bluuebunny/crossref_metadata_2025 huggingface dataset:
Double-stranded RNA induces antiviral transcriptional response through the Dicer-2/Ampk/FoxO axis in an arthropod
Authors: Gao Jie , Liu Chen-Fei , Liu Ping-Ping , Wang Xian-Wei
Published: July 2024

Invertebrates mainly rely on sequence-specific RNA interference (RNAi) to resist viral infections. Increasing studies show that double-stranded RNA (dsRNA) can induce sequence-independent protection and that Dicer-2, the key RNAi player that cleaves long dsRNA into small interfering RNA (siRNA), is necessary for this protection. However, how this protection occurs remains unknown. Herein, we report that it is caused by adenosine triphosphate (ATP)-hydrolysis accompanying the dsRNA-cleavage. Dicer-2 helicase domain is ATP-dependent; therefore, the cleavage consumes ATP. ATP depletion activates adenosine monophosphate-activated protein kinase (Ampk) and induces nuclear localization of Fork head box O (FoxO), a key transcriptional factor for dsRNA-induced genes. siRNAs that do not require processing cannot activate the transcriptional response. This study reveals a unique nonspecific antiviral mechanism other than the specific RNAi in shrimp. This mechanism is functionally similar to, but mechanistically different from, the dsRNA-activated antiviral response in vertebrates and suggests an interesting evolution of innate antiviral immunity.
Interaction of exotic states in a hadronic medium: the Z

c
(3900) case
Authors: Abreu L M , Magalhães R O , Navarra F S , Vieira H P L
Published: July 2024

We investigate the interactions of the charged exotic state Z

c
(3900) in a hadronic medium composed of light mesons. We study processes such as

Z

c

π
→
D

D

¯

,

Z

c

π
→

D

*

D

¯

*

,

Z

c

π
→
D

D

¯

*

and the inverse ones. Using effective Lagrangians and form factors calculated with Quantum Chromodynamics (QCD) sum rules (treating the Z

c
(3900) as a tetraquark) we estimate the vacuum and thermally-averaged cross-sections of these reactions. We find that the Z

c
(3900) has relatively large interaction cross sections with the constituent particles of the hadronic medium. After that, we use the production and suppression cross sections in a rate equation to estimate the time evolution of the Z

c
multiplicity. We include the Z

c
decay and regeneration terms The coalescence model is employed to compute the initial Z

c
multiplicity for the compact tetraquark configuration. Our results indicate that the combined effects of hadronic interactions, hydrodynamical expansion, decay and regeneration affect the final yield, which is bigger than the initial value. Besides, the dependence of the Z

c
final yield with the centrality, center-of-mass energy and the charged hadron multiplicity measured at midrapidity

[

d
N

ch

/

d
η

(
η
<

0.5
)
]

is also investigated.
Molecular dynamics simulation of salt diffusion in constituting phosphazene-based polymer electrolyte
Authors: Kaur Sarabjeet , Swayamjyoti S , Taneja Vibhuti , Padhee Srikant S , Nigam Vineeta , Jena Kailash C
Published: July 2024

A growing demand to visualize polymer models in liquid poses a computational challenge in molecular dynamics (MD) simulation, as this requires emerging models under suitable force fields (FFs) to capture the underlying molecular behaviour accurately. In our present study, we have employed TIP3P potential on water and all atomistic optimized potentials for liquid simulations FFs to study the liquid electrolyte behavior of phosphazene-based polymer by considering its potential use in lithium-ion polymer batteries. We have explored the polymer’s local structure, chain packing, wettability, and hydrophobic tendencies against the silicon surface using a combination of a pseudocontinuum model in MD simulation, and surface-sensitive sum frequency generation (SFG) vibrational spectroscopy. The finding yields invaluable insights into the molecular architecture of phosphazene. This approach identifies the importance of hydrophobic interactions with air and hydrophilic units with water molecules in understanding the behavior and properties of phosphazene-based polymers at interfaces, contributing to its advancements in materials science. The MD study uniquely captures traces of the polymer-ion linkage, which is observed to become more pronounced with the increase in polymer weight fraction. The theoretical observation of this linkage’s influence on lithium-ion diffusion motion offers valuable insights into the fundamental physics governing the behavior of atoms and molecules within phosphazene-based polymer electrolytes in aqueous environments. Further these predictions are corroborated in the molecular-level depiction at the air-aqueous interface, as evidenced from the OH-oscillator strength variation measured by the SFG spectroscopy.The fundamental findings from this study open new avenues for utilizing MD simulation as a versatile methodology to gain profound insights into intermolecular interactions of polymer. It could be useful in the application of biomedical and energy-related research, such as polymer lithium-ion batteries, fuel cells, and organic solar cells.
An adaptive weighted integration method for multipath ultrasonic flowmeter
Authors: Guo Suna , Han Jiawen , Li Baonan , Fang Lide , Zhang Tao , Wang Fan
Published: July 2024

