bluuebunny/crossref_metadata_2025 huggingface dataset:
Spiking Laguerre Volterra networks—predicting neuronal activity from local field potentials
Authors: Kostoglou Kyriaki , Michmizos Konstantinos P , Stathis Pantelis , Sakas Damianos , Nikita Konstantina S , Mitsis Georgios D
Published: July 2024

Objective. Understanding the generative mechanism between local field potentials (LFP) and neuronal spiking activity is a crucial step for understanding information processing in the brain. Up to now, most approaches have relied on simply quantifying the coupling between LFP and spikes. However, very few have managed to predict the exact timing of spike occurrence based on LFP variations. Approach. Here, we fill this gap by proposing novel spiking Laguerre–Volterra network (sLVN) models to describe the dynamic LFP-spike relationship. Compared to conventional artificial neural networks, the sLVNs are interpretable models that provide explainable features of the underlying dynamics. Main results. The proposed networks were applied on extracellular microelectrode recordings of Parkinson’s Disease patients during deep brain stimulation (DBS) surgery. Based on the predictability of the LFP-spike pairs, we detected three neuronal populations with unique signal characteristics and sLVN model features. Significance. These clusters were indirectly associated with motor score improvement following DBS surgery, warranting further investigation into the potential of spiking activity predictability as an intraoperative biomarker for optimal DBS lead placement.
Structure and properties of composite nanostructured coatings on steel
Authors: Petrova Anna
Published: July 2024

In the recent years, the development of nanotechnology has increased the applications of nanoparticles, and the possibility of incorporating them into innovative composite coatings. In this paper, we aim to improve the corrosion resistance of 42CrMo4 and 65G steels by electroless chemical deposition of Ni, reinforced by adding of nanoparticles of nanodiamants (ND), boron (B) or cubic-BN (CBN). Consequently, by this approach we extend the useful-life of these mechanical parts, making them suitable for aerospace and automotive industry.
Formation of medical radioisotope 111In in photonuclear reactions
Authors: Bakhshiyan T.M. , Hovhannisyan G.H.
Published: July 2024

The possibility of photonuclear production of 111In radioisotope has been
investigated. The enriched target 112Sn was irradiated at the linear electron accelerator
LUE-75 of A. Alikhanian National Science Laboratory (Yerevan, Armenia) at the bremsstrahlung
endpoint energy Eγmax = 55 MeV. The cross section per equivalent quantum for
reactions 112Sn(γ,x)111In, 112Sn(γ,n)111Sn,
112Sn(γ,2n)110Sn, 112Sn(γ,3n)109Sn,112
Sn(γ,pn)110mIn, 112Sn(γ,pn)110g110In,
112Sn(γ,p2n)109In have been measured via the method of activation and off-line
γ-ray spectrometric technique. The cross section per equivalent quantum of the 111In
in photonuclear reaction was compared with its cross section in proton induced reaction on cadmium
targets and other possible 111In production routes. It is shown that the photonuclear method
can be used for the production of 111In.
Timing resolution performance of Timepix4 bump-bonded assemblies
Authors: Bolzonella R. , Alozy J. , Ballabriga R. , van Beuzekom M. , Biesuz N.V. , Campbell M. , Cardarelli P. , Cavallini V. , Coco V. , Cotta Ramusino A. , Fiorini M. , Gromov V. , Guarise M. , Llopart Cudie X. , Okamura S. , Romolini G. , Saputi A. , Vitkovskiy A.
Published: July 2024

The timing performance of the Timepix4 application-specific
integrated circuit (ASIC) bump-bonded to a
100 μm thick n-on-p
silicon sensor is presented. A picosecond pulsed infrared laser was
used to generate electron-hole pairs in the silicon bulk in a
repeatable fashion, controlling the amount, position and time of the
stimulated charge signal. The timing resolution for a single pixel
has been measured to 107 ps
r.m.s. for laser-stimulated signals in the silicon sensor
bulk. Considering multi-pixel clusters, the measured timing
resolution reached 33 ps
r.m.s. exploiting oversampling of the timing information over
several pixels.
Design, fabrication and testing of Al/p-Si Schottky and pn junctions for radiation studies
Authors: Giulio Villani E. , Zhang Dengfeng , Malik Adnan , Vickey Trevor , Chen Yebo , Kurth Matthew G. , Liu Peilian , Zhu Hongbo , Koffas Thomas , Klein Christoph Thomas , Vandusen Robert , Aiton Rodney , Mccormick Angela , Tarr Garry
Published: July 2024

Strip and pixels sensors, fabricated on high resistivity
silicon substrate, normally of p-type, are used in detectors
for High Energy Physics (HEP) typically in a hybrid detector
assembly. Furthermore, and owing to their inherent advantages over
hybrid sensors, Monolithic Active Pixel Sensors (MAPS) fabricated in
CMOS technology have been increasingly implemented in HEP
experiments. In all cases, their use in higher radiation areas
(HL-LHC and beyond) will require options to improve their radiation
hardness and time resolution. These aspects demand a deep
understanding of their radiation damage and reliable models to
predict their behaviours at high fluences. As a first step, we
fabricated several Schottky and n-on-p diodes, to
allow a comparison of results and provide a backup solution for test
devices, on 6 or 4-inch p-type silicon wafers with
50 μm epitaxial thickness and of doping concentration as they
are normally used in HEP detectors and CMOS MAPS devices. In this
paper, details of the design and fabrication process, along with
test results of the fabricated devices before irradiation, will be
provided. Additional test results on irradiated devices will be
provided in subsequent publications.
Seasonality of the intraseasonal variability in the upper equatorial western Pacific Ocean currents
Authors: Song Lina , Li Yuanlong , Lee June-Yi , Wang Fan , Wang Jianing
Published: July 2024

