Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of novel GLI1 target genes and regulatory circuits in human cancer cells

Hedgehog (HH) signaling is involved in many physiological processes, and pathway deregulation can result in a wide range of malignancies. Glioma‐associated oncogene 1 (GLI1) is a transcription factor and a terminal effector of the HH cascade. Despite its crucial role in tumorigenesis, our understanding of the GLI1 cellular targets is quite limited. In this study, we identified multiple new GLI1 target genes using a combination of different genomic surveys and then subjected them to in‐depth validation in human cancer cell lines. We were able to validate >90% of the new targets, which were enriched in functions involved in neurogenesis and regulation of transcription, in at least one type of follow‐up experiment. Strikingly, we found that RNA editing of GLI1 can modulate effects on the targets. Furthermore, one of the top targets, FOXS1, a gene encoding a transcription factor previously implicated in nervous system development, was shown to act in a negative feedback loop limiting the cellular effects of GLI1 in medulloblastoma and rhabdomyosarcoma cells. Moreover, FOXS1 is both highly expressed and positively correlated with GLI1 in medulloblastoma samples of the Sonic HH subgroup, further arguing for the existence of FOXS1/GLI1 interplay in human tumors. Consistently, high FOXS1 expression predicts longer relapse‐free survival in breast cancer. Overall, our findings open multiple new avenues in HH signaling pathway research and have potential for translational implications.
Extracts and components of Ficus carica leaves suppress survival, cell cycle, and migration of triple-negative breast cancer MDA-MB-231 cells

Background Products from Ficus carica have been used in traditional medicine to treat many diseases. This study aimed to analyze anticancer effects of extracts of F. carica leaves on the triple-negative breast cancer cell line MDA-MB-231. Materials and methods The human breast cancer cell line MDA-MB-231 was used to evaluate effects of F. carica extracts. Effects of F. carica on cell viability were evaluated using MTT assays. Cell-cycle distribution was examined using cell-cycle analysis. Wound-healing assays were used to evaluate migration of MDA-MB-231. Quantitative reverse-transcription polymerase chain reaction was used to detect levels of Bax, p53, p21, GATA3, ELF5, cyclin-dependent kinases, MMP2, and tissue inhibitors of metalloproteinase. Results We investigated the mechanism of anti-growth effects, and found that the expressions of genes that promote apoptosis were increased. In addition, the treated cells illustrated increased portion at S phase and changed expression of cyclin-dependent kinases, demonstrating cell-cycle arrest at the S phase. Furthermore, treated cells showed decreased cell mobility, which is essential for metastasis. Two of the active components of F. carica leaves, bergapten and psoralen, had similar anticancer effects as F. carica leaf extracts, indicating that these two components might play important roles in anticancer effects of F. carica leaves. Conclusion Our findings suggest that F. carica leaves might be a good source to develop drugs for suppressing cancer-cell growth and migration to treat triple-negative breast cancers.
A Sensor Image Dehazing Algorithm Based on Feature Learning

To solve the problems of color distortion and structure blurring in images acquired by sensors during bad weather, an image dehazing algorithm based on feature learning is put forward to improve the quality of sensor images. First, we extracted the multiscale structure features of the haze images by sparse coding and the various haze-related color features simultaneously. Then, the generative adversarial network (GAN) was used for sample training to explore the mapping relationship between different features and the scene transmission. Finally, the final haze-free image was obtained according to the degradation model. Experimental results show that the method has obvious advantages in its detail recovery and color retention. In addition, it effectively improves the quality of sensor images.
USG-guided continuous erector spinae block as a primary mode of perioperative analgesia in open posterolateral thoracotomy: A report of two cases

The postoperative pain management in open thoracotomy is very crucial as the effective analgesia can prevent respiratory and thrombotic complications and lead to early mobilization and discharge. The thoracic epidural analgesia is the gold standard in such surgeries; however, there are few adverse effects such as hypotension, dural puncture, and contralateral block that always warrants safer alternative. Recently, with the advent of ultrasound, the regional anesthetic techniques are getting more popular to avoid such complications. Erector spinae plane (ESP) block is one of the novel techniques that has been described as a safe thoracic paravertebral block. We are reporting here the continuous ESP block as a primary mode of postoperative analgesia which was continued for 48 h. The intraoperative opioid requirement was very less, and the maximum NRS score in postoperative period was 4 at 12 h, which was well managed with multimodal analgesic regimen along with rescue doses of opioid.
A review of the Cholevinae from the island of Borneo (Coleoptera, Leiodidae)

