bluuebunny/crossref_metadata_2025_split huggingface dataset:
Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress
Authors: Echeveste Medrano Maider J , Leu Andy O , Pabst Martin , Lin Yuemei , McIlroy Simon J , Tyson Gene W , van Ede Jitske , Sánchez-Andrea Irene , Jetten Mike S M , Jansen Robert , Welte Cornelia U 
Published: July 2024

Abstract
Climate change–driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.
Cuticle development and the underlying transcriptome–metabolome associations during early seedling establishment
Authors: Chen Keting , Bhunia Rupam Kumar , Wendt Matthew M , Campidilli Grace , McNinch Colton , Hassan Ahmed , Li Ling , Nikolau Basil J , Yandeau-Nelson Marna D 
Published: July 2024

Abstract
The plant cuticle is a complex extracellular lipid barrier that has multiple protective functions. This study investigated cuticle deposition by integrating metabolomics and transcriptomics data gathered from six different maize seedling organs of four genotypes, the inbred lines B73 and Mo17, and their reciprocal hybrids. These datasets captured the developmental transition of the seedling from heterotrophic skotomorphogenic growth to autotrophic photomorphogenic growth, a transition that is highly vulnerable to environmental stresses. Statistical interrogation of these data revealed that the predominant determinant of cuticle composition is seedling organ type, whereas the seedling genotype has a smaller effect on this phenotype. Gene-to-metabolite associations assessed by integrated statistical analyses identified three gene networks associated with the deposition of different elements of the cuticle: cuticular waxes; monomers of lipidized cell wall biopolymers, including cutin and suberin; and both of these elements. These gene networks reveal three metabolic programs that appear to support cuticle deposition, including processes of chloroplast biogenesis, lipid metabolism, and molecular regulation (e.g. transcription factors, post-translational regulators, and phytohormones). This study demonstrates the wider physiological metabolic context that can determine cuticle deposition and lays the groundwork for new targets for modulating the properties of this protective barrier.
Integrating Mendelian Randomization With Single-Cell Sequencing Data Reveals the Causal Effect and Related Mechanisms of Smoking on Parkinson’s Disease
Authors: Zhang Xinyue , Zhu Zhigang , Zhu Liuhui , Guan Ying , Zhu Zhouhai , Liu Bin , Ren Hui , Yang Xinglong 
Published: July 2024

Abstract

Introduction
Smoking (nicotine) has been reported to possibly be neuroprotective and conducive to patients with early Parkinson’s disease (PD). However, the causal effect of smoking on PD and the molecular mechanisms of smoking-related genes (SRGs) are vague.

Aims and Methods
First, genome-wide association study summary data on smoking (ukb-b-6244) and PD (ieu-b-7) were retrieved from the Integrative Epidemiology Unit OpenGWAS database for Mendelian randomization (MR) analysis. Sensitivity analyses were performed to validate the results of the MR analyses. Subsequently, a differential analysis of PD patients and controls was performed to identify differentially expressed SRGs (DE-SRGs). Finally, the expression of DE-SRGs was analyzed in annotated cell types.

Results
The MR analysis revealed that smoking was a protective factor causally related to PD (p = .008, odds ratio = 0.288). Furthermore, a total of five DE-SRGs enriched in Toll-like receptor signaling pathways were identified in GSE7621 dataset. Regarding the single-cell analysis of the GSE184950 dataset, a total of nine cell types were annotated. The expression of LRRN1 in oligodendrocyte progenitor cells and oligodendrocytes, respectively, differed significantly between PD patients and controls.

Conclusions
Our study supported a causal relationship between smoking and PD and found that five SRGs (MAPK8IP1, LRRN1, LINC00324, HIST1H2BK, and YOD1) enriched in Toll-like receptor signaling pathways might be beneficial in PD. In addition, single-cell sequencing indicated that four SRGs were differentially expressed in different cell types. All four genes except MAPK8IP1 were significantly correlated with the 10 genes calculated by scPagwas. Thus, this evidence provides a theoretical basis for further research on the effect of nicotine (smoking) on PD.