The error introduced by the integration method is an important factor affecting the measurement accuracy of the multipath ultrasonic flowmeter. An adaptive weighted integration method (adaptive weighted integration method for velocity profile of circular section) is proposed to reduce the integration error, taking a DN400 double-side eight-path ultrasonic flowmeter as an example. This method is based on the velocity distribution information in the full flow range and the integration weights are determined by the principle of minimum error. The applicability of this method is verified by numerical simulation and actual fluid flow experiments. The results show that the integration error of the proposed method is superior to the Gauss–Jacobi and optimized weighted integration method for circular section integration methods, and the maximum integration error is reduced from 0.0877% and −0.0355% to 0.0220% in the flow range of 125–2500 t h−1.
Age prediction from 12-lead electrocardiograms using deep learning: a comparison of four models on a contemporary, freely available dataset
Authors: Barros Andrew , German Mesner Ian , Nguyen N Rich , Moorman J Randall
Published: July 2024

Objective. The 12-lead electrocardiogram (ECG) is routine in clinical use and deep learning approaches have been shown to have the identify features not immediately apparent to human interpreters including age and sex. Several models have been published but no direct comparisons exist. Approach. We implemented three previously published models and one unpublished model to predict age and sex from a 12-lead ECG and then compared their performance on an open-access data set. Main results. All models converged and were evaluated on the holdout set. The best preforming age prediction model had a hold-out set mean absolute error of 8.06 years. The best preforming sex prediction model had a hold-out set area under the receiver operating curve of 0.92. Significance. We compared performance of four models on an open-access dataset.
Completion of all the ITER toroidal field coil structures
Authors: Kajitani Hideki , Hemmi Tsutomu , Iguchi Masahide , Sakurai Takeru , Takano Katsutoshi , Tsutsumi Fumiaki , Saito Kengo , Sakamoto Kazuyuki , Tanaka Nobuhiko , Nakahira Masataka , Isono Takaaki
Published: July 2024

All 19 ITER toroidal field coil structures (TFCSs) were successfully fabricated by the Japan Domestic Agency with solving technical challenges. This study presents the results of the welding-deformation control process, which is a remarkable challenge in an efficient fabrication of the TFCSs.
Novel method for in-situ drift velocity measurement in large volume TPCs: the Geometry Reference Chamber of the NA61/SHINE experiment at CERN
Authors: László András , Gera Ádám , Hamar Gergő , Pálfi Botond , Podlaski Piotr , Rumberger Brant , Varga Dezső
Published: July 2024

This paper presents a novel method for low maintenance, low
ambiguity in-situ drift velocity monitoring in large volume Time
Projection Chambers (TPCs). The method was developed and deployed
for the 40 m3 TPC tracker system of the NA61/SHINE
experiment at CERN, which has a one meter of drift length. The
method relies on a low-cost multi-wire proportional chamber placed
next to the TPC to be monitored, downstream with respect to the
particle flux. Reconstructed tracks in the TPC are matched to hits
in the monitoring chamber, called the Geometry Reference Chamber
(GRC). Relative differences in positions of hits in the GRC are used
to estimate the drift velocity, removing the need for an accurate
alignment of the TPC to the GRC. An important design requirement on
the GRC was minimal added complexity to the existing system, in
particular, compatibility with Front-End Electronics cards already
used to read out the TPCs. Moreover, the GRC system was designed to
operate both in large and small particle fluxes. The system is
capable of monitoring the evolution of the drift velocity inside the
TPC down to a one permil precision, with a few minutes of data
collection.
Realization of modularized corrector magnet power supply with N+1 redundancy for TPS facilities
Authors: Wang Baosheng , Liu Kuobin , Wong Yongseng
Published: July 2024

This paper delves into implementing multi-module parallel
current output using the existing TPS storage ring correction magnet
power supply. We have devised a control interface card with N+1
redundancy to facilitate bipolar high-current parallel module
output. To achieve this, we have employed various current feedback
methods, including external DC Current Transducer (DCCT) and
internal module current feedback signals. Following PI compensation,
these feedback signals are amalgamated with reference current
signals to compute compensation values for each module, which are
subsequently disseminated to each Corrector Magnet Power Supply
(CMPS) for modulation, thereby enabling closed-loop current
control. A single CMPS module can deliver ± 48 V/± 10 A
output, while up to eight CMPS modules can be interconnected,
yielding a maximum output of ± 80 A. Through numerous
experimental measurements, the long-term output current stability
remains within 0.6 mA, or 7.5 ppm, with the output current
spectrum predominantly maintained within 500 μA. Furthermore,
the system boasts N+1 redundancy functionality and bipolar output
current characteristics. These exemplary performance attributes
underscore the criticality of our design for future applications of
TPS magnet power supplies.
Research on datumn transformation model in particle accelerator component installation
Authors: Zhang Qiuyu , Wu Enchen , Wang Wei , Li Xiao , Ding Ting , He Xiaoye
Published: July 2024

When the important components of the particle accelerator
are installed, it is required to locate the instrument in the global
coordinate system by measuring the control points of the surrounding
tunnels, which involves the datumn transformation between the global
coordinate system and the station coordinate system, and the
selection of the transformation model has gradually become a
potential breakthrough in solving the problem. Four different models
euler angle, Rodrigues matrix, dual quaternion and twelve parameters
are used to analyze and compare the solution parameters, accuracy
index, iteration efficiency, and the number of selected common
points of the four models with the measured data of 2022 Hefei Light
Source summer. The results show that the deviation of the four model
parameters from the SpatialAnalyzer commercial software is no more
than 3 μm for the translation parameters, and no more than
0.6” for the rotation angle. Among them, the twelve-parameters
and dual quaternion two models are theoretically rigorous, with high
and stable accuracy indexes, and the twelve parameters posteriori
unit weight mean error shows obvious advantages. The twelve
parameters and Rodrigues models have fewer iterations and higher
efficiency. In summary, the dual quaternion model and twelve
parameters method are preferred in the absence of better initial
values. In addition, in the process of datumn transformation, along
with the increase of the number of common points, the accuracies of
all four model solutions show an increasing trend of first fast and
then slow.
Poloidal magnetic field reconstruction by laser-driven ion-beam trace probe in spherical tokamak
Authors: ZHANG 张 Zuyu 祖煜 , XU 徐 Tianchao 田超 , XIAO 肖 Chijie 池阶 , HUANG 黄 Xianli 贤礼 , HE 何 Renchuan 任川 , YUAN 袁 Ruixin 瑞鑫 , YANG 杨 Xiaoyi 肖易
Published: July 2024

