bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPRlnc: a machine learning method for lncRNA-specific single-guide RNA design of CRISPR/Cas9 system
Authors: Yang Zitian , Zhang Zexin , Li Jing , Chen Wen , Liu Changning 
Published: March 2024

Abstract
CRISPR/Cas9 is a promising RNA-guided genome editing technology, which consists of a Cas9 nuclease and a single-guide RNA (sgRNA). So far, a number of sgRNA prediction softwares have been developed. However, they were usually designed for protein-coding genes without considering that long non-coding RNA (lncRNA) genes may have different characteristics. In this study, we first evaluated the performances of a series of known sgRNA-designing tools in the context of both coding and non-coding datasets. Meanwhile, we analyzed the underpinnings of their varied performances on the sgRNA’s specificity for lncRNA including nucleic acid sequence, genome location and editing mechanism preference. Furthermore, we introduce a support vector machine-based machine learning algorithm named CRISPRlnc, which aims to model both CRISPR knock-out (CRISPRko) and CRISPR inhibition (CRISPRi) mechanisms to predict the on-target activity of targets. CRISPRlnc combined the paired-sgRNA design and off-target analysis to achieve one-stop design of CRISPR/Cas9 sgRNAs for non-coding genes. Performance comparison on multiple datasets showed that CRISPRlnc was far superior to existing methods for both CRISPRko and CRISPRi mechanisms during the lncRNA-specific sgRNA design. To maximize the availability of CRISPRlnc, we developed a web server (http://predict.crisprlnc.cc) and made it available for download on GitHub.
Limited interspecific gene flow in the evolutionary history of the icefish genus Chionodraco
Authors: Schiavon Luca , Ceballos Santiago G , Matschiner Michael , Trucchi Emiliano , La Mesa Mario , Riginella Emilio , Lucassen Magnus , Mark Felix C , Bilyk Kevin , Franch Rafaella , Wallberg Andreas , Boscari Elisa , Zane Lorenzo , Papetti Chiara 
Published: March 2024

Abstract
Hybridization and introgression are recognized as mechanisms promoting genetic variability during evolutionary radiations. We examined the impact of introgression in the process of speciation, focusing on the Antarctic icefish genus Chionodraco. Our analyses confirmed that the three Chionodraco species (Chionodraco hamatus, Chionodraco myersi, and Chionodraco rastrospinosus) were genetically distinctive, despite signals of past interspecific gene flow between C. hamatus and C. myersi that likely occurred during interglacial periods. However, in this study, no recent hybrids were identified. The lack of contemporary hybridization may be due to life-history traits and the type of marker used in the analysis. Our study emphasizes the importance of genomic approaches to detect subtle patterns of past hybridization accurately and highlights the significance of historical climate events in the demographic and evolutionary history of Antarctic notothenioids. Polar regions, and especially the Antarctic Peninsula, are now experiencing the fastest climate changes due to global warming. Understanding the impact of past climate events is fundamental to trace current modifications in species’ genetic variability and distributions and predict future evolutionary trajectories. This knowledge is also vital for conservation efforts, including the implementation of marine protected areas.
The effects of dietary net energy on grow-finish performance and carcass characteristics of market gilts managed with immunological suppression of ovarian function and estrus (Improvest)
Authors: Bohrer Benjamin M , Wang Yifei , Landero Jose L , Young Malachy , Hansen Blaine , Pollmann D Steve , Mellencamp Marnie A , Van De Weyer Leanne , Aldaz Alvaro 
Published: March 2024