Implications
In search of explore the potential etiology and pathogenesis of Parkinson’s disease, this study combined MR analysis, transcriptomics, and single-cell sequencing analysis to explore the association between exposure factors and Parkinson’s disease, observe and confirm the relationship and mechanism between the two from the perspective of genetics, and provide more reliable evidence for causal inference.
Genes for the Type-I Reaction Center and Galactolipid Synthesis are Required for Chlorophyll a Accumulation in a Purple Photosynthetic Bacterium
Authors: Tsukatani Yusuke , Azai Chihiro , Noji Tomoyasu , Kawai Shigeru , Sugimoto Saori , Shimamura Shigeru , Shimane Yasuhiro , Harada Jiro , Mizoguchi Tadashi , Tamiaki Hitoshi , Masuda Shinji 
Published: July 2024

Abstract
Anoxygenic photosynthesis is diversified into two classes: chlorophototrophy based on a bacterial type-I or type-II reaction center (RC). Whereas the type-I RC contains both bacteriochlorophyll and chlorophyll, type-II RC-based phototrophy relies only on bacteriochlorophyll. However, type-II phototrophic bacteria theoretically have the potential to produce chlorophyll a by the addition of an enzyme, chlorophyll synthase, because the direct precursor for the enzyme, chlorophyllide a, is produced as an intermediate of BChl a biosynthesis. In this study, we attempted to modify the type-II proteobacterial phototroph Rhodovulum sulfidophilum to produce chlorophyll a by introducing chlorophyll synthase, which catalyzes the esterification of a diterpenoid group to chlorophyllide a thereby producing chlorophyll a. However, the resulting strain did not accumulate chlorophyll a, perhaps due to the absence of endogenous chlorophyll a-binding proteins. We further heterologously incorporated genes encoding the type-I RC complex to provide a target for chlorophyll a. Heterologous expression of type-I RC subunits, chlorophyll synthase and galactolipid synthase successfully afforded detectable accumulation of chlorophyll a in Rdv. sulfidophilum. This suggests that the type-I RC can work to accumulate chlorophyll a and that galactolipids are likely necessary for the type-I RC assembly. The evolutionary acquisition of type-I RCs could be related to prior or concomitant acquisition of galactolipids and chlorophylls.
Do private firms (mis)learn from the stock market?
Authors: Yan Dong 
Published: July 2024

Abstract
This article examines whether and to what extent private firms learn from the stock market. Using a large panel data set for the UK, I find that private firms’ investment responds positively to the valuation of public firms in the same industry. The sensitivity increases with price informativeness. To further pin down the information channel, I construct a price noise measure based on public firms’ unrelated minor segments and show that it positively affects the investment of private firms in the major-segment industry. The results are consistent with models featuring learning from noisy signals and are not driven by alternative channels in the absence of learning. My findings suggest that the stock market can have real effects on private firms through an information-spillover channel, even when these firms do not list their shares on the stock exchanges.
Bilateral cystoid macular edema as the presenting feature of chronic myeloid leukemia
Authors: Brown Ffion E , Al-Janabi Ahmed , Gallagher Kevin 
Published: July 2024

Purpose:
Ophthalmic disease may rarely be a presenting feature of chronic myeloid leukemia (CML).

Methods:
We report a case of a 53-year-old man with type 1 diabetes mellitus who presented with a rapid onset of bilateral blurred vision.

Results:
He was noted to have bilateral macular edema and was initially treated for presumed diabetic macular edema (DME) with intravitreal alifbercept injections. One month later, there was complete resolution of his macular edema. Review of his history and imaging revealed features atypical for DME, specifically; the rapid onset of bilateral blurred vision over 2-3 weeks, numerous cotton wool spots within the macula, the absence of any exudates, the symmetrical macular edema with a “vaulted ceiling” appearance (more typical of cystoid macular edema) and the dramatic response to a single intravitreal aflibercept injection. One week after his intravitreal injection, the patient was diagnosed with CML following marked leucocytosis on a routine blood test by his general practitioner. Although uncommon, sudden onset bilateral edema in the absence of other chronic diabetic changes should prompt consideration of an underlying haematological cause.

Conclusion:
This case highlights the importance of considering CML as a differential diagnosis in patients presenting with sudden onset, bilateral cystoid macular oedema. Vigilance is especially important in patients with co-existing diabetic retinopathy as the clinical features of leukemic retinopathy can overlap. Furthermore, the diagnosis of CML in a patient with diabetes mellitus should prompt extra observation for accelerated worsening of diabetic retinopathy.
Is JAK effective in treating recurrent SAPHO syndrome? TwHF might be a good choice
Authors: Sun Qiong , Gu Qinchen , Jiang Haixu , Li Weizhong , Lin Zhimin , Li Chen , Ying Zhenhua 
Published: July 2024

Background:
Recently, JAKi has also been widely proved to be an effective alternative to conventional treatment for Synovitis acne pustulosis–hyperostosis–osteitis (SAPHO) cases, after failure of multiple drugs including those described above. But what to do when all these treatments fail? We report a case of remission from Tripterygium wilfordii Hook (TwHF) treatment.