Abstract The available knowledge of the round fungus beetle subfamily Cholevinae (Leiodidae) from the island of Borneo is reviewed, and the results of newly studied material presented. The currently known 30 species (of which 14 are newly described herein) represent the genera Micronemadus (one species), Catops (one species), Baryodirus (one species), Ptomaphaginus (14 species), and Ptomaphaminus (13 species). The following new species are described: Micronemadussondaicus Schilthuizen & Perreau, sp. n. , Ptomaphaginusgrandis Schilthuizen & Perreau, sp. n. , P.louis Schilthuizen & Perreau, sp. n. , P.muluensis Schilthuizen & Perreau, sp. n. , and P.isabellarossellini Schilthuizen, Njunjić & Perreau, sp. n. , and Ptomaphaminuskinabatanganensis Njunjić, Schilthuizen & Perreau, sp. n. , P.testaceus Schilthuizen & Perreau, sp. n. , P.nanus Schilthuizen & Perreau, sp. n. , P.marshalli Schilthuizen & Perreau, sp. n. , P.hanskii Schilthuizen & Perreau, sp. n. , P.sarawacensis Schilthuizen & Perreau, sp. n. , P.layangensis Schilthuizen & Perreau, sp. n. , P.microphallus Schilthuizen & Perreau, sp. n. , and P.alabensis Schilthuizen & Perreau, sp. n. It is expected that the cholevine biodiversity of Borneo is still far from completely known. Nonetheless, provisional identification keys to all species known so far are presented.
Effects of Horticultural Therapy on Asian Older Adults: A Randomized Controlled Trial

The effect of horticultural therapy (HT) on immune and endocrine biomarkers remains largely unknown. We designed a waitlist-control randomized controlled trial to investigate the effectiveness of HT in improving mental well-being and modulating biomarker levels. A total of 59 older adults was recruited, with 29 randomly assigned to the HT intervention and 30 to the waitlist control group. The participants attended weekly intervention sessions for the first 3 months and monthly sessions for the subsequent 3 months. Biological and psychosocial data were collected. Biomarkers included IL-1β, IL-6, sgp-130, CXCL12/SDF-1α, CCL-5/RANTES, BDNF (brain-derived neurotrophic factor), hs-CRP, cortisol and DHEA (dehydroepiandrosterone). Psychosocial measures examined cognitive functions, depression, anxiety, psychological well-being, social connectedness and satisfaction with life. A significant reduction in plasma IL-6 level (p = 0.02) was observed in the HT intervention group. For the waitlist control group, significant reductions in plasma CXCL12 (SDF-1α) (p = 0.003), CXCL5 (RANTES) (p = 0.05) and BDNF (p = 0.003) were observed. A significant improvement in social connectedness was also observed in the HT group (p = 0.01). Conclusion: HT, in reducing plasma IL-6, may prevent inflammatory disorders and through maintaining plasma CXCL12 (SDF-1α), may maintain hematopoietic support to the brain. HT may be applied in communal gardening to enhance the well-being of older adults.
Inhibition of adventitious root development in apple rootstocks by cytokinin is based on its suppression of adventitious root primordia formation.

