bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigations of brain-wide functional and structural networks of dopaminergic and CamKIIα-positive neurons in VTA with DREADD-fMRI and neurotropic virus tracing technologies
Authors: Zheng Ning , Gui Zhu , Liu Xiaodong , Wu Yang , Wang Huadong , Cai Aoling , Wu Jinfeng , Li Xihai , Kaewborisuth Challika , Zhang Zhijian , Wang Qitian , Manyande Anne , Xu Fuqiang , Wang Jie 
Published: August 2023

Abstract
Background
The ventral tegmental area (VTA) contains heterogeneous cell populations. The dopaminergic neurons in VTA play a central role in reward and cognition, while CamKIIα-positive neurons, composed mainly of glutamatergic and some dopaminergic neurons, participate in the reward learning and locomotor activity behaviors. The differences in brain-wide functional and structural networks between these two neuronal subtypes were comparatively elucidated.

Methods
In this study, we applied a method combining Designer Receptors Exclusively Activated by Designer Drugs (DREADD) and fMRI to assess the cell type-specific modulation of whole-brain neural networks. rAAV encoding the cre-dependent hM3D was injected into the right VTA of DAT-cre or CamKIIα-cre transgenic rats. The global brain activities elicited by DREADD stimulation were then detected using BOLD-fMRI. Furthermore, the cre-dependent antegrade transsynaptic viral tracer H129ΔTK-TT was applied to label the outputs of VTA neurons.

Results
We found that DREADD stimulation of dopaminergic neurons induced significant BOLD signal changes in the VTA and several VTA-related regions including mPFC, Cg and Septum. More regions responded to selective activation of VTA CamKIIα-positive neurons, resulting in increased BOLD signals in VTA, Insula, mPFC, MC_R (Right), Cg, Septum, Hipp, TH_R, PtA_R, and ViC_R. Along with DREADD-BOLD analysis, further neuronal tracing identified multiple cortical (MC, mPFC) and subcortical (Hipp, TH) brain regions that are structurally and functionally connected by VTA dopaminergic and CamKIIα-positive neurons.

Conclusions
Our study dissects brain-wide structural and functional networks of two neuronal subtypes in VTA and advances our understanding of VTA functions.
The mitochondrial protein TSPO in Alzheimer’s disease: relation to the severity of AD pathology and the neuroinflammatory environment
Authors: Garland Emma F. , Dennett Oliver , Lau Laurie C. , Chatelet David S. , Bottlaender Michel , Nicoll James A. R. , Boche Delphine 
Published: August 2023

AbstractThe 18kD translocator protein (TSPO) is used as a positron emission tomography (PET) target to quantify neuroinflammation in patients. In Alzheimer’s disease (AD), the cerebellum is the pseudo-reference region for comparison with the cerebral cortex due to the absence of AD pathology and lower levels of TSPO. However, using the cerebellum as a pseudo-reference region is debated, with other brain regions suggested as more suitable. This paper aimed to establish the neuroinflammatory differences between the temporal cortex and cerebellar cortex, including TSPO expression. Using 60 human post-mortem samples encompassing the spectrum of Braak stages (I–VI), immunostaining for pan-Aβ, hyperphosphorylated (p)Tau, TSPO and microglial proteins Iba1, HLA–DR and MSR-A was performed in the temporal cortex and cerebellum. In the cerebellum, Aβ but not pTau, increased over the course of the disease, in contrast to the temporal cortex, where both proteins were significantly increased. TSPO increased in the temporal cortex, more than twofold in the later stages of AD compared to the early stages, but not in the cerebellum. Conversely, Iba1 increased in the cerebellum, but not in the temporal cortex. TSPO was associated with pTau in the temporal cortex, suggesting that TSPO positive microglia may be reacting to pTau itself and/or neurodegeneration at later stages of AD. Furthermore, the neuroinflammatory microenvironment was examined, using MesoScale Discovery assays, and IL15 only was significantly increased in the temporal cortex. Together this data suggests that the cerebellum maintains a more homeostatic environment compared to the temporal cortex, with a consistent TSPO expression, supporting its use as a pseudo-reference region for quantification in TSPO PET scans.
Biopharma innovation trends during COVID-19 and beyond: an evidence from global partnerships and fundraising activities, 2011-2022
Authors: Yu Tzu-Hui , Mei Yung-Yu , Tseng Yufeng Jane 
Published: August 2023

Abstract
Background
Co-development alliances and capital-raising activities are essential supports for biopharmaceutical innovation. During the initial outbreak of the COVID-19, the level of these business activities has increased greatly. Yet the magnitude, direction, and duration of the trend remain ambiguous. Real-time real-world data are needed to inform strategic redirections and industrial policies.