Methods:
The patient was treated with nonsteroidal anti-inflammatory drugs, oral prednisone, minocycline, bisphosphonate injection, etanercept, and tofacitinib, but the symptoms did not change significantly. Treatment with TwHF (1.0 mg/kg/day, patient weight 60 kg) was started for 24 weeks.

Results:
After 50 months of unsatisfactory treatment, this patient was finally treated with herbal TwHF, and after 6 months of treatment, the patient’s magnetic resonance imaging and inflammatory indexes were significantly improved, indicating that the disease had been better controlled.

Conclusion:
In this study, TwHF was successful in treating a patient with refractory SAPHO syndrome who was refractory to multiple Western medications without significant adverse effects or toxicities, but further follow-up is needed to determine long-term efficacy. More case reports as well as clinical trials are still needed to confirm whether TwHF can effectively treat refractory SAPHO syndrome.
Slow-velocity eccentric-only resistance training improves symptoms of type 2 diabetic mellitus patients by regulating plasma MMP-2 and -9
Authors: Qian Zhao , Ping Liu , Dongming Xu , Xuelin Zhang 
Published: July 2024

Objective:
This study investigated the intervention effect of slow-velocity eccentric-only resistance training on type 2 diabetic mellitus (T2DM) patients based on the role of matrix metalloproteinase-2 and -9 (MMP-2 and -9) in regulating extracellular matrix homeostasis.

Methods:
50 T2DM patients were randomly divided into the slow-velocity eccentric-only resistance training group (E) and control group (C). The E group performed eccentric-only resistance training 3 times a week, every other day for 10 weeks, while the C group did not. Blood samples were collected before and after training, and subjects were tested for changes in clinical parameters, insulin resistance indices [fasting insulin, homeostatic model assessment insulin resistance (HOMA-IR)], MMP-2 and -9, and hydroxyproline, and muscle strength (12-RM), respectively.

Results:
After 10 weeks of training, the E group showed significant decreases in fasting glucose (P < .05), insulin (P < .05), insulin resistance indices (P < .05), hemoglobin A1c (HbA1c) (P < .01), triglycerides (P = .06) and MMP-2 (P < .05), while total cholesterol (P < .05), MMP-9 (P < .05), hydroxyproline (P < .01), Creatine Kinase (CK) (P < .05), and muscle strength (P < .001) significantly increased. There were no significant changes in the count of neutrophil, lymphocyte and platelet, neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), high-density lipoprotein cholesterol (HDL-c), and low-density lipoprotein cholesterol (LDL-c). Compared with the C group, the E group showed a trend of a significant decrease in triglyceride (P < .05), lymphocyte count (P < .05), fasting glucose (P = .07), and plasma MMP-2 (P < .05), while MMP-9 (P < .05), hydroxyproline (P < .001), and muscle strength (P < .01) significantly increased. However, no significant changes were observed in insulin and insulin resistance indices, HbA1c, total cholesterol, HDL-c, LDL-c, CK, and other inflammatory indicators.

Conclusions:
Slow-velocity eccentric-only resistance training was beneficial for T2DM, but the potential role of MMP-2 and -9 in regulating extracellular matrix homeostasis is very different in T2DM patients.
Fingertip cutaneous metastasis of salivary duct carcinoma secondary to scald: A unique case report and a brief review of literature (following CARE guidelines)
Authors: Peng Ran , Wu Wenqi , Li Xuemin , Zhou Yang , Su Jing , Wang Hao 
Published: July 2024

Rationale:
Salivary duct carcinoma (SDC) is an aggressive form of cancer, with cutaneous metastasis being a rare occurrence. Furthermore, cutaneous metastasis of SDC secondary to a scald is even rarer, and to the best of our knowledge, our case represents the first such instance. Considering the involvement of the fingers in the metastatic site, which may affect limb function and quality of life, we present this case to explore the reason why scald could lead to distant recurrence and better treatment options.