Abstract
The objective was to determine the effects of net energy (NE) during the grow-finish period on live performance and carcass characteristics of market gilts managed with immunological suppression of ovarian function and estrus (Improvest®; IMP) compared with market gilts not managed with Improvest (CON). The 104-d study began when 1,008 gilts (11 wk old; average starting weight of 30.8 kg) were allocated by weight to 48 pens with 21 gilts/pen. Half of the pens were randomly selected to be managed with Improvest while the other half of the pens were not managed with Improvest. Three dietary programs differing in their NE were formulated over five dietary phases (according to standardized ileal digestible lysine requirements) to provide an average of 2,218 kcal/kg (low NE), 2,343 kcal/kg (medium NE), or 2,468 kcal/kg (high NE). The experiment was designed as a 2 × 3 factorial with main effects of Improvest management and NE. For the overall study period, there were no significant interactions (P ≥ 0.20) for average daily feed intake (ADFI), average daily gain (ADG), or Gain:Feed (G:F). There were also no significant interactions between Improvest management and NE (P ≥ 0.30) for carcass characteristics. However, IMP gilts consumed more feed (6.8% greater ADFI; P &lt; 0.01), grew faster (5.0% greater ADG; P &lt; 0.01), were less efficient (1.8% lower G:F; P &lt; 0.01), heavier (3.5 kg hot carcass weight; P &lt; 0.01), and fatter (1.9 mm greater backfat thickness and 1.26% less predicted lean carcass yield; P &lt; 0.01). No difference (P = 0.21) in carcass dressing percentage between IMP and CON gilts was reported. For the overall study period, gilts fed low NE and medium NE diets consumed more feed compared with gilts fed high NE diets (6.8% more ADFI for low NE and 5.7% more for medium NE; P &lt; 0.01), and gilts fed low NE diets grew 2.5% slower (P &lt; 0.01) than gilts fed medium NE diets, while gilts fed high NE diets were intermediate and not different from the other NE treatments. This resulted in gilts fed Low NE diets being the least efficient (3.8% lower G:F than medium NE and 7.1% lower G:F than High NE; P &lt; 0.01). Overall, these data indicate that typical Improvest response levels were sustained at each of the NE treatments evaluated in this study as there were no significant interactions for Improvest management and NE; however, consideration should still be provided to the known production impacts of low NE diets.
Revision of the genus Robbea (Stilbonematinae: Desmodoridae), worldwide abundant marine nematodes with chromophoric Fe–Br inclusions and the description of a new stilbonematine genus
Authors: Scharhauser Florian , Saavedra Daniel E M , Pröts Philipp , Ott Jörg A , Geier Benedikt , Gruber-Vodicka Harald R , Polikarpov Maxim , Bourenkov Gleb , Leisch Nikolaus 
Published: March 2024

Abstract
Nematodes are one of the most widespread and abundant animal taxa across aquatic and terrestrial environments. In marine shallow-water, porous sediments, members of the subfamily Stilbonematinae may be found in high numbers. Stilbonematinae are characterized by their coat of symbiotic bacteria, which give the nematodes a white appearance, while the nematodes themselves are usually colourless. We identified several species of the genus Robbea (Desmodoridae: Stilbonematinae) in which live specimens had a conspicuous dark purple coloration of the glandular sense organs (GSOs), highly specialized epidermal glands that are prominent in the Stilbonematinae. The dark inclusions in the GSOs of Robbea contained high concentrations of iron and bromide, regardless of their habitat. Morphological and phylogenetic analyses show that the genus Robbea is paraphyletic and we define the new genus Cyathorobbea gen. nov. for species with sucker-shaped post-pharyngeal supplements in males. Furthermore, we describe five new Robbea species from around the world. Some Robbea species are morphologically very similar and required the use of principal component analysis of morphometric data to untangle the diversity in this taxon. Our work emphasizes the value of live animal observations that enable the identification of important characters and highlights the overlooked diversity within the Stilbonematinae.
A Review of Current Uses of Amniotic Membrane Transplantation in Ophthalmic Plastic and Reconstructive Surgery
Authors: Parikh Alomi O. , Conger Jordan R. , Li Joy , Sibug Saber Maria , Chang Jessica R. 
Published: March 2024

Purpose:To review and summarize the existing literature on the clinical applications of amniotic membrane transplantation (AMT) in ophthalmic plastic and reconstructive surgery.Methods:A literature review was conducted on the PubMed database using the following search terms: “amniotic membrane” and “eyelid” or “orbit” or “fornix” or “socket” or “lacrimal”.Results:In total 516 articles resulted from the search, of which 62 were included. Numerous cases and case series have been published on the use of amniotic membrane transplantation for ocular surface reconstruction, eyelid and forniceal reconstruction, and cicatricial eyelid abnormalities. Surgical methods of securing the graft vary. Few comparative studies exist; some show a similar or improved result when compared to oral mucous membrane grafting for certain indications.Conclusions:Amniotic membrane transplantation can be a useful tool for the oculoplastic surgeon when faced with a case requiring reconstruction of the posterior lamellae, particularly in patients without other graft donor sites available, and uses of AMT continue to expand. Additional studies directly comparing AMT to other reconstructive techniques would be helpful in choosing between the available surgical techniques and standardizing best practices.
Plasma Exeresis for the Treatment of Benign Eyelid Lesions: A New Surgical Approach
Authors: Ucar Fikret , Unluzeybek Murat 
Published: March 2024

Purpose:
To report the plasma therapy technique and its clinical outcomes in patients with benign eyelid lesions.