The poloidal magnetic field (

plays a critical role in plasma equilibrium, confinement and transport of magnetic confinement devices. Multiple diagnostic methods are needed to complement each other to obtain a more accurate

profile. Recently, the laser-driven ion-beam trace probe (LITP) has been proposed as a promising tool for diagnosing

and radial electric field (

) profiles in tokamaks [Yang X Y et al 2014 Rev. Sci. Instrum.
85 11E429]. The spherical tokamak (ST) is a promising compact device with high plasma beta and naturally large elongation. However, when applying LITP to diagnosing

in STs, the larger

invalidates the linear reconstruction relationship for conventional tokamaks, necessitating the development of a nonlinear reconstruction principle tailored to STs. This novel approach employs an iterative reconstruction method based on Newton’s method to solve the nonlinear equation. Subsequently, a simulation model to reconstruct the

profile of STs is developed and the experimental setup of LITP is designed for EXL-50, a middle-sized ST. Simulation results of the reconstruction show that the relative errors of

reconstruction are mostly below 5%. Moreover, even with 5 mm measurement error on beam traces or 1 cm flux surface shape error, the average relative error of reconstruction remains below 15%, initially demonstrating the robustness of LITP in diagnosing

profiles in STs.
Melville and the Time of War
Authors: Gould Philip
Published: July 2024

This chapter reads Melville’s Civil War poetry, Battle-Pieces and Aspects of the War (1866), in context of the relations between federal power, the writing of history, and reconstruction politics. My reading of numerous poems and his prose “Supplement” to Battle-Pieces attends to the relation between poetic form and theme and reconstruction politics, and argues for Melville’s interventions in Unionist accounts of the war. These poems, I argue, aim to confuse the question of when war ends as a way of suggesting that any clear historical narrative of the Civil War is always underwritten by contemporary political objectives. Melville’s lyrics disrupt Unionist narratives that often rationalized a punitive version of political reconstruction. My reading of Melville further questions why critics have designated him the literary figure best able to see beyond sectional and national ideologies, and it reconsiders his accommodating view of reconstruction in light of the political issue of protecting African-American lives.
Unique presentations of female pattern hair loss evident in Asian and Black women
Authors: Gadre Aditi , Sun Yage , Aguh Crystal
Published: July 2024

While racial variations in the presentation of androgenetic alopecia have been reported in men, similar data are very limited in women. We studied the distribution patterns of 112 women with female pattern hair loss and identified unique presentations in Asian, particularly those of South Asian descent, and Black women. These results may have implications for treatment response rates in different populations.
Associations between brain imaging–derived phenotypes and cognitive functions
Authors: Liu Yi , Shen Ouxi , Zhu Huating , He Yu , Chang Xinyue , Sun Lulu , Jia Yiming , Sun Hongyan , Wang Yinan , Xu Qingyun , Guo Daoxia , Shi Mengyao , Zheng Jin , Zhu Zhengbao
Published: July 2024

We aimed to evaluate the potential causal relationship between brain imaging–derived phenotypes and cognitive functions via Mendelian randomization analyses. Genetic instruments for 470 brain imaging–derived phenotypes were selected from a genome-wide association study based on the UK Biobank (n = 33,224). Statistics for cognitive functions were obtained from the genome-wide association study based on the UK Biobank. We used the inverse variance weighted Mendelian randomization method to investigate the associations between brain imaging–derived phenotypes and cognitive functions, and reverse Mendelian randomization analyses were performed for significant brain imaging–derived phenotypes to examine the reverse causation for the identified associations. We identified three brain imaging–derived phenotypes to be associated with verbal–numerical reasoning, including cortical surface area of the left fusiform gyrus (beta, 0.18 [95% confidence interval, 0.11 to 0.25], P = 4.74 × 10−7), cortical surface area of the right superior temporal gyrus (beta, 0.25 [95% confidence interval, 0.15 to 0.35], P = 6.30 × 10−7), and orientation dispersion in the left superior longitudinal fasciculus (beta, 0.14 [95% confidence interval, 0.09 to 0.20], P = 8.37 × 10−7). The reverse Mendelian randomization analysis indicated that verbal–numerical reasoning had no effect on these three brain imaging–derived phenotypes. This Mendelian randomization study identified cortical surface area of the left fusiform gyrus, cortical surface area of the right superior temporal gyrus, and orientation dispersion in the left superior longitudinal fasciculus as predictors of verbal–numerical reasoning.
Wealth inequality in northwestern Anatolia under the Ottomans, 1460–1870
Authors: Canbakal Hülya , Filiztekin Alpay
Published: July 2024

