bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards Energy-Efficient Semi-Autonomous Operation of Hydraulic Mobile Cranes
Authors: Zhidchenko Victor , Komarov Timofei , Handroos Heikki 
Published: November 2023

Abstract
This paper describes a method for an automatic control of hydraulic mobile crane movement that decreases required energy and allows avoiding obstacles. The method was originally developed for mobile log cranes and provides automatic transportation of the grappled logs to the desired position. The trajectory is calculated taking into account hydraulic energy needed for the movement. The method can also be applied to other machines, such as loader cranes. An input to the method is the positions of the endpoints and a map of the working space that defines the obstacles. To calculate an energy-efficient trajectory, the method uses a modified version of the A* search algorithm. The method includes two steps. First, a set of simulation experiments must be performed with a multi-physics model of the crane. The model should describe mechanical and hydraulic parts of the system and provide the value of hydraulic energy spent in each experiment. The first step represents a learning phase of the algorithm and must be executed once. A set of energy efficiency matrices is generated at this phase, which is used in the second step of the method to calculate a heuristic for the modified A* algorithm. The first step requires several hours of calculations depending on the model complexity and available computational resources. The second step can be executed faster than in a second, which makes it suitable for the real-time operation of the machine. To move the crane by the generated energy-efficient trajectory, a control algorithm was developed by combining feed-forward and PID control.
The paper presents the simulation results obtained with a real-time model of a log truck created using commercial software. The results demonstrate the median value of energy savings of 5 percent compared to the shortest path for the work task of loading and unloading the truck using common endpoint positions of logs. Validation of the method with a real device is planned for future research.
Time to rethink academic publishing: the peer reviewer crisis
Authors: Tropini Carolina , Finlay B. Brett , Nichter Mark , Melby Melissa K. , Metcalf Jessica L. , Dominguez-Bello Maria Gloria , Zhao Liping , McFall-Ngai Margaret J. , Geva-Zatorsky Naama , Amato Katherine R. , Undurraga Eduardo A. , Poinar Hendrik N. , Gilbert Jack A. 
Published: November 2023

ABSTRACT
There is concern that the time taken to publish academic papers in microbiological science has significantly increased in recent years. While the data do not specifically support this, evidence suggests that editors are having to invite more and more reviewers to identify those willing to perform peer review.
Characterization and genome sequence of
Microbacterium foliorum
phage Morrigan, of cluster EA6 with siphovirus morphology
Authors: Guerrero Jennifer A. , Maldonado Nery , Mbajiofor Emmanuella O. , Ramirez Lisette , Valencia Mary Jo , Healy Creehan D. , Garza Alejandro A. , Mizell Samantha A. , Jackson Brianna N. , Vargas Ayala Mayra 
Published: November 2023

ABSTRACT

Bacteriophage Morrigan, which was isolated from soil using
Microbacterium foliorum
NRRL B-24224, is lytic with siphovirus morphology. Morrigan’s 40,509-bp genome has a GC content of 62.8% and 66 putative protein-coding genes, of which 31 could be assigned putative functions. Based on gene content similarity to actinobacteriophages, Morrigan is assigned to subcluster EA6.
p97/VCP targets
Toxoplasma gondii
vacuoles for parasite restriction in interferon-stimulated human cells
Authors: Clough Barbara , Fisch Daniel , Mize Todd H. , Encheva Vesela , Snijders Ambrosius , Frickel Eva-Maria 
Published: November 2023

ABSTRACT

Infection with the parasite
Toxoplasma gondii
leads to production of interferon gamma (IFNγ) that stimulates cells to upregulate defense proteins targeting the parasite for cell intrinsic elimination or growth restriction. Various host defense mechanisms operate at the parasitophorous vacuole (PV) in different human cell types leading to PV disruption, acidification, or membrane envelopment. Ubiquitin and p62 are players in all human host control mechanisms of
Toxoplasma
, but other unifying proteins have not been identified. Here, we show that p97/valosin-containing protein (VCP), as well as its associated proteins ANKRD13A and UBXD1 control
Toxoplasma
infection while recruited to the PV in IFNγ-stimulated endothelial cells. Convergent deposition of ANKRD13A, p97/VCP, and UBXD1 onto the same vacuole is dependent on vacuolar ubiquitination and observed within 2 h post-infection. ANKRD13A, p97/VCP, and UBXD1 all drive the acidification mechanism of the vacuole, which is the IFNγ-dependent control pathway of
Toxoplasma
in endothelial cells. We assessed p97/VCP in
Toxoplasma
control in various human cells and demonstrate that p97/VCP is a universal IFNγ-dependent host restriction factor targeting the
Toxoplasma
PV in epithelial (HeLa) and endothelial cells (human umbilical vein endothelial cells), fibroblasts (human foreskin fibroblast), and macrophages (THP1).

