor \frac {d}{2}\rfloor -1$, equality holds if and only if $\Delta $ is $k$-stacked. Finally, we show that for $d\geq 4$, any simplicial $d$-polytope $P$ that has no missing faces of dimension $\geq d-1$ is redundantly rigid, that is, for each edge $e$ of $P$, there exists an affine $2$-stress on $P$ with a non-zero value on $e$.
Rifampicin and protein concentrations in paired spinal versus ventricular cerebrospinal fluid samples of children with tuberculous meningitis
Authors: Combrinck Jill , Tshavhungwe Phophi , Rohlwink Ursula , Enslin Nico , Thango Nqobile , Lazarus Jed , Kriegler Katie , Castel Sandra , Abdelgawad Noha , Mcilleron Helen , Denti Paolo , Wiesner Lubbe , Figaji Anthony
Published: December 2023

Background

Tuberculous meningitis (TBM) is the most lethal form of TB. To study the disease, drug concentrations in samples obtained from the spinal CSF are usually used to reflect brain concentrations. Emerging data suggest that transport of substances across capillaries in the brain (ventricular CSF) and spinal cord may differ.

Methods

We examined paired, time-linked samples of ventricular CSF (VCSF) and lumbar CSF (LCSF) of 28 patients with TBM and analysed these for rifampicin and total protein concentrations. Clinically indicated samples from procedures to determine the level of CSF block were collected from children being treated for TBM and hydrocephalus. Total protein concentrations were determined using the bicinchoninic acid (BCA) or turbidimetry assay, and rifampicin concentrations were determined using a validated LC coupled with tandem MS method. A paired Wilcoxon signed-rank test was used to determine significance.

Results

TBM was confirmed in 19 cases (68%) using TB culture or GeneXpert Mtb/Rifampicin assay. All other cases were classified as probable. The median total protein concentration in LCSF was 6.0 g/L and in VCSF was 1.3 g/L. The median rifampicin concentration in LCSF was 299 ng/mL and 133 ng/mL in VCSF. The median ratio of LCSF/VSCF for protein was 4.23 and 1.57 for rifampicin.

Conclusions

Total protein and rifampicin concentrations differed significantly between the two compartments, both being higher in LCSF than in VCSF samples (P < 0.0001 for total protein and P = 0.0046 for rifampicin). Further studies are required to explore the causative reasons for the observed differences.
Use of Fourier-transform infrared spectroscopy for real-time outbreak investigation of OXA-48-producing Escherichia coli
Authors: Kon Hadas , Lurie-Weinberger Mor N , Lugassy Carmela , Chen Dafna , Schechner Vered , Schwaber Mitchell J , Hussein Khetam , Alon Tamar , Tarabeia Jalal , Hamo Moran , Firan Ibraheem , Aboalhega Worood , Lomansov Elena , Mendelsohn Sigal , Keren-Paz Alona , Carmeli Yehuda
Published: December 2023

Background

Efficient infection control during carbapenem-resistant Enterobacterales outbreaks demands rapid and simple techniques for outbreak investigations. WGS, the current gold standard for outbreak identification, is expensive, time-consuming and requires a high level of expertise. Fourier-transform infrared (FTIR) spectroscopy (IR Biotyper) is a rapid typing method based on infrared radiation applied to samples, which provides a highly specific absorption spectrum.

Objectives

To investigate an outbreak of OXA-48-producing Escherichia coli in real-time using FTIR and subsequently compare the results with WGS.

Methods

Twenty-one isolates were collected during a nosocomial outbreak, and identification and antibiotic susceptibilities were confirmed by VITEK®2. FTIR was conducted for all isolates, and nine representative isolates were sequenced.

Results

FTIR was able to correctly determine the clonal relatedness of the isolates and to identify the outbreak cluster, as confirmed by WGS. By WGS, isolates in the main FTIR cluster belonged to the same MLST type and core-genome MLST type, and they harboured similar plasmids and resistance genes, whereas the singletons external to the FTIR cluster had different genetic content.