Quantifying spatiotemporal characteristics of intraseasonal variability (ISV) of upper ocean (100 m) zonal currents (U) in the equatorial western Pacific remains difficult due to a lack of direct observations. Here we investigate the characteristics by analyzing five subsurface mooring data at 140°–142° E, 1.7° S–4.7° N, from January 2014 to April 2021. Our analysis revealed that U ISV has an amplitude exceeding 40 cm s−1, comparable to their long-term mean, and pronounced seasonality, with a peaking period in boreal winter–spring (October–April) and a weakening period in summer–autumn (May–September). U ISV intensity in the south of the equator is 50% stronger than that in the north. Analysis of satellite/reanalysis data and model experiments suggests that atmospheric intraseasonal oscillation accounts for 80% of the U ISV seasonality through wind forcing, while the oceanic internal process contributes 20% through nonlinear baroclinic instability. The consistent variation in mixed layer depth indicates the potential roles of oceanic ISVs in seasonal phase locking of El Niño–Southern oscillation. Our results highlight the significance of direct observations for better understanding and estimating ISVs of ocean circulation.
Overlooked cooling effects of albedo in terrestrial ecosystems
Authors: Chen Jiquan , Lei Cheyenne , Chu Housen , Li Xianglan , Torn Margaret , Wang Ying-Ping , Sciusco Pietro , Robertson G Philip
Published: July 2024

Radiative forcing (RF) resulting from changes in surface albedo is increasingly recognized as a significant driver of global climate change but has not been adequately estimated, including by Intergovernmental Panel on Climate Change (IPCC) assessment reports, compared with other warming agents. Here, we first present the physical foundation for modeling albedo-induced RF and the consequent global warming impact (GWIΔα
). We then highlight the shortcomings of available current databases and methodologies for calculating GWIΔα
at multiple temporal scales. There is a clear lack of comprehensive in situ measurements of albedo due to sparse geographic coverage of ground-based stations, whereas estimates from satellites suffer from biases due to the limited frequency of image collection, and estimates from earth system models (ESMs) suffer from very coarse spatial resolution land cover maps and associated albedo values in pre-determined lookup tables. Field measurements of albedo show large differences by ecosystem type and large diurnal and seasonal changes. As indicated from our findings in southwest Michigan, GWIΔα
is substantial, exceeding the RFΔα
values of IPCC reports. Inclusion of GWIΔα
to landowners and carbon credit markets for specific management practices are needed in future policies. We further identify four pressing research priorities: developing a comprehensive albedo database, pinpointing accurate reference sites within managed landscapes, refining algorithms for remote sensing of albedo by integrating geostationary and other orbital satellites, and integrating the GWIΔα
component into future ESMs.
Radiation versus environmental degradation in unencapsulated metal halide perovskite solar cells
Authors: Khanal Megh N , Whiteside Vincent R , Parashar Mritunjaya , Merckx Tamara , Sharma Mohin , Kuang Yinghuan , Aguirre Aranzazu , Afshari Hadi , Hamtaei Sarallah , Aernouts Tom , Vermang Bart , Rout Bibhudutta , Sellers Ian R
Published: July 2024

Here, the radiation hardness of metal halide perovskite solar cells exposed to space conditions versus the effects of environmental degradation are assessed. The relative response of the constituent layers of the architecture to radiation is analyzed, revealing a general resilience of the structure when assessed across varying proton energy levels and fluences. However, despite the tolerance of the structure to irradiation, sensitivity to environmental degradation is observed during the transit of the device between the radiation and characterization facilities. Experimental evidence suggests the NiO
x
/perovskite interface is particularly sensitive to the effects of humidity and/or temperature exposure, while the irradiation of the devices appears to induce thermally activated annealing: improving the solar cells upon radiation exposure.
Optimisation of electron irradiation for creating spin ensembles in hexagonal boron nitride
Authors: Healey Alexander J , Singh Priya , Robertson Islay O , Gavin Christopher , Scholten Sam C , Broadway David A , Reineck Philipp , Abe Hiroshi , Ohshima Takeshi , Kianinia Mehran , Aharonovich Igor , Tetienne Jean-Philippe
Published: July 2024

Boron vacancy centre (

V
B
−

) ensembles in hexagonal boron nitride (hBN) have attracted recent interest for their potential as two-dimensional solid-state quantum sensors. Irradiation is necessary for

V
B
−

creation, however, to date only limited attention has been given to optimising the defect production process, especially in the case of bulk irradiation with high-energy particles, which offers scalability through the potential for creating ensembles in large volumes of material. Here we systematically investigate the effect of electron irradiation by varying the dose delivered to a range of hBN samples, which differ in their purity, and search for an optimum in measurement sensitivity. We find that moderate electron irradiation doses (