IMPORTANCE

Toxoplasma gondii
(Tg) is a ubiquitous parasitic pathogen, infecting about one-third of the global population. Tg is controlled in immunocompetent people by mechanisms that are not fully understood. Tg infection drives the production of the inflammatory cytokine interferon gamma (IFNγ), which upregulates intracellular anti-pathogen defense pathways. In this study, we describe host proteins p97/VCP, UBXD1, and ANKRD13A that control Tg at the parasitophorous vacuole (PV) in IFNγ-stimulated endothelial cells. p97/VCP is an ATPase that interacts with a network of cofactors and is active in a wide range of ubiquitin-dependent cellular processes. We demonstrate that PV ubiquitination is a pre-requisite for recruitment of these host defense proteins, and their deposition directs Tg PVs to acidification in endothelial cells. We show that p97/VCP universally targets PVs in human cells and restricts Tg in different human cell types. Overall, these findings reveal new players of intracellular host defense of a vacuolated pathogen.
A SEVA-based, CRISPR-Cas3-assisted genome engineering approach for
Pseudomonas
with efficient vector curing
Authors: Lammens Eveline-Marie , Volke Daniel Christophe , Schroven Kaat , Voet Marleen , Kerremans Alison , Lavigne Rob , Hendrix Hanne 
Published: November 2023

ABSTRACT

The development of CRISPR-Cas-based engineering technologies has revolutionized the microbial biotechnology field. Over the years, the Class II Type II CRISPR-Cas9 system has become the gold standard for genome editing in many bacterial hosts. However, the Cas9 system does not allow efficient genomic integration in
Pseudomonas putida
, an emerging Synthetic Biology host, without the assistance of lambda-Red recombineering. In this work, we utilize the alternative Class I Type I-C CRISPR-Cas3 system from
Pseudomonas aeruginosa
as a highly efficient genome editing tool for
P. putida
and
P. aeruginosa
. This system consists of two vectors, one encoding the Cas genes, CRISPR array and targeting spacer, and a second Standard European Vector Architecture vector, containing the homologous repair template. Both vectors are Golden Gate compatible for rapid cloning and are available with multiple antibiotic markers, for application in various Gram-negative hosts and different designs. By employing this Cas3 system, we successfully integrated an 820-bp cassette in the genome of
P. putida
and performed several genomic deletions in
P. aeruginosa
within a week, with an efficiency of >83% for both hosts. Moreover, by introducing a universal self-targeting spacer, the Cas3 system rapidly cures all helper vectors, including itself, from the host strain in a matter of days. As such, this system constitutes a valuable engineering tool for
Pseudomonas
, to complement the existing range of Cas9-based editing methods, and facilitates genomic engineering efforts of this important genus.

IMPORTANCE

The CRISPR-Cas3 editing system as presented here facilitates the creation of genomic alterations in
Pseudomonas putida
and
Pseudomonas aeruginosa
in a straightforward manner. By providing the Cas3 system as a vector set with Golden Gate compatibility and different antibiotic markers, as well as by employing the established Standard European Vector Architecture (SEVA) vector set to provide the homology repair template, this system is flexible and can readily be ported to a multitude of Gram-negative hosts. Besides genome editing, the Cas3 system can also be used as an effective and universal tool for vector curing. This is achieved by introducing a spacer that targets the origin-of-transfer, present on the majority of established (SEVA) vectors. Based on this, the Cas3 system efficiently removes up to three vectors in only a few days. As such, this curing approach may also benefit other genomic engineering methods or remove naturally occurring plasmids from bacteria.
Impact of time of culture specimen collection on the recovery ofNeisseria gonorrhoeaeafter a positive nucleic acid amplification test
Authors: Nadal-Barón Patricia , Trejo-Zahinos Jesús , García Jorge Nestor , Salmerón Paula , Sulleiro Elena , Arando Maider , Descalzo Vicente , Álvarez-Lopez Patricia , El Ouazzani Rachid , López Luis , Zarzuela Francesc , Ruiz Edurne , Llinas Montserrat , Blanco-Grau Albert , Curran Adrian , Larrosa María Nieves , Pumarola Tomàs , Hoyos-Mallecot Yannick 
Published: November 2023

