bluuebunny/crossref_metadata_2025 huggingface dataset:
GTPase activity of porcine Mx1 plays a dominant role in inhibiting the N-Nsp9 interaction and thus inhibiting PRRSV replication
Authors: Hu Yue , Wu Xiangju , Tian Yunfei , Jiang Dandan , Ren Jinrui , Li Ziyong , Ding Xiuliang , Zhang Quanfang , Yoo Dongwan , Miller Laura C. , Lee Changhee , Cong Xiaoyan , Li Juntong , Du Yijun , Qi Jing
Published: March 2024

Porcine Mx1 is a type of interferon-induced GTPase that inhibits the replication of certain RNA viruses. However, the antiviral effects and the underlying mechanism of porcine Mx1 for porcine reproductive and respiratory syndrome virus (PRRSV) remain unknown. In this study, we demonstrated that porcine Mx1 could significantly inhibit PRRSV replication in MARC-145 cells. By Mx1 segment analysis, it was indicated that the GTPase domain (68-341aa) was the functional area to inhibit PRRSV replication and that Mx1 interacted with the PRRSV-N protein through the GTPase domain (68-341aa) in the cytoplasm. Amino acid residues K295 and K299 in the G domain of Mx1 were the key sites for Mx1-N interaction while mutant proteins Mx1(K295A) and Mx1(K299A) still partially inhibited PRRSV replication. Furthermore, we found that the GTPase activity of Mx1 was dominant for Mx1 to inhibit PRRSV replication but was not essential for Mx1-N interaction. Finally, mechanistic studies demonstrated that the GTPase activity of Mx1 played a dominant role in inhibiting the N-Nsp9 interaction and that the interaction between Mx1 and N partially inhibited the N-Nsp9 interaction. We propose that the complete anti-PRRSV mechanism of porcine Mx1 contains a two-step process: Mx1 binds to the PRRSV-N protein and subsequently disrupts the N-Nsp9 interaction by a process requiring the GTPase activity of Mx1. Taken together, the results of our experiments describe for the first time a novel mechanism by which porcine Mx1 evolves to inhibit PRRSV replication.

IMPORTANCE

Mx1 protein is a key mediator of the interferon-induced antiviral response against a wide range of viruses. How porcine Mx1 affects the replication of porcine reproductive and respiratory syndrome virus (PRRSV) and its biological function has not been studied. Here, we show that Mx1 protein inhibits PRRSV replication by interfering with N-Nsp9 interaction. Furthermore, the GTPase activity of porcine Mx1 plays a dominant role and the Mx1-N interaction plays an assistant role in this interference process. This study uncovers a novel mechanism evolved by porcine Mx1 to exert anti-PRRSV activities.
Transcriptome fine-mapping in
Fusobacterium nucleatum
reveals FoxJ, a new σ
E
-dependent small RNA with unusual mRNA activation activity
Authors: Ponath Falk , Zhu Yan , Vogel Jörg
Published: March 2024

The oral commensal
Fusobacterium nucleatum
can spread to extra-oral sites, where it is associated with diverse pathologies, including pre-term birth and cancer. Due to the evolutionary distance of
F. nucleatum
to other model bacteria, we lack a deeper understanding of the RNA regulatory networks that allow this bacterium to adapt to its various niches. As a first step in that direction, we recently showed that
F. nucleatum
harbors a global stress response governed by the extracytoplasmic function sigma factor, σ
E
, which displays a striking functional conservation with Proteobacteria and includes a noncoding arm in the form of a regulatory small RNA (sRNA), FoxI. To search for putative additional σ
E
-dependent sRNAs, we comprehensively mapped the 5′ and 3′ ends of transcripts in the model strain ATCC 23726. This enabled the discovery of FoxJ, a ~156-nucleotide sRNA previously misannotated as the 5′ untranslated region (UTR) of
ylmH
. FoxJ is tightly controlled by σ
E
and activated by the same stress conditions as is FoxI. Both sRNAs act as mRNA repressors of the abundant porin FomA, but FoxJ also regulates genes that are distinct from the target suite of FoxI. Moreover, FoxJ differs from other σ
E
-dependent sRNAs in that it also positively regulates genes at the post-transcriptional level. We provide preliminary evidence for a new mode of sRNA-mediated mRNA activation, which involves the targeting of intra-operonic terminators. Overall, our study provides an important resource through the comprehensive annotation of 5′ and 3′ UTRs in
F. nucleatum
and expands our understanding of the σ
E
response in this evolutionarily distant bacterium.

IMPORTANCE

The oral microbe
Fusobacterium nucleatum
can colonize secondary sites, including cancer tissue, and likely deploys complex regulatory systems to adapt to these new environments. These systems are largely unknown, partly due to the phylogenetic distance of
F. nucleatum
to other model organisms. Previously, we identified a global stress response mediated by σ
E
that displays functional conservation with the envelope stress response in Proteobacteria, comprising a coding and noncoding regulatory arm. Through global identification of transcriptional start and stop sites, we uncovered the small RNA (sRNA) FoxJ as a novel component of the noncoding arm of the σ
E
response in
F. nucleatum
. Together with its companion sRNA FoxI, FoxJ post-transcriptionally modulates the synthesis of envelope proteins, revealing a conserved function for σ
E
-dependent sRNAs between Fusobacteriota and Proteobacteria. Moreover, FoxJ activates the gene expression for several targets, which is a mode of regulation previously unseen in the noncoding arm of the σ
E
response.
Assessment of performance characteristics of pavement base course incorporating reclaimed asphalt pavement and asphaltenes
Authors: Kamran Farshad , Jhora Nusrat , Moghaddam Taher Baghaee , Hashemian Leila
Published: March 2024