≈

5
×

10

18

cm−2) appear to offer the best sensitivity, and also observe a dependence on the initial crystal purity. These results pave the way for the scalable and cost-effective production of hBN quantum sensors, and provide insight into the mechanisms limiting

V
B
−

spin properties.
Legal Personhood and Gender Women and Gender Minorities
Authors: Arstein-Kerslake Anna
Published: July 2024

This chapter applies the right to legal personhood in the context of gender, including both women and gender minorities. It uses critical feminist theory to discuss the historical denial of legal agency (an element of legal personhood) to women and gender minorities via labels of ‘hysteria’ and ‘mental illness’. It also discusses modern barriers to legal personhood for these groups, such as the inability to obtain identity documents that accurately reflect gender identity, which are required for the exercise of legal agency. The barriers to legal personhood in the private sphere, such as interpersonal relationships that result in limitations on legal agency, for example, husbands limiting the legal decision-making power of their wives, are also highlighted. Finally, it is argued that the right to legal personhood has the potential to provide new avenues for redistributing power and privilege into the hands of women and gender minorities.
Extending Legacy
Authors: Foster Ann-Marie
Published: July 2024

This chapter traces how family memory of the First World War and early twentieth-century disasters changed and developed from the 1970s to the late 2010s. Following the death of a loved one, siblings, children, nieces, and nephews continued to memorialize the dead, but their memories were increasingly mixed with cultural memories that had begun to circulate. It is in these long-term memory trends that we can see a distinct split, and there were significant differences in the ways that war and disaster memories were influenced by cultural memory. By the 1980s, individuals turned to cultural understandings to contextualize their family histories, which heavily influenced how families presented their history to the world. The centenaries of war and disaster offered families a chance to show their connection to the dead on an (inter)national stage, through websites designed to memorialize the war dead and news stories focusing on family memory of disaster.
Bullshit
Authors: Benatar David
Published: July 2024

This chapter discusses the ethics of bullshit. Almost all the existing literature on bullshit is concerned with what bullshit is. This chapter does devote some attention to that question, along with an explanation of why there is so much of it. However, it does so only as a prelude to discussing the ethical issues concerning bullshit. The initial focus is on how we should respond to the bullshit of others. It is argued that sometimes we should tolerate bullshit and sometimes we should challenge it—‘calling bullshit’. Sometimes challenging bullshit is supererogatory. Even when one does not challenge bullshit oneself, one can have duties to those who do challenge it. The chapter then turns to the question of when, if ever, it is permissible to produce bullshit oneself. It is argued that the general presumption should be against bullshitting, but that this presumption may sometimes be defeated.
Introduction
Authors: Valentim Vicente
Published: July 2024

Radical-right behavior is increasing across Western democracies, often very fast. Previous research has shown, however, that political attitudes and preferences do not change this fast. The Introduction argues that, to understand these patterns, one needs to appreciate the crucial role of social norms as drivers of political behavior. Building on a norms-based theory of political supply and demand, it maintains that growing radical-right behavior is driven by individuals who long held radical-right views, but did not act on them because they thought that they were socially unacceptable. If these voters do not show their views, politicians underestimate how much latent support there is for radical-right policy. This leaves the radical right with less skilled leaders, demobilizing even radical-right voters from voting for them. But, if politicians realize that there is more private support for radical-right policy than is typically observable, they have an incentive to run with a radical-right platform and mobilize silent radical-right views. Their electoral success, in turn, makes radical-right individuals more comfortable showing their views, and impels more politicians to join the radical right.
The three phases of political normalization
Authors: Valentim Vicente
Published: July 2024

This chapter argues that growing radical-right behavior across Western democracies is the result of normalization. It is driven by individuals who already held radical-right views, but previously did not act on them because they were deemed socially unacceptable. Normalization can be defined as a process where social norms against a given political preference weaken. There are three phases to political normalization: first, a latency phase, where the radical right is socially stigmatized, electorally weak, and has low-skilled leaders; second, an activation phase, where a skilled entrepreneur enters the race with a radical-right platform and is able to mobilize radical-right support in the voting booth, but still not in public; and finally, a surfacing phase, where the entrepreneur achieves an electoral breakthrough, making radical-right individuals more comfortable publicly acting on their views and impelling more politicians to join the radical right.
Deep learning pipeline reveals key moments in human embryonic development predictive of live birth after in vitro fertilization
Authors: Mapstone Camilla , Hunter Helen , Brison Daniel , Handl Julia , Plusa Berenika
Published: July 2024

Demand for in vitro fertilization (IVF) treatment is growing; however, success rates remain low partly due to difficulty in selecting the best embryo to be transferred. Current manual assessments are subjective and may not take advantage of the most informative moments in embryo development. Here, we apply convolutional neural networks (CNNs) to identify key windows in pre-implantation human development that can be linked to embryo viability and are therefore suitable for the early grading of IVF embryos. We show how machine learning models trained at these developmental time points can be used to refine overall embryo viability assessment. Exploiting the well-known capabilities of transfer learning, we illustrate the performance of CNN models for very limited datasets, paving the way for the use on a clinic-by-clinic basis, catering for local data heterogeneity.
Is there a clinically meaningful association between paediatric atopic dermatitis and the risk of inflammatory bowel disease?
Authors: Melton Matthew , Feldman Steven R
Published: July 2024