Conclusions

FTIR can operate as a rapid, efficient and reliable first-line tool for outbreak investigations during a real-time ongoing E. coli outbreak, which can contribute to limiting the spread of pathogens.
Effect of Extraction Procedure Substitution on Automated Tacrolimus, Sirolimus, and Cyclosporine Assays
Authors: Chandras Athanasia , Mendu Damodara R , Kirchhoff Daniel C
Published: December 2023

Background

An erroneously high tacrolimus level was reported to a clinician. A root cause analysis investigation failed to determine the cause of the error. It was suspected that the incorrect preanalytical extraction reagent and procedure was used during testing; however, how this would affect the assayed drug concentration was unclear. Here we investigated the effect of the substitution of sirolimus, tacrolimus, and cyclosporine extraction reagents on assayed drug concentration.

Methods

Tacrolimus, sirolimus, and cyclosporine concentration were measured on the Abbott Architect i2000 analyzer. Each assay requires a preanalytical extraction step, with a distinct reagent. We investigated the effect of the substitution of the extraction reagents and procedure between the 3 assays on the measured drug concentration. Two experiments were performed, one on samples of known drug concentration and one on samples with no drug present.

Results

Substituting cyclosporine and sirolimus extraction procedures increased assayed tacrolimus concentrations from 5.6 to 8.47 (+51.25%) and 8.13 (+45.18%) ng/mL, respectively. Extraction procedure substitutions decreased assayed sirolimus from 13.63 to 4.60 (−66.25%) and 8.07 (−40.79%) ng/mL for cyclosporine and tacrolimus. Cyclosporine concentration increased from 274.60 to 391.30 (+42.50%) ng/mL using sirolimus extraction reagents and to 757.30 (+175.78%) ng/mL using tacrolimus extraction reagents. Cross-reactivity was observed between the tacrolimus assay and sirolimus and cyclosporine extraction reagents.

Conclusions

Significant changes, both positive and negative, are observed in assayed drug concentration when incorrect extraction procedures are used in the Abbott i2000 tacrolimus, sirolimus, and cyclosporine assays. Preanalytic extraction procedures should be investigated when performing root cause analysis for erroneous therapeutic drug values.
In situ cryo-electron tomography: a new method to elucidate cytoplasmic zoning at the molecular level
Authors: Chen Lin , Fukata Yuko , Murata Kazuyoshi
Published: December 2023

Cryo-electron microscopy was developed as a powerful tool for imaging biological specimens in near-native conditions. Nowadays, advances in technology, equipment and computations make it possible to obtain structures of biomolecules with near-atomic resolution. Furthermore, cryo-electron tomography combined with continuous specimen tilting allows structural analysis of heterogeneous biological specimens. In particular, when combined with a cryo-focused ion beam scanning electron microscope, it becomes possible to directly analyse the structure of the biomolecules within cells, a process known as in situ cryo-electron tomography. This technique has the potential to visualize cytoplasmic zoning, involving liquid–liquid phase separation, caused by biomolecular networks in aqueous solutions, which has been the subject of recent debate. Here, we review advances in structural studies of biomolecules to study cytoplasmic zoning by in situ cryo-electron tomography.
Mitochondrial quality control via organelle and protein degradation
Authors: Yamano Koji , Kinefuchi Hiroki , Kojima Waka
Published: December 2023