Asphalt pavement is demolished and milled at the end of its service life, resulting in an enormous amount of waste material known as reclaimed asphalt pavement (RAP). Using cold recycling techniques, it is possible to reuse RAP for base course construction. However, using a high amount of RAP could have negative effects on the mechanical properties and durability of the base course. In this study, to improve the performance of asphalt emulsion recycled base course prepared with RAP, asphaltenes derived from Alberta oil-sands bitumen was added to the mixture. The performance properties of the selected mixtures were investigated at high, intermediate, and low temperatures. Testing results and statistical analysis revealed that asphaltenes enhances the high and intermediate temperature performance of the modified mixes significantly. The low-temperature creep compliance of asphaltenes-modified mixtures was slightly lower than the unmodified mixtures, however, the low-temperature properties of the modified mixes were not significantly affected.
Multi-charmed and singled charmed hadrons from coalescence: yields and ratios in different collision systems at LHC
Authors: Minissale Vincenzo , Plumari Salvatore , Sun Yifeng , Greco Vincenzo
Published: March 2024

We study the production of charmed and multi-charmed hadrons in ultra-relativistic Heavy Ion Collisions coupling the transport approach for charm dynamics in the medium to an hybrid hadronization model of coalescence plus fragmentation. In this paper, we mainly discuss the particle yields for single charmed and multi-charmed baryons focusing mainly on the production of $$\Xi _{cc}$$

Ξ

cc

and $$\Omega _{ccc}$$

Ω

ccc

. We provide first predictions for PbPb collision in $$0 \! - \! 10\%\ $$

0

-

10
%

centrality class and then we explore the system size dependence through KrKr , to ArAr and OO collisions, planned within the ALICE3 experiment. In these cases, a monotonic behavior for the yields emerges which can be tested in future experimental data. We found about three order of magnitude increase in the production of $$\Omega _{ccc}$$

Ω

ccc

in PbPb collisions compared with the yield in small collision systems like OO collisions. Furthermore, we investigate the effects on the $$\Omega _{ccc}$$

Ω

ccc

particle yield and spectra coming from the modification of the charm quark distribution due to the different size of the collision systems also comparing it to the case of thermalized charm distributions. These results suggest that observation on the $$\Omega _{ccc}$$

Ω

ccc

spectra and their evolution across system size can give novel information about the partial thermalization of the charm quark distribution as well as to its wave function width. Furthermore, we find that the $$\Omega _{ccc}$$

Ω

ccc

/$$D^0$$

D
0

ratio is an observable more sensitive with respect to $$\Lambda _c$$

Λ
c

/$$D^0$$

D
0

, this ratio is predicted to span over two order of magnitude from large to small systems.
Induced current by a cosmic string and a brane in high-dimensional AdS spacetime
Authors: Santos W. Oliveira dos , de Mello E. R. Bezerra
Published: March 2024

In this paper we investigate the bosonic current induced by a brane and a magnetic flux running along the idealized cosmic string in a $$(D+1)$$

(
D
+
1
)

-dimensional anti-de Sitter (AdS) background. We consider the brane is parallel to the AdS boundary and the cosmic string is orthogonal to them. Moreover, we assume that on the brane the charged bosonic field obeys the Robin boundary condition. The brane divides the space into two regions with different properties of the vacuum state. We show that the only nonzero component of the current density is along the azimuthal direction in both regions. In order to develop this analysis we calculate, for both regions, the positive frequency Wightman functions. Both functions present a part associated with the AdS in presence of a cosmic string only, and the other part induced by the brane. In this paper we consider only the contributions induced by the brane. We show that in both regions the azimuthal current densities are odd functions of the magnetic flux along the string. Different analytic and numerical analysis are performed and an application of our results is provided for the Randall-Sundrum braneworld model with a single brane.
Phase structure of charged AdS black holes surrounded by exotic fluid with modified Chaplygin equation of state
Authors: Sekhmani Y. , Rayimbaev J. , Luciano G. G. , Myrzakulov R. , Gogoi D. J.
Published: March 2024

By considering the concept of the modified Chaplygin gas (MCG) as a single fluid model unifying dark energy and dark matter, we construct a static, spherically charged black hole (BH) solution in the framework of General Relativity. The P–V criticality of the charged anti-de Sitter (AdS) BH with a surrounding MCG is explored in the context of the extended phase space, where the negative cosmological constant operates as a thermodynamical pressure. This critical behavior shows that the small/large BH phase transition is analogous to the van der Waals liquid/gas phase transition. Accordingly, along the P–V phase spaces, we derive the BH equations of state and then numerically evaluate the corresponding critical quantities. Similarly, critical exponents are identified, along with outcomes demonstrating the scaling behavior of thermodynamic quantities near criticality to a universal class. The use of geometrothermodynamic (GT) tools finally offers a new perspective on the discovery of the critical phase transition point. At this stage, we apply a class of GT tools, such as Weinhold, Ruppeiner, HPEM, and Quevedo classes I and II. The findings are therefore non-trivial, as each GT class metric captures at least either the physical limitation point or the phase transition critical point. Overall, this paper provides a detailed study of the critical behavior of the charged AdS BH with surrounding MCG.
Exact massive and massless scalar quasibound states solutions of the Einstein–Maxwell-dilaton (EMD) black hole
Authors: Senjaya David
Published: March 2024