A previously published article has reported a statistically significant association between atopic dermatitis (AD) and inflammatory bowel disease (IBD). We would like to respond to this report, to elaborate on the clinical significance of these data. Based on this report, nearly 8000 patients would need to be seen each year for 1 patient with AD to have a connected case of IBD.
Tim-4 alleviates acute hepatic injury by modulating homeostasis and function of NKT cells
Authors: Wang Yingchun , Wang Yuzhen , Ge Yutong , Wu Zhuanchang , Yue Xuetian , Li Chunyang , Liang Xiaohong , Ma Chunhong , Wang Pin , Gao Lifen
Published: July 2024

T-cell immunoglobulin and mucin domain-containing molecule 4 (Tim-4) is an immune checkpoint molecule, which involves in numerous inflammatory diseases. Tim-4 is mainly expressed on antigen-presenting cells. However, increasing evidence has shown that Tim-4 is also expressed on natural killer T (NKT) cells. The role of Tim-4 in maintaining NKT cell homeostasis and function remains unknown. In this study, we explored the effect of Tim-4 on NKT cells in acute liver injury. This study found that Tim-4 expression on hepatic NKT cells was elevated during acute liver injury. Tim-4 deficiency enhanced IFN-γ, TNF-α expression while impaired IL-4 production in NKT cells. Loss of Tim-4 drove NKT-cell effector lineages to be skewed to NKT1 subset. Furthermore, Tim-4 KO mice were more susceptible to α-Galactosylceramide (α-GalCer) challenge. In conclusion, our findings indicate that Tim-4 plays an important role in regulating homeostasis and function of NKT cells in acute liver injury. Therefore, Tim-4 might become a new regulator of NKT cells and a potential target for the therapy of acute hepatitis.
Ventricular assist device support in paediatric patients with restrictive cardiomyopathy—clinical outcomes and haemodynamics
Authors: Rohde Sofie , Miera Oliver , Sandica Eugen , Adorisio Rachele , Salas-Mera Diana , Wiedemann Dominik , Sliwka Joanna , Amodeo Antonio , Gollmann-Tepeköylü Can , Napoleone Carlo Pace , Angeli Emanuela , Veen Kevin , de By Theo , Meyns Bart
Published: July 2024

OBJECTIVES

Restrictive cardiomyopathy is rare and is generally associated with worse clinical outcomes compared to other cardiomyopathies. Ventricular assist device (VAD) support for these children is seldom applied and often hampered by the surgical difficulties.

METHODS

All paediatric (<19 years) patients with a restricted cardiomyopathy supported by a VAD from the EUROMACS database were included and compared to patients with a dilated cardiomyopathy (retrospective database analyses). Participating centres were retrospectively contacted to provide additional detailed echo and Swan Ganz measurements to analyse the effect of VAD support on pulmonary artery pressure and right ventricular function.

RESULTS

Forty-four paediatric VAD-supported patients diagnosed with restricted cardiomyopathy were included, with a median age at implantation of 5.0 years. Twenty-six of the 44 patient with a restricted cardiomyopathy survived to transplantation (59.1%), 16 died (36.4%) and 2 are still on ongoing VAD support (4.5%) after a median duration of support of 95.5 days (interquartile range 33.3–217.8). Transplantation probability after 1 and 2 years of VAD support in patients with a restricted cardiomyopathy were comparable to patients with a dilated cardiomyopathy (52.3% vs 51.4% and 59.5% vs 60.1%, P = 0.868). However, mortality probability was higher in the restricted cardiomyopathy cohort (35.8% vs 17.0% and 35.8% vs 19.0%, P = 0.005). Adverse event rates were high (cerebrovascular accident in 31.8%, pump thrombosis in 29.5%, major bleeding 25.0%, eventual biventricular support in 59.1%). In the atrially cannulated group, cerebrovascular accident and pump thrombosis occurred in twice as much patients (21.1% vs 40.0%, P = 0.595 and 15.8% vs 40.0%, P = 0.464; probably non-significant due to the small numbers). Pulmonary arterial pressures improved after implantation of a VAD, and 6 patients who were initially labelled as ineligible due to pulmonary hypertension could eventually be transplanted.

CONCLUSIONS

VAD support in children with a restricted cardiomyopathy is rarely performed. Mortality and adverse event rates are high. On the other hand, survival to cardiac transplantation was 59.1% with all patients surviving the 1st 30 days after cardiac transplantation. Pulmonary arterial pressures improved while on support, potentially making cardiac transplantation a viable option for previously ineligible children.
Early-onset atherosclerotic cardiovascular disease
Authors: Mousavi Idine , Suffredini John , Virani Salim S , Ballantyne Christie M , Michos Erin D , Misra Arunima , Saeed Anum , Jia Xiaoming
Published: July 2024