While studies indicate that economic inequality increased in the early modern period, it is debated whether this applied to all regions, and what the causes of change were. This paper studies long-term wealth inequality in the Ottoman Empire, and its possible determinants, using data from Anatolia. Inequality tended to track demographic and economic change, but evidence for a long-term correlation is inconclusive, whereas there is evidence for the long-term disequalizing impact of taxation and changing power relations. The divergence between cities and countryside suggests structural shifts caused by external factors, and comparison with the slow economies of Europe reveals diversity within this group.
TNF-alpha blockade in primary chronic non-bacterial osteomyelitis of the mandible
Authors: de La Rochefoucauld Jeanne , Lhote Raphaël , Benassarou Mourad-Azzedine , Schouman Thomas , Bertolus Chloé , Amoura Zahir , Hié Miguel
Published: July 2024

Objectives

Primary chronic non-bacterial osteomyelitis of the mandible (CNOM) is a rare auto-inflammatory disease of unknown aetiology that bears pathophysiological resemblance to both SAPHO syndrome in adults and chronic recurrent multifocal osteomyelitis (CRMO) in children. Both SAPHO and CRMO respond to TNF-α blockade. Previously reported treatment regimens in CNOM including NSAIDs, corticosteroids, antibiotics, anti-resorptive therapy and surgery all bear disappointing results. TNF-α blockade is suggested as a treatment option by some experts but this is not backed by any clinical data. We sought to retrospectively and exhaustively report our experience of anti-TNF-α therapy in refractory CNOM.

Methods

Fifteen patients with refractory CNOM and high disease burden were referred to our centre. TNF-α blockade was attempted in 10 cases, given its efficacy in neighbouring diseases, its good tolerance profile and failure of previous treatment strategies. We herein retrospectively report detailed outcomes for all patients having received anti-TNF-α therapy for this indication in our centre.

Results

TNF-α-targeting therapy resulted in a rapid and sustained remission in a majority of patients with CNOM, without serious adverse events. Treatment was tapered and stopped without relapse in some patients despite a refractory course of several years. Male sex seems to be associated with a poorer outcome.

Conclusion

Our results suggest that blocking TNF-α is efficient and safe in CNOM.
The Application of Blood Products in Plastic Surgery: A Systematic Review
Authors: Zhuang Jun , Chen Yi , Zheng Xinyue , Wang Cheng , Hu Jintian , Liu Tun
Published: July 2024

Background:

Due to their minimal trauma and relative safety, blood products are becoming increasingly popular in medical aesthetics. In recent years, research on the application of blood products has also been increased. This article will summarize the research progress of emerging blood products in plastic surgery in recent years.

Methods:

We searched the PubMed database for literature related to the application of blood preparation in plastic surgery over the past 5 years and summarized them.

Results:

Commonly used in plastic surgery are platelet-rich plasma, platelet-rich fibrin, concentrated growth factor, platelet-poor plasma, and mesenchymal stem cells derived from blood products. They can be used for wound repair and skin and autologous fat transplantation, and can be combined with laser therapy and facial rejuvenation.

Conclusions:

Understanding the application pathways of blood products in plastic surgery and their respective advantages and disadvantages can help us better choose and use them.
Liver transplantation provides survival benefit at all levels of frailty: From the Multicenter Functional Assessment in Liver Transplantation Study
Authors: Wang Melinda , Chiou Sy Han , Ganger Daniel , Ruck Jessica , Huang Chiung-Yu , Kappus Matthew R. , King Elizabeth A. , Ladner Daniela P. , Rahimi Robert S. , Duarte-Rojo Andres , Volk Michael L. , Tevar Amit D. , Verna Elizabeth C. , Lai Jennifer C.
Published: July 2024

Background and Aims:

Offering LT to frail patients may reduce waitlist mortality but may increase post-LT mortality. LT survival benefit is the concept of balancing these risks. We sought to quantify the net survival benefit with LT by liver frailty index (LFI).

Approach and Results:

We analyzed data in the multicenter Functional Assessment in LT (FrAILT) study from 2012 to 2021. Pre-LT cohort included ambulatory patients with cirrhosis awaiting LT, without HCC; the post-LT cohort included those who underwent LT. Primary outcomes were pre-LT and post-LT mortality. We computed 1-, 3-, and 5-year restricted mean survival times (RMSTs) from adjusted Cox models. The survival benefit was calculated as a net gain in life-years with LT. Pre-LT cohort included 2628 patients: median Model for End-Stage Liver Disease-Sodium was 18 (IQR: 14–22); 731 (28%) were frail; 440 (17%) died before LT. Post-LT cohort included 1335 patients: median Model for End-Stage Liver Disease-Sodium was 20 (IQR: 14–24); 325 (24%) were frail; 103 (8%) died after LT. Pre-LT RMST decreased substantially as LFI increased. Post-LT RMST also decreased as LFI increased but only modestly. There was no LFI threshold at which pre-LT and post-LT RMST intersected—patients had net survival benefits at all LFI values.