In this letter, we will focus on the Klein–Gordon equation with static spherically symmetric black hole solution of the Einstein–Maxwell-dilaton (EMD) theory as its 3+1 background space-time. The Klein–Gordon equation represents quasibound states of both massive and massless scalar fields which are localized in the black hole potential well. By using the covariant Klein–Gordon equation, we investigate the behaviour of both massive and massless scalars in the EMD black hole space-time. We successfully exactly solved the relativistic wave equation and are going to present the novel exact results in this letter. The exact solutions, the wave functions and the energy levels, describe the decaying nature of the relativistic scalar field bound in the curved space-time. The massive scalar quasibound state has complex-valued energy levels where the real part is the massive scalar’s energy while the imaginary part represents the decay. For the massless scalar quasibound state, pure imaginary energy levels are discovered. In this letter, by using the obtained exact scalar particle’s wave functions, we also consider the Hawking radiation of the apparent horizon of the EMD black hole that is calculated via Damour–Ruffini method. In principle, the investigation of black hole quasibound states could provide possibility for laboratory testing of effects whose nature are absolutely related with quantum effects in gravity.
Electromagnetically induced absorption and transparency in a ladder-type atomic system with different dressing mechanisms
Authors: Ti Hao-Wei , Yan Xiang-An , Liu Hao-Gong , Bai Xi-Xi , Huang Xiao-Rui , Guo Zhou , Wang Chen-Jie , Zhang Dan-Dan , Han Xiaoxiang
Published: March 2024

In a Doppler-broadened ladder-type Rubidium atomic system [Formula: see text]–[Formula: see text]–[Formula: see text], three-photon electromagnetically induced absorption (EIA) and transparency (EIT) in two schemes of two coupling lasers with different propagation directions are comprehensively studied. Two coupling fields are entangled tightly with each other and induce constructive interference such that we observe EIA as two coupling fields are counter-propagating. Two coupling fields are independent and cause destructive interference such that only enhanced EIT occurs when two coupling fields are co-propagating, although all of the Doppler-broadened atoms satisfy the condition for three-photon resonance. The experimental results are coincided with the numerically calculated spectra using the dressed perturbation method. The mechanisms of EIT and EIA could also be understood by the dressed-state pictures.
Explaining Firm-Level Manufacturing Outward FDI from India Under Alternate Theoretical Frameworks
Authors: Goldar Anindita
Published: March 2024

The firm-level determinants of outward foreign direct investment (OFDI) intensity of Indian manufacturing firms are analyzed using a random-effects Tobit model for a panel dataset covering over 17,550 firms from 1992–1993 to 2018–2019. The explanatory variables are based on a theoretical synthesis of Dunning’s (1980) [Towards an eclectic theory of international production: Some empirical tests. Journal of International Business Studies, 11(1), 9–31] ownership–location–internationalization (OLI) model and Mathew’s (2002) [Competitive advantage of the latecomer firm: A resource-based account of industrial catch-up strategies. Asia Pacific Journal of Management, 19(4), 467–488] linkage–leverage–learning (LLL) model. The empirical evidence reveals that policy liberalization, size (up to a threshold level), age, business group ownership structure, and the extent of foreign earnings strongly impact the OFDI intensity of Indian manufacturing enterprises. In contrast, outsourcing intensity, technological efforts, product differentiation, export intensity, and use of imported intermediate inputs were found to have a moderate positive impact. A moderate negative impact was found for factors like the global financial crisis, debt-equity ratio, and technology imports, and a strong negative effect for foreign ownership and public-sector ownership structure variables.
Lower Cretaceous holostratigraphy in Svalbard: the Arctic key piece of the Boreal basin puzzle
Authors: Jelby Mads E. , Grundvåg Sten-Andreas , Śliwińska Kasia K. , Alsen Peter , Vickers Madeleine L. , Olaussen Snorre , Stemmerik Lars
Published: March 2024

Lower Cretaceous stratigraphy of the high palaeo-latitude Arctic-Boreal Realm is generally more poorly understood than its lower-latitude Tethyan counterpart, prohibiting regional correlations and evaluation of global climate dynamics during this important high-
p
CO
2
period. In this paper, a holostratigraphic scheme and lithostratigraphic revision are presented for the Valanginian–lower Barremian, siliciclastic ramp succession of the Rurikfjellet Formation in Svalbard, drawn from synthesis of the latest published sedimentological, biostratigraphic, petrophysical, sequence stratigraphic, chemostratigraphic and chronostratigraphic results, supplemented by new measured sections from five localities. The offshore mudstone-dominated Wimanfjellet Member (Valanginian–lower Barremian) is retained, whereas three new members are defined according to their distinct geographical, sedimentological and stratigraphic characteristics. The Adventpynten Member (upper(?) Valanginian–lowermost upper Hauterivian) constitutes a thick, relatively localized succession of mass-transport deposits. The Kikutodden Member (Hauterivian–lower Barremian) is discarded and replaced by the northern Bohemanneset Member and southern Fotografryggen Member, representing respectively: heterogeneous prodelta to delta front deposits; and sandy offshore transition to shoreface deposits. The Rurikfjellet Formation records Valanginian–earliest late Hauterivian shoreline progradation followed by late Hauterivian–early Barremian shoreline retreat and flooding across a low-gradient ramp, which never experienced full regression into continental deposits within the extent of the present-day outcrop belt.
Loss Relaxation Strategy for Noisy Facial Video-based Automatic Depression Recognition
Authors: Song Siyang , Luo Yiming , Tumer Tugba , Fu Changzeng , Valstar Michel , Gunes Hatice
Published: March 2024