Methods
This observational study aims to characterize trends in global biopharma innovation activities throughout the global pandemic outbreak. Our extensive deal dataset is retrieved from the commercial database GlobalData (12,866 partnership deals and 32,250 fundraising deals announced between 2011 and 2022). We perform Chi-squared tests to examine the changes in qualitative deal attributes during and beyond the outbreak. Our deal-level sample is further aggregated into category-level panel data according to deal characteristics such as therapy area, molecule type, and development phase. We run a series of regressions to examine how the monthly investment amount raised in each category changed with the onset of the pandemic, controlling for the US Federal funds rate.

Results
The temporary surge of partnership and capital-raising activities was associated with the increase in infectious disease-related deals. Academic and government institutions played an increased role in supporting COVID-related co-development partnerships in 2020, and biopharma ventures had been securing more investments in the capital market throughout 2020 and 2021. The partnership and investment boom did not last till the later pandemic in 2022. The most significant and enduring trend was the shifting focus toward discovery-phase investments. Our regression model reveals that the discovery-phase fundraising deals did not suffer from a bounce back in the late pandemic, consistent with a persistent focus on early innovation.

Conclusions
Despite the reduced level of partnership and fundraising activities during 2022, we observe a lasting change in focus toward biopharmaceutical innovation after the pandemic outbreak. Our evidence suggests how entrepreneurs and investors should allocate resources in response to the post-pandemic tight monetary environment. We also suggest the need for policy interventions in financing private/public co-development partnerships and non-COVID-related technologies, to maintain their research capacity and generate breakthroughs when faced with unforeseen diseases.
Gut microbiota and intervertebral disc degeneration: a bidirectional two-sample Mendelian randomization study
Authors: Geng Ziming , Wang Jian , Chen Guangdong , Liu Jianchao , Lan Jie , Zhang Zepei , Miao Jun 
Published: August 2023

Abstract
Background
Although previous studies have suggested a close association between gut microbiota (GM) and intervertebral disc degeneration (IVDD), the causal relationship between them remains unclear. Hence, we thoroughly investigate their causal relationship by means of a two-sample Mendelian randomization (MR) study, aiming to determine the impact of gut microbiota on the risk of developing intervertebral disc degeneration.

Methods
Summary data from genome-wide association studies of GM (the MiBioGen) and IVDD (the FinnGen biobank) have been acquired. The inverse variance weighted (IVW) method was utilized as the primary MR analysis approach. Weighted median, MR-Egger regression, weighted mode, and simple mode were used as supplements. The Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) and MR-Egger regression were performed to assess horizontal pleiotropy. Cochran's Q test evaluated heterogeneity. Leave-one-out sensitivity analysis was further conducted to determine the reliability of the causal relationship. A reverse MR analysis was conducted to assess potential reverse causation.

Results
We identified nine gut microbial taxa that were causally associated with IVDD (P < 0.05). Following the Benjamini–Hochberg corrected test, the association between the phylum Bacteroidetes and a higher risk of IVDD remained significant (IVW FDR-corrected P = 0.0365). The results of the Cochrane Q test did not indicate heterogeneity (P > 0.05). Additionally, both the MR-Egger intercept test and the MR-PRESSO global test revealed that our results were not influenced by horizontal pleiotropy (P > 0.05). Furthermore, the leave-one-out analysis substantiated the reliability of the causal relationship. In the reverse analysis, no evidence was found to suggest that IVDD has an impact on the gut microbiota.

Conclusion
Our results validate the potential causal impact of particular GM taxa on IVDD, thus providing fresh insights into the gut microbiota-mediated mechanism of IVDD and laying the groundwork for further research into targeted preventive measures.
Efficacy and safety of traditional Chinese medicine in the treatment of osteonecrosis of the femoral head
Authors: Ouyang Wensi , Meng Yubo , Guo Guimei , Zhao Changwei , Zhou Xiaoling 
Published: August 2023

Abstract
Background
Hip joint-preserving treatment options for osteonecrosis of the femoral head (ONFH) have been a research hotspot in recent years. The combination of Chinese and Western medicine has been used in clinical practice to treat early- and mid-stage ONFH. However, there is still a lack of high-quality evidence to verify the effectiveness and safety of this approach.