ObjectivesCulture ofNeisseria gonorrhoeaeremains essential for antimicrobial resistance (AMR) surveillance. We evaluated the effect of time of specimen collection on culture yield following a positive nucleic acid amplification test (NAAT).MethodsWe retrospectively assessedN. gonorrhoeaeculture yield among asymptomatic individuals (largely men who have sex with men) who attended for sexual health screening and had a positive NAAT. Participants underwent either same-day testing and notification (Drassanes Exprés) or standard screening with deferred testing.ResultsAmong 10 423 screened individuals, 809 (7.7%) tested positive forN. gonorrhoeae. A total of 995 different anatomical sites of infection culture was performed in 583 of 995 (58.6%) of anatomical sites (Drassanes Exprés 278 of 347, 80.1%; standard screening 305 of 648, 47.1%; p<0.001). Recovery was highest when culture specimens were collected within 3–7 days of screening with only a slight drop in recovery when the interval extended to 7 days . Recovery from pharynx was 38 of 149 (25.5%) within 3 days, 19 of 81 (23.4%) after 4–7 days (p=0.7245), 11 of 102 (10.7%) after 8–14 days (p<0.0036) and 1 of 22 (4.5%) with longer delays (p=0.00287). Recovery from rectum was 49 of 75 (65.3%) within 3 days, 28 of 45 (62.2%) after 4–7 days (p=0.7318), 41 of 69 (59.4%) after 8–14 days (p=0.4651) and 6 of 18 (33.3%) with longer delays (p=0.0131). Median culture specimen collection time was 1 day within Drassanes Exprés vs 8 days within standard screening. Consequently, the overall culture yield was slightly higher within Drassanes Exprés (102/278, 36.6% vs 99/305, 32.5%; p=0.2934).ConclusionReducing the interval between screening and collection of culture specimens increasedN. gonorrhoeaerecovery in extragenital samples. Implementing a same-day testing and notification programme increased collection of culture samples and culture yield in our setting, which may help AMR surveillance.
Nitric oxide and potassium channels but not opioid and cannabinoid receptors mediate tramadol-induced peripheral antinociception in rat model of paw pressure withdrawal
Authors: Soares-Santos Raquel R. , Machado Daniel P. , Romero Thiago L. , Duarte Igor D.G. 
Published: November 2023

Tramadol, an analgesic classified as an “atypical opioid”, exhibits both opioid and non-opioid mechanisms of action. This study aimed to explore these mechanisms, specifically the opioid-, cannabinoid-, nitric oxide-, and potassium channel-based mechanisms, which contribute to the peripheral antinociception effect of tramadol, in an experimental rat model. The nociceptive threshold was determined using paw pressure withdrawal. To examine the mechanisms of action, several substances were administered intraplantarly: naloxone, a non-selective opioid antagonist (50 µg/paw); AM251 (80 µg/paw) and AM630 (100 µg/paw) as the selective antagonists for types 1 and 2 cannabinoid receptors, respectively; nitric oxide synthase inhibitors L-NOArg, L-NIO, L-NPA, and L-NIL (24 µg/paw); and the enzyme inhibitors of guanylatocyclase and phosphodiesterase of cGMP, ODQ, and zaprinast. Additionally, potassium channel blockers glibenclamide, tetraethylammonium, dequalinium, and paxillin were used. The results showed that opioid and cannabinoid receptor antagonists did not reverse tramadol's effects. L-NOarg, L-NIO, and L-NPA partially reversed antinociception, while ODQ completely reversed, and zaprinast enhanced tramadol's antinociception effect. Notably, glibenclamide blocked tramadol's antinociception in a dose-dependent manner. These findings suggest that tramadol's peripheral antinociception effect is likely mediated by the nitrergic pathway and sensitive ATP potassium channels, rather than the opioid and cannabinoid pathways.
Influence of Elevation and Anthropogenic Disturbance on Woody Species Composition, Diversity, and Stand Structure in Harego Mountain Forest, Northeastern Ethiopia
Authors: Bogale Worku Belachew , Genete Muluneh Melese , Molla Tesfaye 
Published: November 2023