Automatic depression analysis has been widely investigated on face videos that have been carefully collected and annotated in lab conditions. However, videos collected under real-world conditions may suffer from various types of noise due to challenging data acquisition conditions and lack of annotators. Although deep learning (DL) models frequently show excellent depression analysis performances on datasets collected in controlled lab conditions, such noise may degrade their generalization abilities for real-world depression analysis tasks. In this article, we uncovered that noisy facial data and annotations consistently change the distribution of training losses for facial depression DL models; i.e., noisy data–label pairs cause larger loss values compared to clean data–label pairs. Since different loss functions could be applied depending on the employed model and task, we propose a generic loss function relaxation strategy that can jointly reduce the negative impact of various noisy data and annotation problems occurring in both classification and regression loss functions for face video-based depression analysis, where the parameters of the proposed strategy can be automatically adapted during depression model training. The experimental results on 25 different artificially created noisy depression conditions (i.e., five noise types with five different noise levels) show that our loss relaxation strategy can clearly enhance both classification and regression loss functions, enabling the generation of superior face video-based depression analysis models under almost all noisy conditions. Our approach is robust to its main variable settings and can adaptively and automatically obtain its parameters during training.
Performance and Durability of Hybrid Fuel Cell Systems for Class-8 Long Haul Trucks
Authors: Ahluwalia R. K. , Wang X.
Published: March 2024

Hybrid fuel cell-battery configurations are investigated that overcome thermal management issues in fuel cell powertrains for heavy-duty Class 8 trucks. The battery is sized so that it has sufficient capacity to provide supplemental power and energy on a hill climb transient at end-of-life. A dynamic load sharing strategy is developed to distribute the power demand between the fuel cell system (FCS) and the energy storage system in a manner that optimizes their lifetimes. The FCS end-of-life is identified as the terminal point beyond which the stack cannot generate the rated power with target power density at 0.7 V and 40 °C ambient temperature. Reaching the target lifetime with a-Pt/C cathode catalyst in one hybrid configuration requires voltage clipping to 813 mV, idle power limited to 50 kW, catalyst overloading to 0.45 mg cm−2 total Pt in anode and cathode, and 44% active membrane area oversizing. The stack and FCS drive cycle efficiencies decrease by 4.2% and 5.4%, respectively, during the electrode lifetime. The FCS performance, durability and cost are compared with the targets of 68% peak efficiency, 0.30 mg cm−2 total Pt loading, 2.5 kW/gPGM Pt group metal (PGM) loading, 750 mW cm−2 power density, 25,000-h lifetime and $80/kW cost.
Multi-Objective Operating Parameters Optimization for the Start Process of Proton Exchange Membrane Fuel Cell Stack with Non-Dominated Sorting Genetic Algorithm II
Authors: Liu Zhao , Chen Huicui , Zhang Tong , Meuser Carmen , Unwerth Thomas von
Published: March 2024

Proton exchange membrane fuel cell (PEMFC) is one of the most promising energy conversion devices in the world. Performance, durability, and cost are the key issues currently limiting its large-scale commercial application. This paper proposes a non-dominated sorting genetic algorithm II (NSGA-II) for optimizing operating parameters of the start process to improve the output performance of a PEMFC stack. First, a Simulink model of the PEMFC stack including the anode module, cathode module, water transfer module, output voltage module, and output net power module is established, and the accuracy of the stack model is verified through experiments. The three performances are then optimized simultaneously based on NSGA-II. The results show that the optimized operating parameters for the start process results in a PEMFC stack that outperforms the base case in steady-state voltage, percentage of undershoot, and net power these three indicators with the same response time, demonstrating the success of the method in solving multiple optimization problems. This study presents an effective approach for the multi-objective optimization of the PEMFC stack, which is of guidance for engineering practice.
Mycobacterium tuberculosis Lineage Distribution Using Whole‐Genome Sequencing and Bedaquiline, Clofazimine, and Linezolid Phenotypic Profiles among Rifampicin‐Resistant Isolates from West Java, Indonesia
Authors: Rukmana Andriansjah , Gozali Cynthia , Erlina Linda
Published: March 2024

Tuberculosis (TB) is caused by Mycobacterium tuberculosis infection. Indonesia is ranked second in the world for TB cases. New anti‐TB drugs from groups A and B, such as bedaquiline, clofazimine, and linezolid, have been shown to be effective in curing drug resistance in TB patients, and Indonesia is already using these drugs to treat patients. However, studies comparing the TB strain types with anti‐TB resistance profiles are still relevant to understanding the prevalent strains in the country and their phenotypic characteristics. This study aimed to determine the association between the TB lineage distribution using whole‐genome sequencing and bedaquiline, clofazimine, and linezolid phenotypic profile resistance among M. tuberculosisrifampicin‐resistant isolates from West Java. M. tuberculosis isolates stock of the Department of Microbiology, Faculty of Medicine, Universitas Indonesia, was tested against bedaquiline, clofazimine, and linezolid using a mycobacteria growth indicator tube liquid culture. All isolates were tested for M. tuberculosis and rifampicin resistance using Xpert MTB/RIF. The DNA genome of M. tuberculosis was freshly extracted from a Löwenstein–Jensen medium culture and then sequenced. The isolates showed phenotypically resistance to bedaquiline, clofazimine, and linezolid at 5%, 0%, and 0%, respectively. We identified gene mutations on phenotypically bedaquiline‐resistant strains (2/3), and other mutations also found in phenotypically drug‐sensitive strains. Mykrobe analysis showed that most (88.33%) of the isolates could be classified as rifampicin‐resistant TB. Using Mykrobe and TB‐Profiler to determine the lineage distribution, the isolates were found to belong to lineage 4 (Euro‐American; 48.33%), lineage 2 (East Asian/Beijing; 46.67%), and lineage 1 (Indo‐Oceanic; 5%). This work underlines the requirement to increase the representation of genotype‐phenotype TB data while also highlighting the importance and efficacy of WGS in predicting medication resistance and inferring disease transmission.
Fulminant Myocarditis with SARS-CoV-2 Infection: A Narrative Review from the Case Studies
Authors: Ono Ryohei , Iwahana Togo , Aoki Kaoruko , Kato Hirotoshi , Okada Sho , Kobayashi Yoshio
Published: March 2024