Objective
To systematically evaluate the clinical efficacy and safety of the combination of traditional Chinese medicine (TCM) with Western medicine in the treatment of early- and mid-stage ONFH.

Methods
Multiple electronic databases were searched to identify the randomized controlled trials (RCTs) examining the use of TCM in the treatment of ONFH. Based on the inclusion and exclusion criteria, eligible studies were selected, and the quality of the studies was evaluated using the risk of bias assessment tool recommended by the Cochrane system Evaluator manual 5.1.0. The meta-analysis of the included data was performed using Review Manager 5.4.1 software and Stata 17.0 software.

Results
A total of 47 RCTs involving 3266 subjects were included in the meta-analysis. The results are observed: (1) Harris score: TCM + Western medicine versus Western medicine (SMD = 1.25, 95% Cl: 1.02 to 1.48, P < 0.00001), TCM + physiotherapy versus physiotherapy (SMD = 2.26, 95% Cl: 1.42 to 3.10, P < 0.00001), and TCM + hip preservation surgery versus hip preservation surgery (SMD = 1.28, 95% Cl: 1.03 to 1.53, P < 0.00001); (2) Visual analogue scale score: TCM + Western medicine versus Western medicine (SMD = −3.99, 95% Cl: −7.41 to −0.57, P = 0.02), TCM + physiotherapy versus physiotherapy (SMD = −0.99, 95% Cl: −1.44 to −0.54, P < 0.0001), and TCM + hip preservation surgery versus hip preservation surgery (SMD = −1.08, 95% Cl: −1.75 to −0.40, P = 0.002); (3) Imaging improvement: TCM + physiotherapy versus physiotherapy (RR = 1.42, 95% Cl: 1.15 to 1.76, P = 0.001) and TCM + hip preservation surgery versus hip preservation surgery (RR = 1.21, 95% Cl: 1.11 to 1.31, P < 0.0001); and (4) Occurrence of adverse reaction: TCM + Western medicine versus Western medicine (RR = 0.73, 95% Cl: 0.28 to 1.92, P = 0.53), TCM + physiotherapy versus physiotherapy (RR = 0.46, 95% Cl: 0.03 to 7.33, P = 0.58), and TCM + hip preservation surgery versus hip preservation surgery (RR = 1.11, 95% Cl: 0.36 to 3.45, P = 0.86).

Conclusion
TCM combined with Western medicine is an effective and safe approach for the treatment of ONFH. However, due to the low quality and quantity of the included studies, additional large-scale, high-quality studies are required to verify the above conclusions.
Systematic review registration: https://www.crd.york.ac.uk/prospero/#recordDetails, CRD42023392030.
Comparative analysis of percutaneous endoscopic interlaminar discectomy for highly downward-migrated disc herniation
Authors: Li Ran , Fu Dongming , Han Hao , Zhan Zihao , Wu Yiang , Meng Bin 
Published: August 2023

Abstract
Objectives
This study aimed to evaluate the clinical efficacy and safety of percutaneous endoscopic interlaminar discectomy (PEID) for treating highly downward-migrated disc herniation.

Methods
We conducted a retrospective study on 39 patients with highly downward-migrated disc herniation who underwent PEID treatment between January 2015 and October 2020. The clinical outcomes, including the preoperative and postoperative visual analogue scale (VAS) for the back and leg, Oswestry Disability Index (ODI), and MacNab criteria for surgical success, were evaluated and compared to thirty-seven patients treated with posterior lumbar interbody fusion (PLIF).

Results
The mean operation time of PEID was 93.00(77.00,110.00) min, while that of PLIF was 169.00(157.00,183.00) min. Continued improvement in both PEID and PLIF was observed in the VAS and ODI scores immediately after the surgery to the last follow‐up. The VAS and ODI scores of PEID one week after surgery were significantly different from those of PLIF. One patient with recurrent lumbar disc herniation in the same segment improved after undergoing repeat PEID, two patients had dura tears, and conservative treatment helped relieve the symptoms. The overall percentage of patients with good to excellent results of PELD according to the modified MacNab criteria was 97.43%, while that of PLIF was 94.60%.