Environmental variables like elevation affect species composition, diversity, distribution, density, and horizontal and upward growth. Ecologists are constantly working to better understand how species diversity varies along elevational gradients, particularly in mountainous ecosystems. Therefore, the purpose of this research was to examine the species’ horizontal and vertical structural diversity along the Harego Mountain Forest’s elevational gradient. The area was categorized into lower, middle, and upper elevations. A total of 67 (20 m × 20 m) plots were created along gradients of elevation 2,079–2,516 meters above sea level (m a.s.l.). Information for floristic composition, diversity, stand structure, and environmental variables were measured and recorded for each plot over the three elevational gradients. Data on anthropogenic disturbances were visually evaluated for every plot in every gradient of elevation. For the diversity analysis, Hill’s diversity statistics were employed. To find significant variations between the three elevational gradients in terms of Hill’s diversity number, stand structure, and environmental variables, the one-way analysis of variance with SPSS version 26 at the 0.05 level of significance was carried out. The finding revealed that 50 woody plants that belonged to 35 families and 44 genera in the 67 sample plots with an elevation of 2,079 to 2,516 were identified. Shrubs were dominant in each elevational gradient. Species richness, abundance, and Hill’s diversity number were all significantly (

p
<
0.05

) greater in the upper elevational gradient of the forest. On the other hand, all stand structures were significantly (

p

<
0.05

) higher in the middle elevational gradient. The effect of anthropogenic disturbances and environmental variables were clearly observed in the lower and upper elevational gradients than in the middle elevation. As a result, there were fewer seedlings, saplings, trees, and shrubs in the gradients of lower and higher elevations. For the conservation of the forest, it is crucial to pay special attention to biotic elements at lower elevations and abiotic factors at higher elevations. Accordingly, involving the local community in forest management, reducing anthropogenic pressure in and around the Harego Mountain Forest through tree planting in farmlands and woodlots and implementing physical soil and water conservation structures are recommended.
PRESSING Need of Precision Care in HER2-Positive Colorectal Cancer: The ELEPHANT in the Room
Authors: Raghav Kanwal P.S. , Loree Jonathan M. , Kopetz Scott 
Published: November 2023

Summary
Although dual HER2 inhibition has shown promising clinical activity in patients with RAS wild-type HER2-positive metastatic colorectal cancer, predictive biomarkers of response/resistance are less well characterized. Activating HER2/RTK/MAPK genomic alterations appears to blunt the clinical benefit of dual anti-HER2 therapy and may hold a potential albeit partial role in patient selection.
See related article by Randon et al., p. 436
A vida epistolar de Lima Barreto: entrevista com Lilia Schwarcz
Authors: Ferreira Ligia Fonseca , Moraes Marcos Antonio de 
Published: November 2023

Entrevista realizada em 2023 com a antropóloga e professora Lilia Moritz Schwarcz, autora de Lima Barreto, triste visionário (Companhia das Letras, 2017).
U-CORE: A Unified Deep Cluster-wise Contrastive Framework for Open Relation Extraction
Authors: Zhou Jie , Dong Shenpo , Huang Yunxin , Wu Meihan , Li Haili , Wang Jingnan , Tu Hongkui , Wang Xiaodong 
Published: November 2023