abstract

Recent trends indicate a concerning increase in early-onset atherosclerotic cardiovascular disease (ASCVD) among younger individuals (men aged <55 years women aged <65 years). These findings highlight the pathobiology of ASCVD as a disease process that begins early in life and underscores the need for more tailored screening methods and preventive strategies. Increasing attention has been placed on the growing burden of traditional cardiometabolic risk factors in young individuals while also recognizing unique factors that mediate risk of pre-mature atherosclerosis in this demographic such as substance use, socioeconomic disparities, adverse pregnancy outcomes, and chronic inflammatory states that contribute to the increasing incidence of early ASCVD. Additionally, mounting evidence has pointed out significant disparities in the diagnosis and management of early ASCVD and cardiovascular outcomes based on sex and race. Moving towards a more personalized approach, emerging data and technological developments using diverse tools such as polygenic risk scores and coronary artery calcium scans have shown potential in earlier detection of ASCVD risk. Thus, we review current evidence on causal risk factors that drive the increase in early ASCVD and highlight emerging tools to improve ASCVD risk assessment in young individuals.
External validation and comparison of six cardiovascular risk prediction models in the Prospective Urban Rural Epidemiology (PURE)-Colombia study
Authors: Lopez-Lopez Jose P , Garcia-Pena Angel A , Martinez-Bello Daniel , Gonzalez Ana M , Perez-Mayorga Maritza , Muñoz Velandia Oscar Mauricio , Ruiz-Uribe Gabriela , Campo Alfonso , Rangarajan Sumathy , Yusuf Salim , Lopez-Jaramillo Patricio
Published: July 2024

Aims

To externally validate the SCORE2, AHA/ACC pooled cohort equation (PCE), Framingham Risk Score (FRS), Non-Laboratory INTERHEART Risk Score (NL-IHRS), Globorisk-LAC, and WHO prediction models and compare their discrimination and calibration capacity.

Methods and results

Validation in individuals aged 40–69 years with at least 10 years of follow-up and without baseline use of statins or cardiovascular diseases from the Prospective Urban Rural Epidemiology (PURE)-Colombia prospective cohort study. For discrimination, the C-statistic, and receiver operating characteristic curves with the integrated area under the curve (AUCi) were used and compared. For calibration, the smoothed time-to-event method was used, choosing a recalibration factor based on the integrated calibration index (ICI). In the NL-IHRS, linear regressions were used. In 3802 participants (59.1% women), baseline risk ranged from 4.8% (SCORE2 women) to 55.7% (NL-IHRS). After a mean follow-up of 13.2 years, 234 events were reported (4.8 cases per 1000 person-years). The C-statistic ranged between 0.637 (0.601–0.672) in NL-IHRS and 0.767 (0.657–0.877) in AHA/ACC PCE. Discrimination was similar between AUCi. In women, higher over-prediction was observed in the Globorisk-LAC (61%) and WHO (59%). In men, higher over-prediction was observed in FRS (72%) and AHA/ACC PCE (71%). Overestimations were corrected after multiplying by a factor derived from the ICI.

Conclusion

Six prediction models had a similar discrimination capacity, supporting their use after multiplying by a correction factor. If blood tests are unavailable, NL-IHRS is a reasonable option. Our results suggest that these models could be used in other countries of Latin America after correcting the overestimations with a multiplying factor.
Establishing an itaconic acid production process with Ustilago species on the low-cost substrate starch
Authors: Ernst Philipp , Wirtz Astrid , Wynands Benedikt , Wierckx Nick
Published: July 2024

Ustilago maydis and Ustilago cynodontis are natural producers of a broad range of valuable molecules including itaconate, malate, glycolipids, and triacylglycerols. Both Ustilago species are insensitive toward medium impurities, and have previously been engineered for efficient itaconate production and stabilized yeast-like growth. Due to these features, these strains were already successfully used for the production of itaconate from different alternative feedstocks such as molasses, thick juice, and crude glycerol. Here, we analyzed the amylolytic capabilities of Ustilago species for metabolization of starch, a highly abundant and low-cost polymeric carbohydrate widely utilized as a substrate in several biotechnological processes. Ustilago cynodontis was found to utilize gelatinized potato starch for both growth and itaconate production, confirming the presence of extracellular amylolytic enzymes in Ustilago species. Starch was rapidly degraded by U. cynodontis, even though no α-amylase was detected. Further experiments indicate that starch hydrolysis is caused by the synergistic action of glucoamylase and α-glucosidase enzymes. The enzymes showed a maximum activity of around 0.5 U ml−1 at the fifth day after inoculation, and also released glucose from additional substrates, highlighting potential broader applications. In contrast to U. cynodontis, U. maydis showed no growth on starch accompanied with no detectable amylolytic activity.
Characterization of mycobacteriophage Adephagia cytotoxic proteins
Authors: Freeman Krista G , Lauer Michael J , Jiang Danny , Roscher Jennifer , Sandler Sterling , Mercado Nicholas , Fryberger Robert , Kovalski Julia , Lutz Abigail R , Hughes Lee E , VanDemark Andrew P , Hatfull Graham F
Published: July 2024