One of the severe complications of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is myocarditis. However, the characteristics of fulminant myocarditis with SARS-CoV-2 infection are still unclear. We systematically reviewed the previously reported cases of fulminant myocarditis associated with SARS-CoV-2 infection from January 2020 to December 2022, identifying 108 cases. Of those, 67 were male and 41 female. The average age was 34.8 years; 30 patients (27.8%) were ≤20 years old, whereas 10 (9.3%) were ≥60. Major comorbidities included hypertension, obesity, diabetes mellitus, asthma, heart disease, gynecologic disease, hyperlipidemia, and connective tissue disorders. Regarding left ventricular ejection fraction (LVEF) at admission, 93% of the patients with fulminant myocarditis were classified as having heart failure with reduced ejection fraction (LVEF ≤ 40%). Most of the cases were administered catecholamines (97.8%), and mechanical circulatory support (MCS) was required in 67 cases (62.0%). The type of MCS was extracorporeal membrane oxygenation (n = 56, 83.6%), percutaneous ventricular assist device (Impella®) (n = 19, 28.4%), intra-aortic balloon pumping (n = 12, 12.9%), or right ventricular assist device (n = 2, 3.0%); combination of these devices occurred in 20 cases (29.9%). The average duration of MCS was 7.7 ± 3.8 days. Of the 76 surviving patients whose cardiac function was available for follow-up, 65 (85.5%) recovered normally. The overall mortality rate was 22.4%, and the recovery rate was 77.6% (alive: 83 patients, dead: 24 patients; outcome not described: 1 patient).
Characterization of Phenotypic Variation in Indigenous Chicken Populations in Lower Northern Thailand to Improve Chicken Breeding
Authors: Yaemkong Suphawadee , Phromnoi Siriwadee , Mingchai Chedsada , Jongjitvimol Touchkanin
Published: March 2024

In Thailand, native chickens have a deep-rooted history of cultivation driven by diverse purposes, including food production, aesthetic appeal, exhibition, and cockfighting. Their remarkable adaptability, robustness, and resistance to diseases play pivotal roles in the evolution of chicken breeds. The study of morphological characteristics in native chicken breeds assumes significance for biodiversity conservation, sustainable agriculture, and cultural preservation. These traits not only unveil genetic diversity but also provide insights into adaptation that is crucial for the survival of native chicken populations in varied environmental conditions. The primary aim of this extensive research, conducted from June 2020 to May 2023, is to elucidate the morphological traits of six indigenous chicken breeds in Thailand’s Uttaradit province. The research methodology involved the purposive selection of a research group from chicken farms with a minimum of 5 individuals, followed by a random selection of 20 names meeting specific criteria. The resulting group comprised 134 individuals from Khiew Phalee, Thao Thong, Lueng Hang Khao, Chee, Pra Dhu Hang Dam, and Jae species. The study’s findings highlighted significant differences in eight qualitative morphological characteristics among the distinct chicken breeds, including comb type, beak color, neck plumage color, back plumage color, wing plumage color, long curved tail color, back tail color, and shank color p < 0.01. Moreover, a correlation between body size and sex-specific structures across breeds was discovered, with male chickens exhibiting significantly greater body weight, size, wing length, upper and lower shank length, and toe length than females p<0.0001. Notably, the majority of native chickens displayed the walnut (Hin) beak type, except for Jae chickens, which exhibited the single (Jak) type. Beak colors ranged from blackish-green to ivory, while each breed showcased unique plumage, tail, and shank colors, coupled with varying body sizes. This comprehensive study, covering both qualitative and quantitative parameters, emphasizes the morphological diversities among the six native chicken breeds. The derived data serve as a valuable resource for refining or developing chicken breeds in alignment with the Standard of Perfection for Thai Native Chickens, catering to the evolving needs of the market.
Supplementary Figure 5 from AXL/WRNIP1 Mediates Replication Stress Response and Promotes Therapy Resistance and Metachronous Metastasis in HER2+ Breast Cancer
Authors: Marquez-Palencia Mauricio , Reza Herrera Luis , Parida Pravat Kumar , Ghosh Suvranil , Kim Kangsan , Das Nikitha M. , Gonzalez-Ericsson Paula I. , Sanders Melinda E. , Mobley Bret C. , Diegeler Sebastian , Aguilera Todd A. , Peng Yan , Lewis Cheryl M. , Arteaga Carlos L. , Hanker Ariella B. , Whitehurst Angelique W. , Lorens James B. , Brekken Rolf A. , Davis Anthony J. , Malladi Srinivas
Published: March 2024

Supplementary Figure 5
Supplementary Figure 4 from AXL/WRNIP1 Mediates Replication Stress Response and Promotes Therapy Resistance and Metachronous Metastasis in HER2+ Breast Cancer
Authors: Marquez-Palencia Mauricio , Reza Herrera Luis , Parida Pravat Kumar , Ghosh Suvranil , Kim Kangsan , Das Nikitha M. , Gonzalez-Ericsson Paula I. , Sanders Melinda E. , Mobley Bret C. , Diegeler Sebastian , Aguilera Todd A. , Peng Yan , Lewis Cheryl M. , Arteaga Carlos L. , Hanker Ariella B. , Whitehurst Angelique W. , Lorens James B. , Brekken Rolf A. , Davis Anthony J. , Malladi Srinivas
Published: March 2024