Conclusions
PEID has reliable efficacy and safety for treating highly downward-migrated disc herniation. And the long-term efficacy of PEID is comparable to PLIF. No severe complications occurred after surgery, and most patients’ symptoms were relieved.
Current views on meningeal lymphatics and immunity in aging and Alzheimer’s disease
Authors: Rego Shanon , Sanchez Guadalupe , Da Mesquita Sandro 
Published: August 2023

AbstractAlzheimer’s disease (AD) is an aging-related form of dementia associated with the accumulation of pathological aggregates of amyloid beta and neurofibrillary tangles in the brain. These phenomena are accompanied by exacerbated inflammation and marked neuronal loss, which altogether contribute to accelerated cognitive decline. The multifactorial nature of AD, allied to our still limited knowledge of its etiology and pathophysiology, have lessened our capacity to develop effective treatments for AD patients. Over the last few decades, genome wide association studies and biomarker development, alongside mechanistic experiments involving animal models, have identified different immune components that play key roles in the modulation of brain pathology in AD, affecting its progression and severity. As we will relay in this review, much of the recent efforts have been directed to better understanding the role of brain innate immunity, and particularly of microglia. However, and despite the lack of diversity within brain resident immune cells, the brain border tissues, especially the meninges, harbour a considerable number of different types and subtypes of adaptive and innate immune cells. Alongside microglia, which have taken the centre stage as important players in AD research, there is new and exciting evidence pointing to adaptive immune cells, namely T and B cells found in the brain and its meninges, as important modulators of neuroinflammation and neuronal (dys)function in AD. Importantly, a genuine and functional lymphatic vascular network is present around the brain in the outermost meningeal layer, the dura. The meningeal lymphatics are directly connected to the peripheral lymphatic system in different mammalian species, including humans, and play a crucial role in preserving a “healthy” immune surveillance of the CNS, by shaping immune responses, not only locally at the meninges, but also at the level of the brain tissue. In this review, we will provide a comprehensive view on our current knowledge about the meningeal lymphatic vasculature, emphasizing its described roles in modulating CNS fluid and macromolecule drainage, meningeal and brain immunity, as well as glial and neuronal function in aging and in AD.
Spectrum of diabetes mellitus in patients with Shwachman-Diamond syndrome: case report and review of the literature
Authors: Navasardyan Lusine V. , Furlan Ingrid , Brandt Stephanie , Schulz Ansgar , Wabitsch Martin , Denzer Christian 
Published: August 2023

Abstract
Background
Shwachman-Diamond syndrome (SDS) is a rare congenital disorder caused by mutations in the SBDS gene and characterized by exocrine pancreatic deficiency, hematologic dysfunction, and skeletal growth failure. Although the hematologic features and characteristics of the somatic disorders commonly associated with SDS are well known, emerging data from case reports and patient registries suggest that SDS may also be associated with an increased risk of diabetes mellitus. However, currently available data on SDS-associated diabetes are limited and do not allow conclusions regarding prevalence and incidence rates, clinical course, and outcomes.

Case presentation
Here we report the case of a 5-year-old girl with SDS who underwent bone marrow transplantation at the age of 3 months and developed autoantibody-positive type 1 diabetes mellitus at the age of 1.8 years. The manifestation and course of diabetes development were mild, complicated by concurrent spontaneous episodes of hypoglycemia even before the onset of antidiabetic treatment. Currently, adequate metabolic control can be achieved by dietary intervention.

Conclusions
Considering that the SBDS protein regulates mitosis and ribosomal biosynthesis and that its suppression may cause immunologic instability and chronic inflammation, this case provides insight into the phenotype of rare Shwachman-Diamond syndrome-associated diabetes mellitus, which may be characterized by significant age-dependent differences in clinical course.
Did the early full genome sequencing of yeast boost gene function discovery?
Authors: Tantoso Erwin , Eisenhaber Birgit , Sinha Swati , Jensen Lars Juhl , Eisenhaber Frank 
Published: August 2023

Abstract
Background
Although the genome of Saccharomyces cerevisiae (S. cerevisiae) was the first one of a eukaryote organism that was fully sequenced (in 1996), a complete understanding of the potential of encoded biomolecular mechanisms has not yet been achieved. Here, we wish to quantify how far the goal of a full list of S. cerevisiae gene functions still is.