Mitochondria are essential eukaryotic organelles that produce ATP as well as synthesize various macromolecules. They also participate in signalling pathways such as the innate immune response and apoptosis. These diverse functions are performed by >1,000 different mitochondrial proteins. Although mitochondria are continuously exposed to potentially damaging conditions such as reactive oxygen species, proteases/peptidases localized in different mitochondrial subcompartments, termed mitoproteases, maintain mitochondrial quality and integrity. In addition to processing incoming precursors and degrading damaged proteins, mitoproteases also regulate metabolic reactions, mitochondrial protein half-lives and gene transcription. Impaired mitoprotease function is associated with various pathologies. In this review, we highlight recent advances in our understanding of mitochondrial quality control regulated by autophagy, ubiquitin–proteasomes and mitoproteases.
NRIP1 regulates cell proliferation in lung adenocarcinoma cells
Authors: Watanabe Fumihiko , Sato Shigemitsu , Hirose Takuo , Endo Moe , Endo Akari , Ito Hiroki , Ohba Koji , Mori Takefumi , Takahashi Kazuhiro
Published: December 2023

Nuclear receptor interacting protein 1 (NRIP1) is a transcription cofactor that regulates the activity of nuclear receptors and transcription factors. Functional expression of NRIP1 has been identified in multiple cancers. However, the expression and function of NRIP1 in lung adenocarcinoma have remained unclear. Thus, we aimed to clarify the NRIP1 expression and its functions in lung adenocarcinoma cells. NRIP1 and Ki-67 were immunostained in the tissue microarray section consisting of 64 lung adenocarcinoma cases, and the association of NRIP1 immunoreactivity with clinical phenotypes was examined. Survival analysis was performed in lung adenocarcinoma data from The Cancer Genome Atlas (TCGA). Human A549 lung adenocarcinoma cell line with an NRIP1-silencing technique was used in vitro study. Forty-three of 64 cases were immunostained with NRIP1. Ki-67–positive cases were more frequent in NRIP1-positive cases as opposed to NRIP1-negative cases. Higher NRIP1 mRNA expression was associated with poor prognosis in the TCGA lung adenocarcinoma data. NRIP1 was mainly located in the nucleus of A549 cells. NRIP1 silencing significantly reduced the number of living cells, suppressed cell proliferation, and induced apoptosis. These results suggest that NRIP1 participates in the progression and development of lung adenocarcinoma. Targeting NRIP1 may be a possible therapeutic strategy against lung adenocarcinoma.
Exploring protein lipidation by mass spectrometry-based proteomics
Authors: Tsumagari Kazuya , Isobe Yosuke , Imami Koshi , Arita Makoto
Published: December 2023

Protein lipidation is a common co- or post-translational modification that plays a crucial role in regulating the localization, interaction and function of cellular proteins. Dysregulation of lipid modifications can lead to various diseases, including cancer, neurodegenerative diseases and infectious diseases. Therefore, the identification of proteins undergoing lipidation and their lipidation sites should provide insights into many aspects of lipid biology, as well as providing potential targets for therapeutic strategies. Bottom-up proteomics using liquid chromatography/tandem mass spectrometry is a powerful technique for the global analysis of protein lipidation. Here, we review proteomic methods for profiling protein lipidation, focusing on the two major approaches: the use of chemical probes, such as lipid alkyne probes, and the use of enrichment techniques for endogenous lipid-modified peptides. The challenges facing these methods and the prospects for developing them further to achieve a comprehensive analysis of lipid modifications are discussed.
Genome-wide analysis and characterization of HSP gene families (HSP20, HSP40, HSP60, HSP70, HSP90) in the yellow fever mosquito (Aedes aegypti) (Diptera: Culicidae)
Authors: Turan Murat
Published: December 2023