Supplementary Figure 4
Supplementary Figure 3 from AXL/WRNIP1 Mediates Replication Stress Response and Promotes Therapy Resistance and Metachronous Metastasis in HER2+ Breast Cancer
Authors: Marquez-Palencia Mauricio , Reza Herrera Luis , Parida Pravat Kumar , Ghosh Suvranil , Kim Kangsan , Das Nikitha M. , Gonzalez-Ericsson Paula I. , Sanders Melinda E. , Mobley Bret C. , Diegeler Sebastian , Aguilera Todd A. , Peng Yan , Lewis Cheryl M. , Arteaga Carlos L. , Hanker Ariella B. , Whitehurst Angelique W. , Lorens James B. , Brekken Rolf A. , Davis Anthony J. , Malladi Srinivas
Published: March 2024

Supplementary Figure 3
Table S5 from Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial–Mesenchymal Transition
Authors: Fang Liang , Zhang Li , Wang Mengran , He Yuhao , Yang Jiao , Huang Zengjin , Tan Ying , Fang Ke , Li Jun , Sun Zhiyuan , Li Yanping , Tang Yisen , Liang Weizheng , Cui Huanhuan , Zhu Qionghua , Wu Zhe , Li Yiming , Hu Yuhui , Chen Wei
Published: March 2024

Table S5. The list of peaks and genes enriched in DDX6-eCLIP-seq
Table S3 from Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial–Mesenchymal Transition
Authors: Fang Liang , Zhang Li , Wang Mengran , He Yuhao , Yang Jiao , Huang Zengjin , Tan Ying , Fang Ke , Li Jun , Sun Zhiyuan , Li Yanping , Tang Yisen , Liang Weizheng , Cui Huanhuan , Zhu Qionghua , Wu Zhe , Li Yiming , Hu Yuhui , Chen Wei
Published: March 2024

Table S3. The list of candidate genes
Data from Chronic Stress Dampens Lactobacillus Johnsonii–Mediated Tumor Suppression to Enhance Colorectal Cancer Progression
Authors: Cao Qiuhua , Zhao Mingrui , Su Yali , Liu Siliang , Lin Yanting , Da Huijuan , Yue Chongxiu , Liu Yiming , Jing Dongquan , Zhao Qixiang , Liu Ning , Du Juan , Zuo Zhanjie , Fu Yao , Chen Anqi , Birnbaumer Lutz , Yang Yong , Dai Beiying , Gao Xinghua
Published: March 2024

Abstract
Colorectal cancer development and outcome are impacted by modifiable risk factors, including psychologic stress. The gut microbiota has also been shown to be linked to psychologic factors. Here, we found a marked deteriorative effect of chronic stress in multiple colorectal cancer models, including chemically induced (AOM/DSS), genetically engineered (APCmin/+), and xenograft tumor mouse models. RNA sequencing data from colon tissues revealed that expression of stemness-related genes was upregulated in the stressed colorectal cancer group by activated β-catenin signaling, which was further confirmed by results from ex vivo organoid analyses as well as in vitro and in vivo cell tumorigenicity assays. 16S rRNA sequencing of the gut microbiota showed that chronic stress disrupted gut microbes, and antibiotic treatment and fecal microbiota transplantation abolished the stimulatory effects of chronic stress on colorectal cancer progression. Stressed colorectal cancer mice displayed a significant decrease in Lactobacillus johnsonii (L. johnsonii) abundance, which was inversely correlated with tumor load. Moreover, protocatechuic acid (PCA) was identified as a beneficial metabolite produced by L. johnsonii based on metabolome sequencing and LC/MS-MS analysis. Replenishment of L. johnsonii or PCA blocked chronic stress-induced colorectal cancer progression by decreasing β-catenin expression. Furthermore, PCA activated the cGMP pathway, and the cGMP agonist sildenafil abolished the effects of chronic stress on colorectal cancer. Altogether, these data identify that stress impacts the gut microbiome to support colorectal cancer progression.
Significance:
Chronic stress stimulates cancer stemness by reducing the intestinal abundance of L. johnsonii and its metabolite PCA to enhance β-catenin signaling, forming a basis for potential strategies to circumvent stress-induced cancer aggressiveness.

See related commentary by McCollum and Shah, p. 645
Table S1 from ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms
Authors: Arribas Alberto J. , Napoli Sara , Cascione Luciano , Barnabei Laura , Sartori Giulio , Cannas Eleonora , Gaudio Eugenio , Tarantelli Chiara , Mensah Afua A. , Spriano Filippo , Zucchetto Antonella , Rossi Francesca M. , Rinaldi Andrea , Castro de Moura Manuel , Jovic Sandra , Bordone Pittau Roberta , Stathis Anastasios , Stussi Georg , Gattei Valter , Brown Jennifer R. , Esteller Manel , Zucca Emanuele , Rossi Davide , Bertoni Francesco
Published: March 2024

Panel of kinases analyzed in the Phospho Flow experiments of parental and resistant cells by flow cytometry.
Figure S3 from ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms
Authors: Arribas Alberto J. , Napoli Sara , Cascione Luciano , Barnabei Laura , Sartori Giulio , Cannas Eleonora , Gaudio Eugenio , Tarantelli Chiara , Mensah Afua A. , Spriano Filippo , Zucchetto Antonella , Rossi Francesca M. , Rinaldi Andrea , Castro de Moura Manuel , Jovic Sandra , Bordone Pittau Roberta , Stathis Anastasios , Stussi Georg , Gattei Valter , Brown Jennifer R. , Esteller Manel , Zucca Emanuele , Rossi Davide , Bertoni Francesco
Published: March 2024