Cytokinin (CK) inhibits adventitious root (AR) formation in stem cuttings. Little is known, however, about the mechanism underlying the inhibitory effect. In this study, 2 mg l-1 of exogenous 6-benzyl adenine (6-BA) was administered to 3 and 7-day-old apple rootstocks 'M.26' cuttings (3 and 7 days 6-BA) by transferring them from a rooting medium containing indole-3-butanoic acid to the medium containing 6-BA. Anatomical and morphological observations revealed that the exogenous application of 6-BA inhibited primordia formation in the 3 days 6-BA but not the 7 days 6-BA group. The concentration of auxin (IAA), the ratios of IAA/CK and IAA/abscisic acid were lower in 3 days 6-BA than in 7 days 6-BA. Expression analysis of genes known to be associated with AR formation was also analyzed. In the 3 days 6-BA group, high level of CK inhibited the synthesis and transport of auxin, as a result, low endogenous auxin level suppressed the auxin signaling pathway genes, as were other AR development and cell cycle related genes; all of which had an inhibitory impact on AR primordium formation. On the contrary, low CK level in the 7 days 6-BA, reduced the inhibitory impact on auxin levels, leading to an upregulated expression of genes known to promote AR primordia formation. Collectively, our data indicated that 3-7 days is the time period in which AR primordia formation occurs in cuttings of 'M.26' and that the inhibition of AR development by CK is due to the suppression of AR primordia development over 3-7 days period after culturing in rooting medium.
Toothed whale and shark depredation indicators: A case study from the Reunion Island and Seychelles pelagic longline fisheries

Depredation in marine ecosystems is defined as the damage or removal of fish or bait from fishing gear by predators. Depredation raises concerns about the conservation of species involved, fisheries yield and profitability, and reference points based on stock assessment of depredated species. Therefore, the development of accurate indicators to assess the impact of depredation is needed. Both the Reunion Island and the Seychelles archipelago pelagic longline fisheries targeting swordfish (Xiphias gladius) and tuna (Thunnus spp.) are affected by depredation from toothed whales and pelagic sharks. In this study, we used fishery data collected between 2004 and 2015 to propose depredation indicators and to assess depredation levels in both fisheries. For both fisheries, the interaction rate (depredation occurrence) was significantly higher for shark compared to toothed whale depredation. However, when depredation occurred, toothed whale depredation impact was significantly higher than shark depredation impact, with higher depredation per unit effort (number of fish depredated per 1000 hooks) and damage rate (proportion of fish depredated per depredated set). The gross depredation rate in the Seychelles was 18.3%. A slight increase of the gross depredation rate was observed for the Reunion Island longline fleet from 2011 (4.1% in 2007–2010 and 4.4% in 2011–2015). Economic losses due to depredation were estimated by using these indicators and published official statistics. A loss of 0.09 EUR/hook due to depredation was estimated for the Reunion Island longline fleet, and 0.86 EUR/hook for the Seychelles. These results suggest a southward decreasing toothed whale and shark depredation gradient in the southwest Indian Ocean. Seychelles depredation levels are among the highest observed in the world revealing this area as a “hotspot” of interaction between pelagic longline fisheries and toothed whales. This study also highlights the need for a set of depredation indicators to allow for a global comparison of depredation rates among various fishing grounds worldwide.
Bilateral ultrasound-guided erector spinae plane block for postoperative analgesia in choledochal cyst resection surgery

499 Saudi Journal of Anesthesia / Volume 12 / Issue 3 / July‐September 2018 3. Gupta PK, Hopkins PM. Diagnosis and management of malignant hyperthermia. BJA Educ 2017;17:249‐54. 4. Parness J, Bandschapp O, Girard T. The myotonias and susceptibility to malignant hyperthermia. Anesth Analg 2009;109:1054‐64. 5. Weatherred T, Qadeer A, Florentino I. Multiple Anesthetics in a Child with Schwartz‐ Jampel Syndrome. Poster Presentation at Society for Pediatric Anesthesia Meeting. Las Vegas, NV; March, 2013. Available from: http://www2.pedsanesthesia. org/meetings/2013winter/posters/ uploads/268—NM‐199.pdf. [Last accessed on 2018 Feb 18].
Therapeutic implications of how TNF links apolipoprotein E, phosphorylated tau, α‐synuclein, amyloid‐β and insulin resistance in neurodegenerative diseases