Patient concerns:
An 85-year-old man diagnosed with SDC in the parotid gland found enlarged masses at the fingertips as a consequence of a burn, 6 years after his initial treatment.

Diagnoses:
Cutaneous metastasis of SDC in the parotid gland and left thumb loss due to surgery.

Interventions:
Radiotherapy was offered, targeting at the masses on the fingers, with dose at 15 Gy in 3 fractions, 12 Gy in 3 fractions, 15 Gy in 3 fractions for both hands and additional 21 Gy in 7 fractions only for left hand.

Outcomes:
The tumors shrank after 2 months of radiotherapy and the patient recovered well. Side effects included nail hyperplasia and paronychia.

Lessons:
Connections between scald and distant metastasis of malignant tumors in this case needed further investigation. Considering reserving function of the fingers while dealing with metastasis, radiotherapy is recommended rather than surgery.
Clinical value of ultrasound-guided full-needle path anesthesia in transperineal prostate biopsy: An observational study
Authors: Lu DianYuan , Zhou JunYu , Cai JianRong , Liu Lan , Ni Ye 
Published: July 2024

Background:
The pain sensation in a transperineal prostate biopsy was obvious. This study explored the clinical value of ultrasound-guided full-needle path anesthesia in transperineal prostate biopsy.

Methods:
Two hundred patients who underwent ultrasound-guided transperineal prostate biopsy at our department were randomly divided into 2 groups. The control group received routine local infiltration anesthesia, and the experimental group received ultrasound-guided full-needle path anesthesia. Immediately after biopsy, visual analog scoring was used to evaluate pain during the biopsy process. Seven days postbiopsy, telephone follow-up revealed symptoms, such as hematuria and discomfort during urination. The measured data were expressed as x ± s. The 2 groups were compared using the t test, and the differences were statistically significant (P < .05).

Results:
There were no significant differences in age, prostate-specific antigen (PSA) level, or prostate volume between the 2 groups, and all patients underwent prostate biopsy. The pain score of visual analog score was (2.55 ± 0.88), urination discomfort was (1.86 ± 0.67) days and hematuria time was (2.87 ± 0.91) days in the experimental group after biopsy. In the control group, the pain score of visual analog scale was (4.32 ± 0.94), the urination discomfort was (2.3 ± 0.77) days, and the hematuria time was (2.85 ± 0.83) days. Pain scores and urination discomfort were compared between the 2 groups (P < .01). Pain and urination discomfort associated with prostate biopsy in the experimental group were significantly lower than those in the control group.

Conclusion:
Ultrasound-guided full needle path anesthesia can alleviate pain sensation in patients undergoing transperineal prostate biopsy and has high clinical value.
Bacterascites caused by Salmonella spp. following a cesarean section: A case report
Authors: Wu Ya-Chu , Ho Wang-Chun , Kao Sheng-Po , Ding Dah-Ching 
Published: July 2024

Rationale:
Bacterascites are a rare complication of cesarean sections (C/S). Here, we report the case of a patient with bacterascites after an emergent C/S.

Patient concern:
A 41-year-old female reported diffuse abdominal tightness and pain for a week after C/S, who received C/S at 38 4/7 weeks due to superimposed preeclampsia and prolonged labor.

Diagnoses:
Bacterascites caused by Salmonella species after C/S was diagnosed.

Interventions:
Initial treatment included cefmetazole and metronidazole. On day 2, paracentesis was performed, followed by albumin and hydroxyethyl starch administration. By day 3, the patient developed pulmonary edema, necessitating Lasix administration. On day 6, ascites culture revealed Salmonella species resistant to third-generation cephalosporins, leading to meropenem therapy adjustment. This resulted in improved symptoms. Meropenem was continued for 14 days to complete the treatment regimen.

Outcomes:
Follow-up ultrasonography revealed a decrease in ascites. As the patient clinical condition improved, she was discharged on day 20 and scheduled for outpatient department follow-up. No recurrence of ascites was observed during the subsequent follow-up period of 3 months. No ascites were noted 8 days after discharge.