Mycobacterium phage Adephagia is a cluster K phage that infects Mycobacterium smegmatis and some strains of Mycobacterium pathogens. Adephagia has a siphoviral virion morphology and is temperate. Its genome is 59,646 bp long and codes for one tRNA gene and 94 predicted protein-coding genes; most genes not associated with virion structure and assembly are functionally ill-defined. Here, we determined the Adephagia gene expression patterns in lytic and lysogenic growth and used structural predictions to assign additional gene functions. We characterized 66 nonstructural genes for their toxic phenotypes when expressed in M. smegmatis, and we show that 25 of these (38%) are either toxic or strongly inhibit growth, resulting in either reduced viability or small colony sizes. Some of these genes are predicted to be involved in DNA metabolism or regulation, but others are of unknown function. We also characterize the HicAB-like toxin–antitoxin (TA) system encoded by Adephagia (gp91 and gp90, respectively) and show that the gp90 antitoxin is lysogenically expressed, abrogates gp91 toxicity, and is required for normal lytic and lysogenic growth.
A chromosome-level genome assembly of Drosophila madeirensis, a fruit fly species endemic to the island of Madeira
Authors: Tomihara Kenta , Llopart Ana , Yamamoto Daisuke
Published: July 2024

Drosophila subobscura is distributed across Europe, the Near East, and the Americas, while its sister species, Drosophila madeirensis, is endemic to the island of Madeira in the Atlantic Ocean. D. subobscura is known for its strict light-dependence in mating and its unique courtship displays, including nuptial gift-giving. D. subobscura has also attracted the interest of researchers because of its abundant variations in chromosomal polymorphisms correlated to the latitude and season, which have been used as a tool to track global climate warming. Although D. madeirensis can be an important resource for understanding the evolutionary underpinning of these genetic characteristics of D. subobscura, little work has been done on the biology of this species. Here, we used a HiFi long-read sequencing data set to produce a de novo genome assembly for D. madeirensis. This assembly comprises a total of 111 contigs spanning 135.5 Mb and has an N50 of 24.2 Mb and a BUSCO completeness score of 98.6%. Each of the 6 chromosomes of D. madeirensis consisted of a single contig except for some centromeric regions. Breakpoints of the chromosomal inversions between D. subobscura and D. madeirensis were characterized using this genome assembly, updating some of the previously identified locations.
Pouch Salvage of Long Rectal Cuff Syndrome: Excision of Retained Rectum and Mesorectum With Conversion to Ileoanal Anastomosis
Authors: Goldenshluger Michael , Rieder Florian , Holubar Stefan D
Published: July 2024

Lay Summary

The diagnosis of long rectal cuff syndrome may be considered in patients with persistent rectal bleeding after ileal pouch–anal anastomosis. Pouch salvage with excision of residual rectum and conversion to an ileoanal anastomosis offers patients the chance to achieve stoma-free survival.
Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus
Authors: Kaneko Masayuki , Omori Tatsuki , Igai Katsura , Mabuchi Takako , Sakai-Tazawa Miho , Nishihara Arisa , Kihara Kumiko , Yoshimura Tsuyoshi , Ohkuma Moriya , Hongoh Yuichi
Published: July 2024

Anaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts’ fermentative metabolism by consuming excess H2. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of the Cononympha protists in the hindgut of the termite Coptotermes formosanus. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here “Candidatus Methanobrevibacter cononymphae”, is associated with both Cononympha leidyi and Cononympha koidzumii and that its infection rate in Cononympha cells varied from 0.0% to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in both Cononympha species and also on the gut wall. Thus, “Ca. Methanobrevibacter cononymphae” is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by a Cononympha cell. The genome of “Ca. Methanobrevibacter cononymphae” showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase gene fdhA, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.
Lingdan: enhancing encoding of traditional Chinese medicine knowledge for clinical reasoning tasks with large language models
Authors: Hua Rui , Dong Xin , Wei Yu , Shu Zixin , Yang Pengcheng , Hu Yunhui , Zhou Shuiping , Sun He , Yan Kaijing , Yan Xijun , Chang Kai , Li Xiaodong , Bai Yuning , Zhang Runshun , Wang Wenjia , Zhou Xuezhong
Published: July 2024

Objective

The recent surge in large language models (LLMs) across various fields has yet to be fully realized in traditional Chinese medicine (TCM). This study aims to bridge this gap by developing a large language model tailored to TCM knowledge, enhancing its performance and accuracy in clinical reasoning tasks such as diagnosis, treatment, and prescription recommendations.

Materials and Methods

This study harnessed a wide array of TCM data resources, including TCM ancient books, textbooks, and clinical data, to create 3 key datasets: the TCM Pre-trained Dataset, the Traditional Chinese Patent Medicine (TCPM) Question Answering Dataset, and the Spleen and Stomach Herbal Prescription Recommendation Dataset. These datasets underpinned the development of the Lingdan Pre-trained LLM and 2 specialized models: the Lingdan-TCPM-Chat Model, which uses a Chain-of-Thought process for symptom analysis and TCPM recommendation, and a Lingdan Prescription Recommendation model (Lingdan-PR) that proposes herbal prescriptions based on electronic medical records.

Results

The Lingdan-TCPM-Chat and the Lingdan-PR Model, fine-tuned on the Lingdan Pre-trained LLM, demonstrated state-of-the art performances for the tasks of TCM clinical knowledge answering and herbal prescription recommendation. Notably, Lingdan-PR outperformed all state-of-the-art baseline models, achieving an improvement of 18.39% in the Top@20 F1-score compared with the best baseline.