Results
The scientific literature about S. cerevisiae protein-coding genes has been mapped onto the yeast genome via the mentioning of names for genomic regions in scientific publications. The match was quantified with the ratio of a given gene name’s occurrences to those of any gene names in the article. We find that ~ 230 elite genes with ≥ 75 full publication equivalents (FPEs, FPE = 1 is an idealized publication referring to just a single gene) command ~ 45% of all literature. At the same time, about two thirds of the genes (each with less than 10 FPEs) are described in just 12% of the literature (in average each such gene has just ~ 1.5% of the literature of an elite gene). About 600 genes have not been mentioned in any dedicated article. Compared with other groups of genes, the literature growth rates were highest for uncharacterized or understudied genes until late nineties of the twentieth century. Yet, these growth rates deteriorated and became negative thereafter. Thus, yeast function discovery for previously uncharacterized genes has returned to the level of ~ 1980. At the same time, literature for anyhow well-studied genes (with a threshold T10 (≥ 10 FPEs) and higher) remains steadily growing.

Conclusions
Did the early full genome sequencing of yeast boost gene function discovery? The data proves that the moment of publishing the full genome in reality coincides with the onset of decline of gene function discovery for previously uncharacterized genes. If the current status of literature about yeast molecular mechanisms can be extrapolated into the future, it will take about another ~ 50 years to complete the yeast gene function list. We found that a small group of scientific journals contributed extraordinarily to publishing early reports relevant to yeast gene function discoveries.
High-resolution melting (HRM)-based detection of polymorphisms in the malic enzyme and glucose-6-phosphate isomerase genes for Leishmania infantum genotyping
Authors: Buffi Gloria , Ceccarelli Marcello , Diotallevi Aurora , Abruzzese Michelalberto , Bruno Federica , Castelli Germano , Vitale Fabrizio , Andreoni Francesca , Bencardino Daniela , Magnani Mauro , Galluzzi Luca 
Published: August 2023

Abstract
Background
Leishmaniasis is a zoonotic disease endemic in the Mediterranean region where Leishmania infantum is the causative agent of human and canine infection. Characterization of this parasite at the subspecies level can be useful in epidemiological studies, to evaluate the clinical course of the disease (e.g. resistant strains, visceral and cutaneous forms of leishmaniasis) as well as to identify infection reservoirs. Multilocus enzyme electrophoresis (MLEE), a method currently recognized as the reference method for characterizing and identifying strains of Leishmania, is cumbersome and time-consuming and requires cultured parasites. These disadvantages have led to the development of other methods, such as multilocus microsatellite typing (MLMT) and multilocus sequence typing (MLST), for typing Leishmania parasites; however, these methods have not yet been applied for routine use. In this study, we first used MLST to identify informative polymorphisms on single-copy genes coding for metabolic enzymes, following which we developed two rapid genotyping assays based on high-resolution melting (HRM) analysis to explore these polymorphisms in L. infantum parasites.

Methods
A customized sequencing panel targeting 14 housekeeping genes was designed and MLST analysis was performed on nine L. infantum canine and human strains/isolates. Two quantitative real-time PCR-HRM assays were designed to analyze two informative polymorphisms on malic enzyme (ME) and glucose-6-phosphate isomerase (GPI) genes (390T/G and 1831A/G, respectively). The two assays were applied to 73 clinical samples/isolates from central/southern Italy and Pantelleria island, and the results were confirmed by DNA sequencing in a subset of samples.

Results
The MLST analysis, together with sequences available in the Genbank database, enabled the identification of two informative polymorphisms on the genes coding for ME and GPI. The fast screening of these polymorphisms using two HRM-based assays in 73 clinical samples/isolates resulted in the identification of seven genotypes. Overall, genotype 1 (sequence type 390T/1831G) was the most highly represented (45.2%) in the overall sample and correlated with the most common L. infantum zymodemes (MON-1, MON-72). Interestingly, in Pantelleria island, the most prevalent genotype (70.6%) was genotype 6 (sequence type 390T/1831A).

Conclusions
Applying our HRM assays on clinical samples allowed us to identify seven different genotypes without the need for parasite isolation and cultivation. We have demonstrated that these assays could be used as fast, routine and inexpensive tools for epidemiological surveillance of L. infantum or for the identification of new infection reservoirs.

Graphical abstract