Conclusions:

Pre-LT and, to a lesser degree, post-LT mortality increased as LFI increased. Transplant offered a survival benefit at all LFI values, driven by a reduction in pre-LT mortality. No threshold of LFI was identified at which the risk of post-LT mortality exceeded pre-LT mortality. LT offers net survival benefits even in the presence of advanced frailty among those selected for LT.
Impact of Extracellular Matrix Injury on the Calcification of Artificial Bovine Pericardial Leaflets: An Experimental Study
Authors: Yu Honghuan , Yang Xinfeng , Wang Long , Xing Kai , Zhang Tao , Ma Xiaochun , Liu Xiaolin , Wang Zhengjun
Published: July 2024

To investigate the role of extracellular matrix (ECM) injury in bioprosthetic valve calcification, we constructed an ECM damage model by applying a 15 N stress to the bovine pericardium sample in both transverse and longitudinal directions after tissue cross-linking, whereas no stress was applied in the control group. Then we implanted two pieces of bovine pericardium on both sides of the dorsal midline in Wistar rats from both groups and measured the calcium content of the implanted bovine pericardium. The results showed that the calcium content of experimental group was significantly higher than that of control group (p < 0.05). Second, we implanted prosthetic valves made from bovine pericardium in the experimental and control groups into small-tailed Han sheep (Ovis aries). After 180 days, the prosthetic valve was removed for gross and histopathological observation as well as quantitative analysis of calcium. We found a higher average calcium content in bovine pericardium from the experimental group than that from controls. Furthermore, calcium salt deposition was detected on the ventricular surface of valves along with roughened valve leaflets in the experimental group. Our data support the hypothesis that the bovine pericardium with ECM injury is more prone to calcification.
The Effect of Postoperative Sleeping Position on Knee Extension and Range of Motion Following Primary Total Knee Arthroplasty
Authors: Goodwin Tyler M. , Brazier Brett G. , Cien Adam J. , Riggle Patrick K. , Popovich John M. , Penny Phillip C. , Cochran Jason M.
Published: July 2024

Total knee arthroplasty (TKA) is an orthopaedic operation that improves quality of life and reduces pain in patients with disabling arthritis of the knee. One commonly recognized complication is flexion contracture of the knee. Early physical therapy helps prevent flexion contracture and improve range of motion (ROM) postoperatively. This study evaluated postoperative sleeping position and its effect on terminal knee extension and ROM following primary TKA. We hypothesized that patients who slept in the supine position would achieve earlier knee extension and greater ROM when compared to those in the lateral recumbent position. A total of 150 consecutive primary TKAs were performed by a single surgeon (J.M.C.) from April 2014 to December 2014. The data were collected prospectively to determine preoperative ROM, postoperative ROM, and sleeping position. Mean postoperative terminal extension ROM at 1 month was 2.9 degrees in the supine group versus 6.0 degrees (p< .001) in the lateral group. No significant demographic differences between the two groups at baseline were found. Our results demonstrate that sleeping position affects initial postoperative terminal extension, however, not overall ROM. We found a statistically significant difference in extension when comparing patients in the supine versus lateral group. Patients who slept in the lateral position lacked 6 degrees of extension which is greater than the 5 degrees needed for normal gait mechanics. Those in the supine group lacked 2.9 degrees of extension, allowing for normal gait mechanics. This study identifies an easy, effective means of increasing patients initial ability to achieve knee extension and satisfaction following TKA.
Peripheral Blood and Bone Marrow Findings in Treatment-Naive Patients With Cytopenia(s)/Myeloid Neoplasms Harboring Both a Germline and a Somatic DDX41 Mutation
Authors: Bruehl Frido K. , Elbaz Younes Ismail , Bosler David S. , Kelemen Katalin , Jiang Liuyan , Reichard Kaaren K.
Published: July 2024

DDX41-associated cytopenia(s)/myeloid neoplasms (DDX41-C/MNs) are an emerging pathologic entity. We examined the hematopathologic findings in DDX41-C/MNs with both a germline and somatic DDX41 mutation (DDX41-C/MNs-GS). We reviewed the peripheral blood and bone marrow (BM) findings from treatment-naive patients with DDX41-C/MNs-GS. Thirty cases were identified: 10% (3/30) were classified as clonal cytopenia(s) of unknown significance (CCUS), 17% (5/30) as myelodysplastic neoplasm/syndrome (MDS) with <5% blasts, 20% (6/30) as MDS with 5% to 9% blasts, 20% (6/30) as MDS with 10% to 19% blasts, and 33% (10/30) as acute myeloid leukemia (AML). All patients were cytopenic; circulating blasts were rare (23%, 7/30). 63% (19/30) showed dysmegakaryopoiesis. Dyserythropoiesis and dysgranulopoiesis were uncommon; seen in 20% (6/30) and 7% (2/30), respectively. Sixty-six percent (19/29) of cases were normocellular; 43% (13/30) showed erythroid predominance. Flow cytometry revealed an unremarkable blast myeloid phenotype. Blasts were intermediate sized with round nuclei, distinct nucleoli, and light blue cytoplasm with azurophilic granules. The karyotype was predominantly normal (93%, 26/28). All germline mutations were deleterious: 53% (16/30) truncating and 47% (14/30) missense. The most common somatic variant was the R525H mutation in 70% (21/30). The BM diagnostic spectrum in DDX41-C/MNs that harbor both a germline and somatic DDX41 mutation is broad—ranging from CCUS to AML. We describe consistent hematopathologic findings that pathologists may expect in these cases.
Quantitative Liver Imaging in Children
Authors: Yoon Haesung , Kim Jisoo , Lim Hyun Ji , Lee Mi-Jung
Published: July 2024