Conclusion

This study marks a pivotal step in merging advanced LLMs with TCM, showcasing the potential of artificial intelligence to help improve clinical decision-making of medical diagnostics and treatment strategies. The success of the Lingdan Pre-trained LLM and its derivative models, Lingdan-TCPM-Chat and Lingdan-PR, not only revolutionizes TCM practices but also opens new avenues for the application of artificial intelligence in other specialized medical fields. Our project is available at https://github.com/TCMAI-BJTU/LingdanLLM.
Divergent planes of nutrition in mature rams influences body composition, hormone and metabolite concentrations, and offspring birth measurements, but not semen characteristics or offspring growth
Authors: Bochantin-Winders Kerri A , Baumgaertner Friederike , Hurlbert Jennifer L , Menezes Ana Clara B , Kirsch James D , Dorsam Sheri T , Schauer Christopher S , Dahlen Carl R
Published: July 2024

Objectives of this experiment were to characterize the effects of ram plane of nutrition on body composition, concentrations of hormones and metabolites, sperm characteristics, and offspring outcomes. Mature Rambouillet rams (n = 24, BW = 82.9 ± 2.63 kg) were individually housed and randomly assigned to either a positive (POS; n = 8), maintenance (MAINT; n = 8), or negative (NEG; n = 8) plane of nutrition for an 84-day feeding period. Rams were fed a common diet, with daily feed allocations adjusted weekly based on body weight (BW) to achieve the targeted weight gain or loss (approximately 12% of initial BW). On 0, 28, 56, and 84-d, body condition score (BCS) and scrotal circumference (SC) were recorded, and blood and semen were collected. Following the feeding period, rams were placed in pens with 10 ewes each for a 28-d breeding period. Ewes were managed similarly throughout gestation and body weight and measurements were recorded at birth and weaning. Data were analyzed as repeated measures in time where appropriate with the mixed procedure of SAS, and individual ram was the experimental unit for all analysis. Ram BW was influenced by a treatment × day interaction (P < 0.001), with POS (0.12 ± 0.01 kg) having greater daily weight change than MAINT (0.1 ± 0.01 kg), which was greater than NEG (-0.12 ± 0.01 kg). Ram BCS and SC were influenced by treatment × day interactions (P ≤ 0.01), being similar on day 0 but POS being greater than NEG by day 56. Concentrations of triiodothyronine (T3) and T3:T4 ratio exhibited treatment × day interactions (P ≤ 0.02), as POS had greater values than NEG by day 84 (P ≤ 0.02). Concentration of insulin-like growth factor-1 was greater in POS than MAINT and NEG (P ≤ 0.02), and non-esterified fatty acids and thyroxine (T4) were influenced by a day effect (P ≤ 0.01), but testosterone was unaffected (P ≥ 0.09). Minimal differences in semen volume, sperm concentration, motility, or morphology were observed among treatments (P ≥ 0.31). A similar proportion of ewes bred by rams in the respective treatments lambed and weaned lambs (P ≥ 0.54). Birth weight, chest circumference, and shoulder-hip length were greater (P ≤ 0.05) in NEG lambs compared with POS and MAINT; however, no differences were detected in weaning weight and weaning body measurements (P ≥ 0.40). Findings suggest paternal nutrition during the period of sperm development may influence offspring outcomes, potentially as a result of in-utero programming of paternal origin.
Identifying integrated pest management resource needs among Virginia Master Gardeners
Authors: Frank Daniel L , Blevins-Wycoff Stephanie
Published: July 2024

Two survey questionnaires distributed to Master Gardener (MG) volunteers in Virginia provide valuable insights into their awareness, understanding, and utilization of integrated pest management (IPM). Survey responses reveal a varied level of familiarity with IPM, with a notable percentage of respondents lacking knowledge of the term and differing perceptions of its focus on non-chemical or chemical pest control methods. While respondents generally recommended IPM solutions more than half the time, factors limiting their decision to do so included comfort level, limited understanding or knowledge, lack of training, lack of client interest, and lack of resources. The survey results highlight an agreement among respondents regarding the adequacy of state Cooperative Extension Service materials in addressing IPM. Pest management guides, websites, and fact sheets were the IPM resources most frequently used and perceived as effective. Respondents expressed a preference for fact sheets as the top resource material to enhance public training programs, followed by other multimedia content. Moreover, the survey results provide insights into the specific pest-related needs of Virginia MGs, revealing their priorities in terms of arthropod, vertebrate pest, plant disease, and weed resource topics. Overall, the data from the surveys offers a comprehensive understanding of MG perspectives on IPM, identifying areas for program improvement and providing guidance for the development of targeted resources to enhance MG knowledge and facilitate more effective public outreach.
Going urban: variation in personality traits of an invasive species along an urbanization gradient
Authors: Tranquillo Claudia , Santicchia Francesca , Romeo Claudia , Bisi Francesco , Panzeri Mattia , Preatoni Damiano , Martinoli Adriano , Alberdi Antton , Wauters Lucas A
Published: July 2024