The heat shock protein (HSP) gene families, present across prokaryotes to eukaryotes, play vital roles in growth, development, and heat resistance processes. While HSP proteins have been identified and characterized in various species, this study achieved the first genome-wide identification and characterization of HSP proteins in the Aedes aegypti genome. This study identified and assessed 80 potential HSP genes in Ae. aegypti. The phylogenetic relationships of HSP genes were investigated in Ae. aegypti, Anopheles stephensi, and Drosophila melanogaster. Additionally, the structural features, chromosomal locations, protein characteristics, 3D structure, protein–protein interactions, and microsatellites associated with HSP proteins were examined in Ae. aegypti. The phylogenetic analysis of HSP gene families revealed distinct intra-group relationships for each HSP group. Each family exhibited relatively conserved genetic structures and motif components. In the expression analysis of growth and development, high expression was observed in certain HSP20 and HSP70 genes, while others exhibited low expression. Notably, sex-dependent expression differences were observed, particularly in HSP20 genes. These findings, the relationships, evolution, and modification of HSP gene families are illuminated by these comprehensive findings, and a better understanding of the mechanisms underlying growth, development, and heat resistance in vector organisms is facilitated.
Firmicutes and Bacteroidetes contribute to mass gain variation in female obligate hibernators
Authors: Degregori Samuel , Johnson Gina C , Barber Paul H , Blumstein Daniel T
Published: December 2023

Obtaining body condition is an important life history challenge that directly impacts individual fitness and is particularly important for hibernating animals, whose maintenance of adequate body fat and mass is essential for survival. It is well-documented that host-associated microorganisms play a vital role in animal physiology and behavior. Recent work demonstrates that gut microbes are associated with fat accumulation and obesity, particularly the phyla Firmicutes and Bacteroidetes. The focus of most microbiome studies has been on human health or involved lab-reared animals used as a model system. However, these microbes likely are important for individual fitness in wild populations and provide potential mechanistic insights into the adaptability and survival of wildlife. Here we tested whether symbiotic microorganisms within the phyla of Firmicutes and Bacteroidetes were associated with summer mass gain in an exceptionally well-studied wild population of yellow-bellied marmots (Marmota flaviventer) by analyzing 207 fecal samples collected over 5 summer active seasons. Results showed that marmots with higher mass gain rates had a greater relative abundance of Firmicutes. In contrast, a higher relative abundance of Bacteroidetes was associated with lower mass gain rates, but only for marmots living in harsher environments. Similar patterns were found at the family level where Ruminococcaceae, a member of Firmicutes, was associated with higher mass gain rates, and Muribaculaceae, a member of Bacteroidetes, was associated with lower mass gain rates in harsher environments. Although correlative, these results highlight the potential importance of symbiotic gut microbiota to mass gain in the wild—a trait associated with survival and fitness in many taxonomic groups.
A new extinct desert rodent from the Holocene of South America and its bearing on the diversity of Octodontidae (Hystricognathi)
Authors: Verzi Diego H , Olivares A Itatí , De Santi Nahuel A , Morgan Cecilia C , López José Manuel , Chiavazza Horacio
Published: December 2023

A Late Holocene (ca. 3,100 to 380 BP) sample of the viscacha rat genus Octomys (Octodontidae) from the Vaquerías Gruta 1 site (VQ-G1) in western Argentina is reported. Phylogenetic and morphometric comparative analyses with living octodontids support that the VQ-G1 sample is related to the desert specialists Tympanoctomys and Octomys, and is sister to the only living species of the latter, O. mimax. The estimated morphological distance to O. mimax is greater than that between pairs of congeneric octodontid species, and even greater than that between some species belonging to different genera. This suggests that the sample represents a new species, whose young age prevents interpreting it as an anagenetic ancestor of O. mimax. If the new species is the result of cladogenesis, its absence in the current fauna represents actual extinction, which among caviomorphs is added to those of †Clyomys riograndensis, †Dicolpomys fossor, †Ctenomys viarapaensis, and †Galea tixiensis—also extinct in the Late Holocene. Thus, the VQ-G1 sample provides evidence of changes in diversity and distribution undergone by small mammals in southern South America during that time. The potential contribution of the Holocene record may be key to elucidate this issue from both an evolutionary and a conservation perspective. This requires a detailed systematic approach to determine whether the taxa under study are truly independent evolutionary units, as well as geographically broad sampling efforts to distinguish the changes affecting distribution from those producing irreversible changes in diversity.