In children and adults, quantitative imaging examinations determine the effectiveness of treatment for liver disease. However, pediatric liver disease differs in presentation from liver disease in adults. Children also needed to be followed for a longer period from onset and have less control of their bodies, showing more movement than adults during imaging examinations, which leads to a greater need for sedation. Thus, it is essential to appropriately tailor and accurately perform noninvasive imaging tests in these younger patients. This article is an overview of updated imaging techniques used to assess liver disease quantitatively in children. The common initial imaging study for diffuse liver disease in pediatric patients is ultrasound. In addition to preexisting echo analysis, newly developed attenuation imaging techniques have been introduced to evaluate fatty liver. Ultrasound elastography is also now actively used to evaluate liver conditions, and the broad age spectrum of the pediatric population requires caution to be taken even in the selection of probes. Magnetic resonance imaging (MRI) is another important imaging tool used to evaluate liver disease despite requiring sedation or anesthesia in young children because it allows quantitative analysis with sequences such as fat analysis and MR elastography. In addition to ultrasound and MRI, we review quantitative imaging methods specifically for fatty liver, Wilson disease, biliary atresia, hepatic fibrosis, Fontan-associated liver disease, autoimmune hepatitis, sinusoidal obstruction syndrome, and the transplanted liver. Lastly, concerns such as growth and motion that need to be addressed specifically for children are summarized.
A long-headed Cambrian soft-bodied vertebrate from the American Great Basin region
Authors: Lerosey-Aubril Rudy , Ortega-Hernández Javier
Published: July 2024

The fossil record suggests that chordates might have been minor components of marine ecosystems during the first major diversification of animal life in the Cambrian. Vertebrates are represented by a handful of rare soft-bodied stem-lineage taxa known from Konservat-Lagerstätten, including
Myllokunmingia
and
Yunnanozoon
from the Stage 3 of South China, and
Emmonsaspis
and
Metaspriggina
from Stage 4-Drumian deposits of northeast USA and British Columbia. Here, we describe the first soft-bodied vertebrate from the American Great Basin, a region home to a dozen Cambrian Konservat-Lagerstätten. Found in the Drumian Marjum Formation of Utah,
Nuucichthys rhynchocephalus
gen. et sp. nov. is characterized by a finless torpedo-shaped body that includes a snout-like anterior head bearing anterolateral eyes, approximately 25 thick myomeres, a large branchial chamber with a keel and approximately seven putative dorsal bars and a spiniform caudal process. Using Bayesian inference, our analysis recovers
Nuucichthys
within the vertebrate stem, closer to the crown than
Pikaia
,
Yunnanozoon
and
Myllokunmingia
, where it forms a polytomy with its Laurentian relatives,
Emmonsaspis
and
Metaspriggina
, and a scion consisting of conodonts and crown-group vertebrates. Based on the eye orientation and absence of fins
,
we tentatively reconstruct
Nuucichthys
as a pelagic organism with limited swimming abilities (planktonektic).
Genome-based reclassification of Sphingopyxis lutea Chhetri et al. 2023 as a later heterotypic synonym of Sphingopyxis jiangsuensis Gao et al. 2023
Authors: Chen Xiaoman , Wang Di , Qu Qinan , Zhang Xiying , Wei Yuli
Published: July 2024

Sphingopyxis lutea DHUNG17T was compared with Sphingopyxis jiangsuensis XHP0097T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of S. lutea DHUNG17T shared high similarity (99.9 %) to that of S. jiangsuensis XHP0097T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Sphingopyxis. The average amino acid identity, average nucleotide identity and digital DNA–DNA hybridization values between S. lutea DHUNG17T and S. jiangsuensis XHP0097T were below 99.0, 99.1 and 92.2±1.7 %, respectively, all of which were greater than the species delineation threshold for AAI (95.5 %), ANI (95–96 %) and dDDH (70 %), strongly indicating that the two strains represented a single species. Based on the combined phylogenetic, genomic and phenotypic characterization presented here, we propose Sphingopyxis lutea as a later heterotypic synonym of Sphingopyxis jiangsuensis.
Phylogenomic analyses of the genus Actinoplanes: description of four novel genera
Authors: Roman Ivan , Fedorenko Victor , Gromyko Oleksandr
Published: July 2024

The genus Actinoplanes comprises 57 species (in February 2024) that are important components of ecosystems and are widely used in biotechnology, especially pharmaceuticals. Phylogenetic analysis of the family Micromonosporaceae (based on the 16S rRNA gene sequence) allowed us to group members of different genera into separate clades; however, the genus Actinoplanes was divided into three separate clades. Such phylogenetic heterogeneity could be due to the limitations of 16S rRNA gene analysis. In response to this heterogeneity, genomic phylogeny was performed. Phylogenomic reconstruction based on 324 single-copy orthologous genes allowed us to divide the genus Actinoplanes first into four clades and then, based on average nucleotide identity analysis, into five clades. Finally, chemotaxonomic analysis of each clade confirmed each clade’s distinctiveness and the necessity to reclassify the genus Actinoplanes. The obtained data allowed us to divide the genus Actinoplanes into five genera: Actinoplanes, Paractinoplanes, Winogradskya, Symbioplanes and Amorphoplanes.
Winogradskyella pelagia sp. nov., isolated from coastal sediment
Authors: Li Fan , Sun Yang-Yang , Zhang Ya-Jing , Liu Xin-Jiang , Du Zong-Jun , Gong Ya
Published: July 2024