Methods:
This is a retrospective, noncomparative, interventional study. The study included 71 eyes of 66 patients who underwent plasma exeresis for benign eyelid lesions in our clinic between February 2018 and December 2022. Patient symptoms, cosmetic outcomes, and complications were evaluated.

Results:
The lesions were removed with a single plasma exeresis treatment in all patients. The mean size of the lesion at its largest part was 5.5 ± 1.2 mm (range, 3.0–8.8 mm). No complications were encountered during the procedure. The mean procedure time was 4.0 ± 0.7 minutes (range, 3–6 minutes). Postoperatively, only 3 cases (4.2%) with tarsal conjunctival extension had mild irritation symptoms such as pain, discomfort, and redness. The treated areas were fully improved cosmetically, and all patients were satisfied with the cosmetic outcomes.

Conclusions:
The plasma therapy technique for removing benign eyelid lesions offers minimally invasive surgery, less discomfort, fast recovery, and successful anatomical and cosmetic outcomes.
Definitions, outcomes and perspectives for oligometastatic bladder cancer: towards a standardized terminology
Authors: Calleris Giorgio , von Deimling Markus , Kesch Claudia , Soria Francesco , Gontero Paolo , Ploussard Guillaume , Laukhtina Ekaterina , Pradere Benjamin 
Published: March 2024

Purpose of review
Oligometastatic (om) cancer is considered as a transitional state in between locally confined disease and widespread metastases, accessible to a multimodal treatment, combining systemic and local therapy. In urothelial bladder cancer (BCa), the definitions and the approaches to this condition are poorly standardised and mainly based on retrospective data. We aim to portray the framework for uro-oncologic terminology in omBCa and go through the latest evidence and the future perspectives.

Recent findings
Retrospective and registry data support the potential benefits of multimodality treatment for carefully selected omBCa patients, especially following a good response to systemic treatment. In 2023, a Delphi consensus has defined omBCa, allowing maximum three metastatic lesions, theoretically amenable to radical local treatment. In de-novo omBCa, surgical treatment of primary tumour might improve overall survival (OS), according to a matched registry analysis; also, consolidative radiotherapy was associated with better OS in two recent cohorts. Furthermore, metastasis-directed therapy (MDT) has shown high local control rates and promising OS (14.9–51 months) in a meta-analysis; benefits might be more pronounced for single-site omBCa and nodal or lung lesions.

Summary
From a clinical perspective, in de-novo omBCa, the local treatment of primary and metastatic sites might improve disease control and survival, in selected patients; in the oligorecurrent setting, MDT achieves good local symptom control with limited side effects; in selected cases, it could convey a survival benefit, too. From a research perspective, well designed prospective evidence is eagerly awaited, based on recently adopted shared definitions for omBCa.
Can 18F-FES PET Improve the Evaluation of 18F-FDG PET in Patients With Metastatic Invasive Lobular Carcinoma?
Authors: Liu Cheng , Ma Guang , Xu Xiaoping , Song Shaoli , Yang Zhongyi 
Published: March 2024

Purpose
Invasive lobular carcinoma (ILC) exhibits a low affinity for 18F-FDG. The estrogen receptor (ER) is commonly expressed in ILCs, suggesting a potential benefit of targeting with the ER probe 18F-FES in this patient population. The objective of this study was to evaluate the diagnostic performance of 18F-FES imaging in patients with metastatic ILC and compare it with that of 18F-FDG.

Methods
We conducted a retrospective analysis of 20 ILC patients who underwent concurrent 18F-FES and 18F-FDG PET/CT examinations in our center. 18F-FES and 18F-FDG imaging were analyzed to determine the total count of tracer-avid lesions in nonbone sites and their corresponding organ systems, assess the extent of anatomical regions involved in bone metastases, and measure the SUVmax values for both tracers.

Results
Among 20 ILC patients, 65 nonbone lesions were found to be distributed in 13 patients, and 16 patients were diagnosed with bone metastasis, which was distributed in 54 skeletal anatomical regions. The detection rate of 18F-FDG in nonbone lesions was higher than that of 18F-FES (57 vs 37, P < 0.001). 18F-FES demonstrated a superior ability to detect nonbone lesions in 4 patients, whereas 18F-FDG was superior in 5 patients (P > 0.05). Among 9/16 patients with bone metastasis, 18F-FES demonstrated a significant advantage in the detection of bone lesions compared with 18F-FDG (P = 0.05). Furthermore, patients with only 18F-FES–positive lesions (12/12) were administered endocrine regimens, whereas patients lacking 18F-FES uptake (2/3) predominantly received chemotherapy.