The fast-growing expansion of urban areas pose severe pressures on wildlife. However, some generalist native mammals thrive in urbanized landscapes, while invasive alien species (IAS) are often more abundant in cities than in rural habitats. Variation in phenotypes—such as differences in personality traits—can influence the probability to colonize anthropized areas, especially in the case of IAS where certain traits are related to invasion success. Here, we investigated the expression of activity, exploration, and social tendency in the invasive alien Eastern Gray Squirrel (Sciurus carolinensis) in replicated study sites along a rural–urban gradient in Northern Italy. Personality traits expression was estimated using an open field test (OFT) followed by a mirror image stimulation (MIS) test. We found that squirrels were more active in urban than in suburban and rural sites, and behaved more sociable in urban than in suburban sites. Conversely, exploration did not differ along the gradient. Results also reveal the presence of a behavioral syndrome: activity (OFT), social tendency, and activity–exploration (MIS). We suggest that variation in activity level and social behavior in urban habitats could favor some species to respond positively to urbanization. This study sheds light on the underexplored personality–urbanization relationship in IAS, helping to understand the complex process of invasion.
Sandwich freezing and freeze substitution of Arabidopsis plant tissues for electron microscopy
Authors: Yamaguchi Masashi , Sato Mayuko , Takahashi-Nakaguchi Azusa , Okamoto Michiyo , Toyooka Kiminori , Chibana Hiroji
Published: July 2024

Sandwich freezing is a method of rapid freezing by sandwiching specimens between two copper disks, and it has been used for observing exquisite close-to-native ultrastructure of living yeast and bacteria. Recently, this method has been found to be useful for preserving cell images of glutaraldehyde-fixed cultured cells, as well as animal and human tissues. In the present study, this method was applied to observe the fine structure of living Arabidopsis plant tissues and was found to achieve excellent ultrastructural preservation of cells and tissues. This is the first report of applying the sandwich freezing method to observe plant tissues.
Therapeutic plasma exchange for hyperviscosity syndrome in IgA multiple myeloma
Authors: Yurtsever Nalan , Binns Thomas C , Hendrickson Jeanne E , Tormey Christopher A , Lee Edward S
Published: July 2024

Hyperviscosity syndrome (HVS) is defined as the symptomatic presentation of increased blood thickness due to various clinical conditions such as hypergammaglobulinemia. HVS secondary to immunoglobulin (Ig)A multiple myeloma has been infrequently reported. Although the efficiency of IgM or IgG removal by therapeutic plasma exchange (TPE) is well described, the efficiency of IgA removal by TPE is not as well known. Here, we describe a case of HVS due to IgA myeloma in a patient who received 2 TPE treatments, with subsequent symptomatic improvement as well as decrease in IgA and viscosity levels.
Halo densities and pericenter distances of the bright Milky Way satellites as a test of dark matter physics
Authors: Andrade Kevin E , Kaplinghat Manoj , Valli Mauro
Published: July 2024

We provide new constraints on the dark matter halo density profile of Milky Way (MW) dwarf spheroidal galaxies (dSphs) using the phase-space distribution function (DF) method. After assessing the systematics of the approach against mock data from the Gaia Challenge project, we apply the DF analysis to the entire kinematic sample of well-measured MW dwarf satellites for the first time. Contrary to previous findings for some of these objects, we find that the DF analysis yields results consistent with the standard Jeans analysis. In particular, in this study we rediscover (i) a large diversity in the inner halo densities of dSphs (bracketed by Draco and Fornax), and (ii) an anticorrelation between inner halo density and pericenter distance of the bright MW satellites. Regardless of the strength of the anticorrelation, we find that the distribution of these satellites in density versus pericenter space is inconsistent with the results of the high-resolution N-body simulations that include a disc potential. Our analysis motivates further studies on the role of internal feedback and dark matter microphysics in these dSphs.
Why does the Milky Way have a metallicity floor?
Authors: Smith Britton D , O’Shea Brian W , Khochfar Sadegh , Turk Matthew J , Wise John H , Norman Michael L
Published: July 2024

The prevalence of light element enhancement in the most metal-poor stars is potentially an indication that the Milky Way has a metallicity floor for star formation around $\sim 10^{-3.5}$ Z$_{\odot }$. We propose that this metallicity floor has its origins in metal-enriched star formation in the minihaloes present during the Galaxy’s initial formation. To arrive at this conclusion, we analyse a cosmological radiation hydrodynamics simulation that follows the concurrent evolution of multiple Population III star-forming minihaloes. The main driver for the central gas within minihaloes is the steady increase in hydrostatic pressure as the haloes grow. We incorporate this insight into a hybrid one-zone model that switches between pressure-confined and modified free-fall modes to evolve the gas density with time according to the ratio of the free-fall and sound-crossing time-scales. This model is able to accurately reproduce the density and chemo-thermal evolution of the gas in each of the simulated minihaloes up to the point of runaway collapse. We then use this model to investigate how the gas responds to the absence of H$_{2}$. Without metals, the central gas becomes increasingly stable against collapse as it grows to the atomic cooling limit. When metals are present in the halo at a level of $\sim 10^{-3.7}$ Z$_{\odot }$, however, the gas is able to achieve gravitational instability while still in the minihalo regime. Thus, we conclude that the Galaxy’s metallicity floor is set by the balance within minihaloes of gas-phase metal cooling and the radiation background associated with its early formation environment.