An orange-pigmented, Gram-stain-negative, strictly aerobic, non-flagellated and rod-shaped bacterium, designated strain DF17T, was isolated from coastal sediment collected from Jingzi Wharf, Weihai, PR China. The optimal growth conditions were determined to be at 30 °C, pH 7.5, and in 3 % (w/v) NaCl. According to phylogenetic analysis of the 16S rRNA gene sequence, strain DF17T showed the highest sequence similarity of 96.9 % to Winogradskyella aquimaris KCTC 23502T. The DNA G+C content was 35.8 mol%, and the major fatty acids were iso-C15 : 1 G, iso-C15 : 0, and iso-C17 : 0 3-OH. The major polar lipids were two aminoglycolipids, one phosphatidylethanolamine and four unidentified lipids. The predominant respiratory quinone was menaquinone-6 (MK-6). The average nucleotide identity, digital DNA–DNA hybridization, and amino acid identity values between strain DF17T and other Winogradskyella species were below the species delineation thresholds of 69.35–72.95 %, 16.9–19.6 % and 71.25–78.93 %, respectively. On the basis of its phenotypic, genetic and physiological characteristics, strain DF17T is suggested to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella pelagia sp. nov. is proposed. The type strain is DF17T (MCCC 1H00456T=KCTC 82421T).
Automated cell annotation in scRNA-seq data using unique marker gene sets
Authors: Truong Linh , Truong Thao , Nguyen Huy
Published: July 2024

Single-cell RNA sequencing has revolutionized the study of cellular heterogeneity, yet accurate cell type annotation remains a significant challenge. Inconsistent labels, technological variability, and limitations in transferring annotations from reference datasets hinder precise annotation. This study presents a novel approach for accurate cell type annotation in scRNA-seq data using unique marker gene sets. By manually curating cell type names and markers from 280 publications, we verified marker expression profiles across these datasets and unified the nomenclature to consistently identify 166 cell types and subtypes. Our customized algorithm, which builds on the AUCell method, achieves accurate cell labeling at single-cell resolution and surpasses the performance of reference-based tools like Azimuth, especially in distinguishing closely related subtypes. To enhance accessibility and practical utility for researchers, we have also developed a user-friendly application that automates the cell typing process, enabling efficient verification and supporting comprehensive downstream analyses.
Inflammatory Neuropathy in Mouse and Primate Models of Colorectal Cancer
Authors: Gaffney Caitlyn M. , Casaril Angela M. , Mahmud Iqbal , Wei Bo , Valadez Karen M. , Kolb Elizabeth A. , Cherry Fisher R. , Guise Theresa A. , Lorenzi Philip L. , Shi Lei , Hodo Carolyn L. , Shepherd Andrew J.
Published: July 2024

Colorectal cancer survivors are at increased risk of developing neurological issues, particularly peripheral neuropathy and chronic pain. Although pre-existing neuropathy is a risk factor for chronic pain, tumor-induced neuropathy has not been firmly established in pre-clinical models. Consistent with clinical observations, we show that mice with colorectal cancer develop peripheral neuropathy, which was associated with subtle locomotor deficits, without overt hypersensitivity. We detected widespread differences in pro-inflammatory cytokines and lipid metabolites in peripheral nerves from tumor-bearing mice. Macrophage accumulation, myelin decompaction and ryanodine receptor oxidation were associated with dysfunctional calcium homeostasis and reduced spike amplitude in sensory neurons. Inflammatory neuropathy and macrophage accumulation were also observed in peripheral nerves of rhesus macaques with colorectal cancer. These findings suggest colorectal cancer is causally linked to a subacute form of chronic inflammatory demyelinating polyneuropathy across species, which may represent an under-reported, yet important risk factor for neurological dysfunction in colorectal cancer survivors.
Therapeutic DBS for OCD Suppresses the Default Mode Network
Authors: Slepneva Natalya , Basich-Pease Genevieve , Reid Lee , Frank Adam C , Norbu Tenzin , Krystal Andrew D , Sugrue Leo P , Motzkin Julian C , Larson Paul S , Starr Philip A , Morrison Melanie A , Lee A Moses
Published: July 2024

Background: Deep brain stimulation (DBS) of the anterior limb of the internal capsule (ALIC) is an emerging treatment for severe, refractory obsessive-compulsive disorder (OCD). The therapeutic effects of DBS are hypothesized to be mediated by direct modulation of a distributed cortico-striato-thalmo-cortical network underlying OCD symptoms. However, the exact underlying mechanism by which DBS exerts its therapeutic effects still remains unclear. Method: In five participants receiving DBS for severe, refractory OCD (3 responders, 2 non-responders), we conducted a DBS On/Off cycling paradigm during the acquisition of functional MRI to determine the network effects of stimulation across a variety of bipolar configurations. We also performed tractography using diffusion-weighted imaging (DWI) to relate the functional impact of DBS to the underlying structural connectivity between active stimulation contacts and functional brain networks. Results: We found that therapeutic DBS had a distributed effect, suppressing BOLD activity within regions such as the orbitofrontal cortex, dorsomedial prefrontal cortex, and subthalamic nuclei compared to non-therapeutic configurations. Many of the regions suppressed by therapeutic DBS were components of the default mode network (DMN). Moreover, the estimated stimulation field from the therapeutic configurations exhibited significant structural connectivity to core nodes of the DMN. Conclusions: Therapeutic DBS for OCD suppresses BOLD activity within a distributed set of regions within the DMN relative to non-therapeutic configurations. We propose that these effects may be mediated by interruption of communication through structural white matter connections surrounding the DBS active contacts.
The structure of full-length AFPK supports the ACP linker in a role that regulates iterative polyketide and fatty acid assembly
Authors: Schubert Heidi L , Li Feng , Hill Christopher P. , Schmidt Eric W.
Published: July 2024