While cytokines such as TNF have long been recognized as essential to normal cerebral physiology, the implications of their chronic excessive production within the brain are now also increasingly appreciated. Syndromes as diverse as malaria and lead poisoning, as well as non‐infectious neurodegenerative diseases, illustrate this. These cytokines also orchestrate changes in tau, α‐synuclein, amyloid‐β levels and degree of insulin resistance in most neurodegenerative states. New data on the effects of salbutamol, an indirect anti‐TNF agent, on α‐synuclein and Parkinson's disease, APOE4 and tau add considerably to the rationale of the anti‐TNF approach to understanding, and treating, these diseases. Therapeutic advances being tested, and arguably useful for a number of the neurodegenerative diseases, include a reduction of excess cerebral TNF, whether directly, with a specific anti‐TNF biological agent such as etanercept via Batson's plexus, or indirectly via surgically implanting stem cells. Inhaled salbutamol also warrants investigating further across the neurodegenerative disease spectrum. It is now timely to integrate this range of new information across the neurodegenerative disease spectrum, rather than keep seeing it through the lens of individual disease states.
A novel fusion gene PLEKHA6‐NTRK3 in langerhans cell histiocytosis

Langerhans cell histiocytosis (LCH) is the most common histiocytosis with constitutive activation of the RAS–RAF–MEK–ERK (MAPKinase) cell signaling pathway. We analyzed 89 cases of BRAF and MAP2K1 mutations by Sanger sequencing, of which 18 cases showed that these two gene mutations are negative. Whole genome sequencing of suitable specimens in these negative cases revealed a translocation from the 3 intron of PLEKHA6 to the 13 intron of NTRK3 in one case. We identified that this translocation could cause a novel fusion mutation, PLEKHA6‐NTRK3. Overexpression of the PLEKHA6‐NTRK3 mutant in NIH 3T3 cells enhanced MAPKinase pathway activation, promote cell growth. Our result suggested that a new mutation need be included in LCH molecular screening panel to better define its prevalence in LCH.
Comparison of Vocalization Patterns in Piglets Which Were Crushed to Those Which Underwent Human Restraint

Simple Summary Piglet crushing (the process by which a sow sits or lies on and crushes her piglet) is a welfare issue in pig husbandry. In order to understand why crushing occurs, and avoid hardship to a piglet, recordings of distressed piglets are often used to simulate crushing events to measure sows’ behavior. Unfortunately, it is not known if the call produced by the distressed piglet is similar to a piglet being crushed, making the evaluation of the results difficult. We recorded calls of piglets during crushing and compared the calls to those produced by restrained piglets. When crushed, piglets have a deeper call than piglets which are restrained by a human. Restrained piglets call as loudly as crushed piglets. In conclusion, sufficient differences exist between restrained and crushed piglets that restrained calls alone should not be used to understand the conditions in which a sow will respond to the distress calls of her piglets. Future research should include measuring sow behavior in response to Crushed and Restrained calls. Abstract Though many studies focused on piglet crushing utilizing piglet vocalizations to test sow response, none have verified the properties of test vocalizations against actual crushing events. Ten sows were observed 48 h after parturition, and crushing events were recorded from all sows. When a crushing event occurred, a second piglet within the same litter was used to solicit a vocalization through manual restraint to compare restrained piglets’ call properties to those of crushed piglets’. A total of 659 Restrained calls and 631 Crushed calls were collected. Variables were gathered at the loudest point in a call, and as an average across the entire call. Crushed piglets had a lower fundamental frequency (p < 0.01; Crushed: 523.57 ± 210.6 Hz; Restrained: 1214.86 ± 203.2 Hz) and narrower bandwidth (p < 0.01; Crushed: 4897.01 ± 587.3 Hz; Restrained: 6674.99 ± 574.0 Hz) when analyzed at the loudest portion of a call. Overall, piglets which were crushed had a lower mean peak frequency than those which were restrained (p = 0.01; 1497.08 ± 239.4 Hz and 2566.12 ± 235.0 Hz, respectively). Future research should focus on measuring sow reactivity to Crushed and Restrained piglets to continue to improve research practices.
The DPSIR Model for Environmental Risk Assessment of Municipal Solid Waste in Dar es Salaam City, Tanzania