Abstract
Within Open Relation Extraction (ORE) tasks, the Zero-shot ORE method is to generalize undefined relations from predefined relations, while the Unsupervised ORE method is to extract undefined relations without the need for annotations. However, despite the possibility of overlap between predefined and undefined relations in the training data, a unified framework for both Zero-shot and Unsupervised ORE has yet to be established. To address this gap, we propose U-CORE: A Unified Deep Cluster-wise Contrastive Framework for both Zero-shot and Unsupervised ORE, by leveraging techniques from Contrastive Learning (CL) and Clustering.1 U-CORE overcomes the limitations of CL-based Zero-shot ORE methods by employing Cluster-wise CL that preserves both local smoothness as well as global semantics. Additionally, we employ a deep-cluster-based updater that optimizes the cluster center, thus enhancing the accuracy and efficiency of the model. To increase the stability of the model, we adopt Adaptive Self-paced Learning that effectively addresses the data-shifting problems. Experimental results on three well-known datasets demonstrate that U-CORE significantly improves upon existing methods by showing an average improvement of 7.35% ARI on Zero-shot ORE tasks and 15.24% ARI on Unsupervised ORE tasks.
Learning to Paraphrase Sentences to Different Complexity Levels
Authors: Chi Alison , Chen Li-Kuang , Chang Yi-Chen , Lee Shu-Hui , Chang Jason S. 
Published: November 2023

Abstract
While sentence simplification is an active research topic in NLP, its adjacent tasks of sentence complexification and same-level paraphrasing are not. To train models on all three tasks, we present two new unsupervised datasets. We compare these datasets, one labeled by a weak classifier and the other by a rule-based approach, with a single supervised dataset. Using these three datasets for training, we perform extensive experiments on both multitasking and prompting strategies. Compared to other systems trained on unsupervised parallel data, models trained on our weak classifier labeled dataset achieve state-of-the-art performance on the ASSET simplification benchmark. Our models also outperform previous work on sentence-level targeting. Finally, we establish how a handful of Large Language Models perform on these tasks under a zero-shot setting.
Fibroblast Activation Protein–Targeted PET/CT With Al18F-NODA-FAPI-04 for In Vivo Imaging of Tendon Healing in Rat Achilles Tendon Injury Models
Authors: Liu Zhenfeng , Zhou Haiying , Li Pengfei , Wang Zewei , Tu Tian , Ezzi Sohaib Hasan Abdullah , Kota Vishnu Goutham , Hasan Abdulla Mohamed Hasan Abdulla , Alhaskawi Ahmad , Dong Yanzhao , Huang Yuqiao , Dong Mengjie , Su Xinhui , Lu Hui 
Published: November 2023

Background: Fibroblast activation protein (FAP) has shown high expression in inflammatory responses and fibrosis. Hypothesis: We speculated that FAP could serve as a diagnostic and monitoring target in the tendon healing process. Study Design: Controlled laboratory study. Methods: A total of 72 Sprague-Dawley rats were randomly divided into a tendon crush group and a half-partial tendon laceration group. Four rats in each group were injected with radiotracers weekly for 4 weeks after surgery, with aluminum fluoride–labeled 1,4,7-triazacyclononane-N,N′,N″-triacetic acid–conjugated FAP inhibitor (Al18F-NODA-FAPI-04) administered on the first day of each week and 18F-fludeoxyglucose (18F-FDG) on the next day. Small animal positron emission tomography (PET) imaging was performed, and tendon tissue was collected for pathology and quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis each week after surgery. Results: One week after surgery, both radiotracers showed signal concentration at the lesion site, which was the highest radioactive uptake observed during 4 weeks postoperatively, consistent with the severity of the lesion. Consistent trends were observed for inflammatory cytokines during qRT-PCR analysis. Additionally, Al18F-NODA-FAPI-04 PET exhibited a more precise lesion pattern, attributed to its high specificity for naive fibroblasts when referring to histological findings. Over time, the uptake of both radiotracers at the injury site gradually decreased, with 18F-FDG experiencing a more rapid decrease than Al18F-NODA-FAPI-04. In the fourth week after surgery, the maximum standardized uptake values of Al18F-NODA-FAPI-04 in the injured lesion almost reverted to the baseline levels, indicating a substantial decrease in naive fibroblasts and inflammatory cells and a reduction in inflammation and fibrosis, especially compared with the first week. Corresponding trends were also revealed in pathological and qRT-PCR results. Conclusion: Our findings suggest that inflammation is a prominent feature during the early stage of tendon injury. Al18F-NODA-FAPI-04 PET allows accurate localization and provides detailed morphological imaging, enabling continuous monitoring of the healing progress and assessment of injury severity.