Conclusions

18F-FES is more effective than 18F-FDG in detecting bone metastasis in ILC, but it does not demonstrate a significant advantage in nonbone lesions. Additionally, the results of examination with 18F-FES have the potential to guide patient treatment plans.
FDG PET/CT Findings of a Small Cell Carcinoma of the Lung Presented as Diffuse Dermatomyositis
Authors: Li Xinyu , Tian Bin , Bai Xia 
Published: March 2024

Abstract
Patients with dermatomyositis are prone to have occult malignancy. A previously healthy 68-year-old man with dermatomyositis underwent FDG PET/CT to detect possible malignancy of unknown origin. The images showed not only diffuse increased activity in the muscle, which was related to the known dermatomyositis, but also intense activity in the anterior chest with foci of abnormal activity throughout the body. Pathology examination confirmed small cell carcinoma of the lung with widespread metastases.
Macrophages foster adaptive anti-tumor immunity by ZEB1-dependent cytotoxic T cell chemoattraction
Authors: Fuchs Kathrin , Armstark Isabell , van Roey Ruthger , Hajjaj Yussuf , D’Avanzo Elisabetta , Liguori Renato , Ferrazzi Fulvia , Ackermann Jochen , Amon Lukas , Alfredo Marwin , Faas Maria , Hübner Julian , Hoffmann Markus H , Krönke Gerhard , Becker Christoph , Dudziak Diana , Nimmerjahn Falk , Brabletz Simone , Stemmler Marc P. , Brabletz Thomas , Schuhwerk Harald 
Published: March 2024

AbstractTumor-associated macrophages (TAMs) shape the tumor microenvironment (TME) and exert a decisive impact on anti-tumor immunity. Understanding TAM function is therefore critical to understand anti-tumor immune responses and to design immunotherapies. Here, we describe the transcription factor ZEB1, a well-known driver of epithelial-to-mesenchymal transition, as an intrinsic regulator of TAM function in adaptive anti-tumor immunity. By combining cell type-specific deletion of Zeb1 with syngeneic models of colorectal and pancreatic cancer, we discovered an unexpected function of ZEB1 in the TAM-mediated control of T cell trafficking. ZEB1 supports secretion of a subset of chemokines including CCL2 and CCL22 by promoting their transcription and translation as well as by safeguarding protein processing. ZEB1 thereby elevates cytotoxic T cell (CTL) recruitmentin vitroandin vivoand fosters immunosurveillance during tumor as well as lung metastatic outgrowth. Our study spotlights ZEB1 as a crucial facilitator of adaptive anti-tumor immunity and uncovers a potential therapeutic window of opportunity for cytokine-guided enhancement of CTL infiltration into tumors and metastases.
High-Resolution Spatial Transcriptomic Atlas of Mouse Soleus Muscle: Unveiling Single Cell and Subcellular Heterogeneity in Health and Denervation
Authors: Hsu Jer-En , Ruiz Lloyd , Hwang Yongha , Guzman Steve , Cho Chun-Seok , Cheng Weiqiu , Si Yichen , Macpherson Peter , Schrank Mitchell , Jun Goo , Kang Hyun-Min , Kim Myungjin , Brooks Susan , Lee Jun Hee 
Published: March 2024

AbstractSkeletal muscle is essential for both movement and metabolic processes, characterized by a complex and ordered structure. Despite its importance, a detailed spatial map of gene expression within muscle tissue has been challenging to achieve due to the limitations of existing technologies, which struggle to provide high-resolution views. In this study, we leverage the Seq-Scope technique, an innovative method that allows for the observation of the entire transcriptome at an unprecedented submicron spatial resolution. By applying this technique to the mouse soleus muscle, we analyze and compare the gene expression profiles in both healthy conditions and following denervation, a process that mimics aspects of muscle aging. Our approach reveals detailed characteristics of muscle fibers, other cell types present within the muscle, and specific subcellular structures such as the postsynaptic nuclei at neuromuscular junctions, hybrid muscle fibers, and areas of localized expression of genes responsive to muscle injury, along with their histological context. The findings of this research significantly enhance our understanding of the diversity within the muscle cell transcriptome and its variation in response to denervation, a key factor in the decline of muscle function with age. This breakthrough in spatial transcriptomics not only deepens our knowledge of muscle biology but also sets the stage for the development of new therapeutic strategies aimed at mitigating the effects of aging on muscle health, thereby offering a more comprehensive insight into the mechanisms of muscle maintenance and degeneration in the context of aging and disease.
CAR-engineered lymphocyte persistence is governed by a FAS ligand/FAS auto-regulatory circuit
Authors: Yi Fei , Cohen Tal , Zimmerman Natalie , Dündar Friederike , Zumbo Paul , Eltilib Razan , Brophy Erica J. , Arkin Hannah , Feucht Judith , Gormally Michael V. , Hackett Christopher S. , Kropp Korbinian N. , Etxeberria Inaki , Chandran Smita S. , Park Jae H. , Hsu Katharine C. , Sadelain Michel , Betel Doron , Klebanoff Christopher A. 
Published: March 2024