Lessons:
Postoperative bacterascites with Salmonella were diagnosed. Antibiotic treatment and therapeutic paracentesis were effective for this condition.
Ruptured primary ovarian pregnancy: A case report with a literature review
Authors: Qing Xuemei , Xie Min , Zhang Yong , Ma Ying 
Published: July 2024

Rationale:
Ovarian pregnancy is a rare form of ectopic pregnancy, accounting for 0.5% to 3% of the total number of ectopic pregnancies. Its diagnostic rate is very low and it can be easily misdiagnosed before laparoscopy, due to the clinical presentation being very similar to tubal pregnancy. The ovarian blood supply is abundant, and in case of rupture of ovarian pregnancy, intra-abdominal hemorrhage or even hemorrhagic shock may occur, endangering the patient’s life. We report a case of ruptured primary ovarian pregnancy through natural conception.

Patient concerns:
This patient had a history of menopause with lower abdominal pain and tenderness. Ultrasound showed a thick-walled cystic echo in the left adnexal region, a dark area of fluid in the pelvis, and an irregular, slightly strong echo posterior to the uterus. Unclotted blood was punctured from the posterior fornix, and her hemoglobin was decreasing with a serum β-human chorionic gonadotropin of 1800.00 mIU/mL.

Diagnoses:
Through early recognition of clinical manifestations, ultrasonography, laparoscopic exploration, and the final histopathologic examination, this patient was diagnosed with an ovarian pregnancy.

Interventions:
Then, removal of the left ovarian pregnancy lesion was performed, which was visible as villi. And Methotrexate 50 mg was administered locally.

Outcomes:
Through conservative surgical treatment, she recovered well and was discharged with a satisfactory follow-up.

Lessons:
Gynecologists should be alert to patients with menopausal lower abdominal pain with or without vaginal bleeding and consider ectopic pregnancy in rare sites, such as ovarian pregnancy. Surgery is the mainstay of treatment, and early laparoscopic exploration may be beneficial in clarifying the diagnosis and performing the concurrent surgical treatment.
All-optical mapping of Ca2+transport and homeostasis in dendrites
Authors: Hayward Rebecca Frank , Cohen Adam E. 
Published: July 2024

AbstractCalcium mediates many important signals in dendrites. However, the basic transport properties of calcium in dendrites have been difficult to measure: how far and how fast does a local influx of calcium propagate? We developed an all-optical system for simultaneous targeted Ca2+import and concentration mapping. We co-expressed a blue light-activated calcium selective channelrhodopsin, CapChR2, with a far-red calcium sensor, FR-GECO1c, in cultured rat hippocampal neurons, and used patterned optogenetic stimulation to introduce calcium into cells with user-defined patterns of space and time. We determined a mean steady-state length constant for Ca2+transportϕ∼ 5.8 μm, a half-life for return to baselinet1/2∼ 1.7 s, and an effective diffusion coefficientD∼ 20 μm2/s, though there were substantial differences in Ca2+dynamics between proximal and distal dendrites. At high Ca2+concentration, distal dendrites showed nonlinear activation of Ca2+efflux, which we pharmacologically ascribed to the NCX1 antiporter. Genetically encoded tools for all-optical study of Ca2+transport and handling provide a powerful capability for studying this important messenger.
Representing Transcription Factor Dimer Binding Sites Using Forked-Position Weight Matrices and Forked-Sequence Logos
Authors: Dyer Matthew , Tirado-Magallanes Roberto , Ghayour-Khiavi Aida , Quy Xiao Xuan Lin , Santana Walter , Usefi Hamid , Thomas-Chollier Morgane , Jha Sudhakar , Thieffry Denis , Benoukraf Touati 
Published: July 2024

AbstractCurrent position weight matrices and sequence logos may not be sufficient for accurately modeling transcription factor binding sites recognized by a mixture of homodimer and heterodimer complexes. To address this issue, we developedforkedTF, an R-library that allows the creation of Forked-Position Weight Matrices (FPWM) and Forked-Sequence Logos (F-Logos), which better capture the heterogeneity of TF binding affinities based on interactions and dimerization with other TFs. Furthermore, we have enhanced the standard PWM format by incorporating additional information on co-factor binding and DNA methylation. Precomputed FPWM and F-Logos are made available in theMethMotif 2024database, thereby providing ready-to-use resources for analyzing TF binding dynamics. Finally,forkedTFis designed to support the TRANSFAC format, which is compatible with most third-party bioinformatics tools that utilize PWMs. TheforkedTFR-library is open source and can be accessed on GitHub athttps://github.com/benoukraflab/forkedTF.