We present the full structures of two animal fatty acid synthase (FAS)-like polyketide synthases (AFPKs), PKS1 and PKS2 fromElysia chlorotica.Unlike the related FAS enzymes that use malonate to produce reduced lipids, EcPKS1 and EcPKS2 accept methylmalonyl-CoA to produce oxidized polypropionate products. When incubated with inhibitory malonyl-CoA (MC), the resulting EcPKS2(MC) structure revealed MC bound to the acyltransferase active site and the phosphopantetheinylated acyl carrier protein (ACP-pPant) bound to the ketosynthase (KS) active site. Remarkably, the entire linker from one modifying region to the ACP was visible in full-length EcPKS2(MC), revealing an asymmetric mega-enzyme structure. Mutations disrupting the affinity between the ACP linker and modifying domains altered substrate selectivity and active site selection, despite an expectation that the interactions are transient and that the wild-type linker alternates between the observed ordered and disordered conformations during the competing catalytic cycles of the homodimeric protein. A second structure, EcPKS2(AC), was acylated both on the KS catalytic cysteine and on the ACP-pPant. The ACP was docked at the dehydratase site, revealing further interactions between ACP and these FAS-like enzymes. The results suggest an unexpected role for the ACP linker in the control of substrate and product selectivity across the AFPK/FAS clade in animals and highlight ACP interfaces and mega-enzyme dynamics over the course of the catalytic cycle.
Gene expression changes in long-term memory unlikely to replicate in the long term
Authors: Mukamel Eran A. , Yu Zhaoxia
Published: July 2024

Identifying the cellular effects of memory-forming experiences on neurons which enable subsequent memory recall is a fundamental aim of neuroscience. The search for the engram could benefit from single cell RNA sequencing, which can estimate the mRNA expression of all genes in large samples of individual brain cells from animals exposed to specific experiences. A recent study used spatial transcriptomics and single cell RNA-sequencing to identify “transcriptional signatures in subpopulations of neurons and astrocytes that were memory-specific and persisted for weeks”1. However, because the authors did not account for multiple statistical comparisons2and instead used an “unadjusted” threshold for statistical significance, the reported findings are likely dominated by false positives3. Moreover, the statistical analysis treated individual cells as independent samples without accounting for correlations across cells derived from the same biological tissue sample. Reanalysis of the study’s data using appropriate, widely accepted statistical procedures, identifies no significant differentially expressed genes. This suggests the data do not support the author’s claim to have identified cell type-specific transcriptional signatures of memory in the mouse basolateral amygdala.
Sensitive Detection of Structural Differences using a Statistical Framework for Comparative Crystallography
Authors: Hekstra Doeke R. , Wang Harrison K. , Klureza Margaret A. , Greisman Jack B. , Dalton Kevin M.
Published: July 2024

Chemical and conformational changes underlie the functional cycles of proteins. Comparative crystallography can reveal these changes over time, over ligands, and over chemical and physical perturbations in atomic detail. A key difficulty, however, is that the resulting observations must be placed on the same scale by correcting for experimental factors. We recently introduced a Bayesian framework for correcting (scaling) X-ray diffraction data by combining deep learning with statistical priors informed by crystallographic theory. To scale comparative crystallography data, we here combine this framework with a multivariate statistical theory of comparative crystallography. By doing so, we find strong improvements in the detection of protein dynamics, element-specific anomalous signal, and the binding of drug fragments.
SOLeNNoID: A Deep Learning Pipeline For Solenoid Residue Detection in Protein Structures
Authors: Nikov Georgi , Pretorius Daniella , Murray James W.
Published: July 2024

Solenoid proteins are a subset of tandem repeat proteins, which are structurally distinct from globular proteins. Solenoid proteins are defined by their modular, elongated structures, dependent on interactions between adjacent repeats. These proteins are found across all domains of life and have many important functions such as protein binding, enzymatic catalysis, ice binding and nucleic acid binding. Furthermore, engineered variants of solenoid proteins such as DARPins and designed PPR proteins have therapeutic commercial applications. In order to advance the study of natural solenoid proteins and the design of novel solenoid proteins, accurate tools for solenoid detection and annotation are required. As solenoid structures are more conserved than solenoid sequences and owing to recent developments in protein structure prediction, structure-based solenoid detection is preferred. Here we propose SOLeNNoID - a deep learning pipeline for solenoid residue prediction in protein structures. We cover all three solenoid sub-classes: alpha-, alpha/beta- and beta-solenoids. We use a CNN architecture to reason over protein distance matrices and compare our method to existing structure-based methods. Finally, we produce predictions on the entire PDB and demonstrate a 71 percent increase in solenoid-containing entries over the gold-standard RepeatsDB database using our method.

GitHub

https://github.com/gnik2018/SOLeNNoID

Zenodo

TBC