(A) Multidimensional scaling plot showing a 2-dimensional projection of distances across parental and resistant clones for RNA (GEP, top left), methylation (top right) and miRNA (bottom left) profiles. Magenta dots for resistant and pink for parental. (B) Vulcano plots on methylation (top left), gene expression (RNA-seq, top right) and microRNA (RNA-seq, bottom left) profiles of Karpas1718 resistant compared to parental. GEP-miRNA profiles integration. Moderated t-test (limma R Package) was performed comparing resistant to parental: delta Beta-value (methylation), fold change (RNA-seq), adj.P-value for Bonferroni correction of the nominal p-value. Dots represents genes and triangles represent miRNAs. Red corresponds to higher values in resistant, and blue higher values in parental. The genes or miRNAs inversely correlated with methylation are highlighted in darker color: hypomethylated and overexpressed in dark red (neg-corr UP) and hypermethylated and repressed in dark blue (neg-corr DN).
Figure S19 and references for supplementary figures from ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms
Authors: Arribas Alberto J. , Napoli Sara , Cascione Luciano , Barnabei Laura , Sartori Giulio , Cannas Eleonora , Gaudio Eugenio , Tarantelli Chiara , Mensah Afua A. , Spriano Filippo , Zucchetto Antonella , Rossi Francesca M. , Rinaldi Andrea , Castro de Moura Manuel , Jovic Sandra , Bordone Pittau Roberta , Stathis Anastasios , Stussi Georg , Gattei Valter , Brown Jennifer R. , Esteller Manel , Zucca Emanuele , Rossi Davide , Bertoni Francesco
Published: March 2024

Factors associated with resistance to idelalisib in cell lines are expressed in clinical specimens. Expression levels of genes related to idelalisib resistance were studied across different subtypes of B cell lymphoma: (A) n=48 (5), (B) n=80 (6). B-CLL: chronic lymphocytic leukemia, B.FL: follicular lymphoma, LBNH: non-specified non-Hodgkin B cell lymphoma, MALT: MZL of the mucosa associated tissue, MCL: Mantle cell lymphoma, NMZL: nodal marginal zone lymphoma, SMZL: splenic marginal zone lymphoma. Expression levels of genes related to idelalisib resistance were studied across the subtypes of diffuse large B cell lymphoma (DLBCL, two series: (C) n=181 and (D) n=223 from GSE10846 (7). ABC: activated B cell like DLBCL, GCB: germinal center B cell like DLBCL, type3: type3 DLBCL. Red for highly expressed gene in B cells (CD79A), blue for not expressed gene in B cells (IGFBP1), black for the gene of interest. (E) Gene set enrichment analyses comparing resistant versus parental for the top-200 genes positively correlated genes with HBEGF in SMZL clinical specimens (6). NES: normalized enrichment score, p-val: nominal p-value, FDR: false discovery rate.
Table S7 from Bifunctional Inhibitor Reveals NEK2 as a Therapeutic Target and Regulator of Oncogenic Pathways in Lymphoma
Authors: McCrury Mason , Swafford Kennith , Shuttleworth Sydnye L. , Mehdi Syed Hassan , Acharya Baku , Saha Debasmita , Naceanceno Kevin , Byrum Stephanie D. , Storey Aaron J. , Xu Ying-Zhi , Doshier Claire , Patel Vijay , Post Ginell R. , De Loose Annick , Rodriguez Analiz , Shultz Leonard D. , Zhan Fenghuang , Yoon Donghoon , Frett Brendan , Kendrick Samantha
Published: March 2024

Differentially expressed proteins identified from the total proteomic analysis in SUDHL5 treated with NBI-961 relative to DMSO vehicle control.
Figure S5 from Bifunctional Inhibitor Reveals NEK2 as a Therapeutic Target and Regulator of Oncogenic Pathways in Lymphoma
Authors: McCrury Mason , Swafford Kennith , Shuttleworth Sydnye L. , Mehdi Syed Hassan , Acharya Baku , Saha Debasmita , Naceanceno Kevin , Byrum Stephanie D. , Storey Aaron J. , Xu Ying-Zhi , Doshier Claire , Patel Vijay , Post Ginell R. , De Loose Annick , Rodriguez Analiz , Shultz Leonard D. , Zhan Fenghuang , Yoon Donghoon , Frett Brendan , Kendrick Samantha
Published: March 2024

Original blot images from Supplementary Figure S9. Uncropped blot images of (A) Figure S9A and (B) Figure S9B. The blot in (B) also contained samples from a replicate of the SUDHL5 untreated cell lysate that was incubated without and with phosphatase with an additional molecular weight ladder to separate the two sample sets. Each blot was imaged in both the Dylight 650 and 800 channels and shown as the respective image (NEK2 from 650 in top panels and ACTIN from 800 in lower panels). All blots were immunoblotted with a mixture of anti-NEK2 and anti-ACTIN primary antibodies, resolved with a mixture of secondary antibodies Dylight 650 and Dylight 800 and imaged using the BioRad ChemiDoc MP as described in the methods.
Fig. S8 from Radiation Synergizes with IL2/IL15 Stimulation to Enhance Innate Immune Activation and Antitumor Immunity
Authors: Li Xuefeng , Huntoon Kristin , Wang Yifan , Lee DaeYong , Dong Shiyan , Antony Abin , Walkey Carl , Kim Betty Y.S. , Jiang Wen
Published: March 2024

Fig. S8
Fig. S7 from Radiation Synergizes with IL2/IL15 Stimulation to Enhance Innate Immune Activation and Antitumor Immunity
Authors: Li Xuefeng , Huntoon Kristin , Wang Yifan , Lee DaeYong , Dong Shiyan , Antony Abin , Walkey Carl , Kim Betty Y.S. , Jiang Wen
Published: March 2024