Environmental risk has become an area of major concern and research, drawing special attention. This study on the environmental risk assessment (ERA) of Dar es Salaam Municipal Solid Waste comes at a time when the Government of Tanzania is becoming increasingly concerned about dealing with high levels of pollution from municipal solid waste (MSW). The paper employed the Driving force-Pressure-State-Impact-Response (DPSIR) model to establish an environmental risk indicator system and the analytical hierarchy process (AHP) to calculate and analyze risk values, based on the actual situation of MSW in the city of Dar es Salaam. It lists several measures that have been taken in response to the current significantly high levels of pollution, which have assisted in maintaining the environmental risk index (ERI) at a medium level (0.4–0.6) during the period from 2006–2017. However, these measures have not been adequate enough to manage the external pressure. The ERI has been increasing gradually, calling for timely formulation of demand-specific waste management policies to reduce the possibility of reaching the critical point in near future. With the use of the DPSIR model for ERA, this study has become highly valuable, providing empirical justification to reduce environmental risk from MSW, which is one of the main sources of environmental pollution in the urban areas of developing countries.
MicroRNA-124 Dysregulation is Associated With Retinal Inflammation and Photoreceptor Death in the Degenerating Retina.

Purpose We sought to determine the role and retinal cellular location of microRNA-124 (miR-124) in a neuroinflammatory model of retinal degeneration. Further, we explored the anti-inflammatory relationship of miR-124 with a predicted messenger RNA (mRNA) binding partner, chemokine (C-C motif) ligand 2 (Ccl2), which is crucially involved in inflammatory cell recruitment in the damaged retina. Methods Human AMD donor eyes and photo-oxidative damaged (PD) mice were labeled for miR-124 expression using in situ hybridization. PDGFRa-cre RFP mice were used for Müller cell isolation from whole retinas. MIO-M1 immortalized cells and rat primary Müller cells were used for in vitro analysis of miR-124 expression and its relationship with Ccl2. Therapeutic efficacy was tested with intravitreal administration of miR-124 mimic in mice, with electroretinography used to determine retinal function. IBA1 immunohistochemistry and photoreceptor row counts were used for assessment of inflammation and cell death. Results MiR-124 expression was correlated with progressive retinal damage, inflammation, and cell death in human AMD and PD mice. In addition, miR-124 expression was inversely correlated to Ccl2 expression in mice following PD. MiR-124 was localized to both neuronal-like photoreceptors and glial (Müller) cells in the retina, with a redistribution from neurons to glia occurring as a consequence of PD. Finally, intravitreal administration of miR-124 mimics decreased retinal inflammation and photoreceptor cell death, and improved retinal function. Conclusions This study has provided an understanding of the mechanism behind miR-124 in the degenerating retina and demonstrates the usefulness of miR-124 mimics for the modulation of retinal degenerations.
Visualization Taxonomy based on the Specification of User's Goal and Data Dimensions

In this paper we present a visual task taxonomy based on user goals derived via our extensive study, different data dimensions, and available visualization types. This taxonomy will be used in the creation of a visualization system that will assist users in the selection of more appropriate visualizations based on the speciﬁcation of the task they want to perform and the available data dimensions
Optical Coherence Tomography and Management of a Retinal Granuloma in Presumed Ocular Sarcoidosis

ABSTRACT Purpose: To highlight the utility of EDI-OCT and periocular steroid administration for the treatment of a retinal granuloma due to presumed ocular sarcoidosis. Methods: Retrospective case-study of a single patient. Results: A 45-year-old African-American male with blurred vision in the right eye was found to have a macula-involving retinal granuloma. Laboratory, imaging, and clinical findings were consistent with a diagnosis of presumed ocular sarcoidosis. Optical coherence tomography (OCT) and fundus photographs were used to document granuloma evolution. Oral prednisone 60mg was initiated and tapered to 10mg within 2 months. Due to systemic side-effects and inadequate treatment response with prednisone, 5 sub-Tenon’s triamcinolone acetonide (PSTA) injections were then administered over 7 months, and oral prednisone was discontinued at 6 months. Conclusion: This case demonstrated marked granuloma regression occurring with improvement in visual acuity, highlighting the utility of OCT and PSTA in managing retinal sarcoid granulomas.