AbstractChimeric antigen receptor (CAR)-engineered T and NK cells can cause durable remission of B-cell malignancies; however, limited persistence restrains the full potential of these therapies in many patients. The FAS ligand (FAS-L)/FAS pathway governs naturally-occurring lymphocyte homeostasis, yet knowledge of which cells express FAS-L in patients and whether these sources compromise CAR persistence remains incomplete. Here, we constructed a single-cell atlas of diverse cancer types to identify cellular subsets expressingFASLG, the gene encoding FAS-L. We discovered thatFASLGis limited primarily to endogenous T cells, NK cells, and CAR-T cells while tumor and stromal cells express minimalFASLG. To establish whether CAR-T/NK cell survival is regulated through FAS-L, we performed competitive fitness assays using lymphocytes modified with or without a FAS dominant negative receptor (ΔFAS). Following adoptive transfer, ΔFAS-expressing CAR-T and CAR-NK cells became enriched across multiple tissues, a phenomenon that mechanistically was reverted throughFASLGknockout. By contrast,FASLGwas dispensable for CAR-mediated tumor killing. In multiple models, ΔFAS co-expression by CAR-T and CAR-NK enhanced antitumor efficacy compared with CAR cells alone. Together, these findings reveal that CAR-engineered lymphocyte persistence is governed by a FAS-L/FAS auto-regulatory circuit.
Deciphering Mechanochemical Influences of Emergent Actomyosin Crosstalk using QCM-D
Authors: Kerivan Emily M. , Amari Victoria N. , Weeks William B. , Hardin Leigh H. , Tobin Lyle , Azzam Omayma Y. Al , Reinemann Dana N. 
Published: March 2024

AbstractPurposeCytoskeletal protein ensembles exhibit emergent mechanics where behavior exhibited in teams is not necessarily the sum of the components’ single molecule properties. In addition, filaments may act as force sensors that distribute feedback and influence motor protein behavior. To understand the design principles of such emergent mechanics, we developed an approach utilizing QCM-D to measure how actomyosin bundles respond mechanically to environmental variables that alter constituent myosin II motor behavior.MethodsQCM-D is used for the first time to probe alterations in actin-myosin bundle viscoelasticity due to changes in skeletal myosin II concentration and motor nucleotide state. Actomyosin bundles were constructed on a gold QCM-D sensor using a microfluidic setup, and frequency and dissipation change measurements were recorded for each component addition to decipher which assay constituents lead to changes in bundle structural compliancy.ResultsLowering myosin concentration is detected as lower shifts in frequency and dissipation, while the relative changes in frequency and dissipation shifts for both the first and second actin additions are relatively similar. Strikingly, buffer washes with different nucleotides (ATP vs. ADP) yielded unique signatures in frequency and dissipation shifts. As myosin II’s ADP-bound state tightly binds actin filaments, we observe an increase in frequency and decrease in dissipation change, indicating a decrease in viscoelasticity, likely due to myosin’s increased affinity for actin, conversion from an active motor to a static crosslinker, and ability to recruit additional actin filaments from the surface, making an overall more rigid sensor coating. However, lowering the ADP concentration results in increased system compliancy, indicating that transient crosslinking and retaining a balance of motor activity perhaps results in a more cooperative and productive force generating system.ConclusionsQCM-D can detect changes in actomyosin viscoelasticity due to molecular-level alterations, such as motor concentration and nucleotide state. These results provide support for actin’s role as a mechanical force-feedback sensor and demonstrate a new approach for deciphering the feedback mechanisms that drive emergent cytoskeletal ensemble crosstalk and intracellular mechanosensing. This approach can be adapted to investigate environmental influences on more complex cytoskeletal ensemble mechanics, including addition of other motors, crosslinkers, and filament types.