Fig. S7
Figure S8 from Improving Intracellular Delivery of an Antibody–Drug Conjugate Targeting Carcinoembryonic Antigen Increases Efficacy at Clinically Relevant Doses In Vivo
Authors: Nessler Ian , Rubahamya Baron , Kopp Anna , Hofsess Scott , Cardillo Thomas M. , Sathyanarayan Nalini , Donnell Jennifer , Govindan Serengulam V. , Thurber Greg M.
Published: March 2024

Binding to CEACAM5 and CEACAM6. Binding of XAb and hMN14 were tested against CEACAM5 and CEACAM6. Mouse and human Fc binding beads (Bangs Laboratories) were incubated with XAb and hMN14, respectively. Then varying concentrations of biotinylated CEACAM5 or CEACAM6 were added, followed by streptavidin AF647 to quantify CEACAM binding (therefore, the affinity measured is monovalent). Fluorescence is normalized to adjust for different numbers of binding sites on mouse and human beads. The XAb binds both CEACAM5 and CEACAM6 (KD = 1.03 and 1.04 nM, respectively). hMN-14 only binds CEACAM5 (KD = 2.2 nM). However, XAb does not bind HT-1080 cells but binds HT-1080 cells transfected with CEACAM5 at a higher level than other CEACAM5 antibodies (Fig. S2, (1)). The results are consistent with XAb binding multiple epitopes on CEACAM5 to crosslink the receptor and induce rapid internalization. In addition, bivalent binding of two different antigens would not be anticipated to drive clustering-based internalization.
Fig. S23 from Radiation Synergizes with IL2/IL15 Stimulation to Enhance Innate Immune Activation and Antitumor Immunity
Authors: Li Xuefeng , Huntoon Kristin , Wang Yifan , Lee DaeYong , Dong Shiyan , Antony Abin , Walkey Carl , Kim Betty Y.S. , Jiang Wen
Published: March 2024

Fig. S23
Fig. S21 from Radiation Synergizes with IL2/IL15 Stimulation to Enhance Innate Immune Activation and Antitumor Immunity
Authors: Li Xuefeng , Huntoon Kristin , Wang Yifan , Lee DaeYong , Dong Shiyan , Antony Abin , Walkey Carl , Kim Betty Y.S. , Jiang Wen
Published: March 2024

Fig. S21
Figure S2 from Improving Intracellular Delivery of an Antibody–Drug Conjugate Targeting Carcinoembryonic Antigen Increases Efficacy at Clinically Relevant Doses In Vivo
Authors: Nessler Ian , Rubahamya Baron , Kopp Anna , Hofsess Scott , Cardillo Thomas M. , Sathyanarayan Nalini , Donnell Jennifer , Govindan Serengulam V. , Thurber Greg M.
Published: March 2024

SE-HPLC Plot at 280nm for XAb-SN-38. XAb-SN-38 was retained for ~7 minutes similar to the unconjugated ADC.
Fig. S15 from Radiation Synergizes with IL2/IL15 Stimulation to Enhance Innate Immune Activation and Antitumor Immunity
Authors: Li Xuefeng , Huntoon Kristin , Wang Yifan , Lee DaeYong , Dong Shiyan , Antony Abin , Walkey Carl , Kim Betty Y.S. , Jiang Wen
Published: March 2024

Fig. S15
Fig. S11 from Radiation Synergizes with IL2/IL15 Stimulation to Enhance Innate Immune Activation and Antitumor Immunity
Authors: Li Xuefeng , Huntoon Kristin , Wang Yifan , Lee DaeYong , Dong Shiyan , Antony Abin , Walkey Carl , Kim Betty Y.S. , Jiang Wen
Published: March 2024

Fig. S11
Data from ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms
Authors: Arribas Alberto J. , Napoli Sara , Cascione Luciano , Barnabei Laura , Sartori Giulio , Cannas Eleonora , Gaudio Eugenio , Tarantelli Chiara , Mensah Afua A. , Spriano Filippo , Zucchetto Antonella , Rossi Francesca M. , Rinaldi Andrea , Castro de Moura Manuel , Jovic Sandra , Bordone Pittau Roberta , Stathis Anastasios , Stussi Georg , Gattei Valter , Brown Jennifer R. , Esteller Manel , Zucca Emanuele , Rossi Davide , Bertoni Francesco
Published: March 2024

Abstract
BTK and PI3K inhibitors are among the drugs approved for the treatment of patients with lymphoid neoplasms. Although active, their ability to lead to long-lasting complete remission is rather limited, especially in the lymphoma setting. This indicates that tumor cells often develop resistance to the drugs. We started from a marginal zone lymphoma cell line, Karpas-1718, kept under prolonged exposure to the PI3Kδ inhibitor idelalisib until acquisition of resistance, or with no drug. Cells underwent transcriptome, miRNA and methylation profiling, whole-exome sequencing, and pharmacologic screening, which led to the identification of the overexpression of ERBB4 and its ligands HBEGF and NRG2 in the resistant cells. Cellular and genetic experiments demonstrated the involvement of this axis in blocking the antitumor activity of various BTK/PI3K inhibitors, currently used in the clinical setting. Addition of recombinant HBEGF induced resistance to BTK/PI3K inhibitors in parental cells and in additional lymphoma models. Combination with the ERBB inhibitor lapatinib was beneficial in resistant cells and in other lymphoma models already expressing the identified resistance factors. An epigenetic reprogramming sustained the expression of the resistance-related factors, and pretreatment with demethylating agents or EZH2 inhibitors overcame the resistance. Resistance factors were also shown to be expressed in clinical specimens. In conclusion, we showed that the overexpression of ERBB4 and its ligands represents a novel mechanism of resistance for lymphoma cells to bypass the antitumor activity of BTK and PI3K inhibitors and that targeted pharmacologic interventions can restore sensitivity to the small molecules.