Miracle-dz/UniFAR-FTUs huggingface dataset:
Sympathetic context of the disease - a new era in glaucoma management

Primary open angle glaucoma (POAG) is a multifactorial optic neuropathy, which progresses in a chronic manner. Several etiological factors are involved, including genetic factors, race, age, IOP or vascular, systemic factors. IOP has an established role in the initiation and evolution of glaucoma, but its interactions with additional risk factors are complex. We propose the notion of the Glaucoma Etiological Area (GEA), as a representation of all the elements acting in collaboration in the physiopathology of each glaucoma case. When combined in different proportions, these elements may trigger the typical glaucomatous optic neuropathy (GON). We know that the statistical values of IOP are valid for normal eyes, but the glaucoma eye is not a normal eye. The notion of GEA can open a new perspective to interpret IOP values and to assess the true value of IOP control as a treatment for glaucoma. Applying the GEA theory allows us to tune the role of IOP. Additional factors, such as ocular properties (RGCL status, CCT, IOP fluctuation curve), ocular comorbidities (PEX, PDS), systemic comorbidities (arterial hypertension, vasospastic diseases such as migraines or Reynaud’s syndrome) or patient’s attitude towards glaucoma management (treatment compliance, access to follow-up and treatment) may greatly influence the evolution of GON and should be viewed holistically when developing a management plan for each patient. Applying the notion of GEA in clinical practice allows a more realistic approach of the pathophysiology of the disease and for a glaucoma treatment that is tailored to each patient. Abbreviations: AG = advanced glaucoma, BP = blood pressure, CCT = central corneal thickness, CIGTS = Collaborative Initial Glaucoma Treatment Study, CNTGS = Collaborative Normal-Tension Glaucoma Study, EMGT = Early Manifest Glaucoma Trial, GEA = glaucoma etiological area, GON = glaucomatous optic neuropathy, IOP = intraocular pressure, NTG = Normal Tension Glaucoma, OHTS = Ocular Hypertension Study, PDS = Pigmentary dispersion syndrome, PEX = Pseudoexfoliation syndrome, POAG - primary open-angle glaucoma, RGCL = retinal ganglion cell layer, VFL = visual field loss
Researching gender inequalities in academic labor during the COVID‐19 pandemic: Avoiding common problems and asking different questions

Abstract As the COVID‐19 pandemic unfolds, a growing body of international literature is analyzing the effects of the pandemic on academic labor and, specifically, on gender inequalities in academia. In that literature, much attention has been devoted to comparing the unequal impacts of COVID‐19 on the research activities of women and men, with studies demonstrating that women's research productivity has been disproportionately disrupted, in ways that are likely to have detrimental effects in the short‐ and long‐term. In this paper, I discuss that emerging literature on gender inequalities in pandemic academic productivity. I reflect on the questions asked, the issues centered and the assumptions made within this literature, devoting particular attention to how authors conceptualize academic labor and productivity, on one hand, and gender, on the other. I show that this literature makes major contributions to exposing old and new gender inequalities in academia, but argue that it also risks reproducing some problematic assumptions about gender and about academic work. Discussing those assumptions and their effects, I identify some important questions for us to consider as we expand this literature and deepen our understanding of the complex gendered effects of COVID‐19 on academic labor.
The complete mitochondrial genome sequences of Japanese earthworms Metaphire hilgendorfi and Amynthas yunoshimensis (Clitellata: Megascolecidae)

Abstract Many studies have reported the complete mitochondrial genome sequences of Chinese Megascolecidae earthworms, however, there have been no reports on sequences originating from Japanese Megascolecidae earthworms. In this study, we determined complete mitochondrial genome sequences of two Japanese earthworms belonging to the Pheretima complex within the Megascolecidae family. Metaphire hilgendorfi is one of the most common earthworms in Japan and Amynthas yunoshimensis was found to be morphologically similar to M. hilgendorfi. The complete mitochondrial genomes of M. hilgendorfi (15,186 bp; LC573968) and A. yunoshimensis (15,109 bp; LC573969) contained typical 13 protein coding genes, 22 tRNA genes, and 2 rRNA genes. The phylogenetic analysis revealed that these two species were sister species. Therefore, our findings will further contribute to phylogenetic and genetic diversity analyses of Megascolecidae earthworms.
A generalized mechanism for superexchange

The concepts of bond orbitals and unrestricted Hartree-Fock orbitals are used in an attempt to explain the mechanism of superexchange between magnetic cations via an intermediate anion. The resulting theory predicts the same results as the standard theories when the cation-anion-cation angle is 180°. For other values of this angle, however, the nature and strength of the interaction depends on the distribution of bonds round the anion and is not solely a function of angle. The theory is applied to compounds having the corundum-ilmenite and spinel structures, where it correlates the magnetic structures and transition temperatures for a number of compounds and enables these properties to be predicted for others.
A density‐functional study of the intermolecular interactions of benzene

We have tested the performance of three frequently used density functionals (LDA, LDA+B, and LDA+B+LYP) in a study of the intermolecular interactions of benzene. Molecular geometries are satisfactory, with the gradient‐corrected density functionals yielding slightly better results. The quadrupole moment is significantly underestimated by all three functionals. LDA performs fortuitously comparatively well for both binding energies and geometries of the dimer and the solid, whereas in LDA+B, and LDA+B+LYP the dimer interaction is purely repulsive, leading to the complete absence of cohesion in the solid. These results are consistent with density‐functional theory calculations for noble gas dimers. However, when the dispersion energy calculated from a model potential is included, LDA fails. Binding energies are overestimated by unacceptable amounts, and intermolecular distances are too small. In contrast, dispersion corrected LDA+B and LDA+B+LYP perform reasonably well, although discrepancies are still large.
The ocular surface bacterial contamination and its management in the prophylaxis of post cataract surgery endophthalmitis

Objective: To investigate the recent pieces of evidence regarding the bacterial ocular surface contamination and its treatment in the prophylaxis of post-cataract surgery endophthalmitis. Methods: We conducted a literature research on the topic of interest and selected the most relevant data. Results: The studies reported a relatively high rate of positive conjunctival culture and the most frequently isolated organism was Coagulase negative Staphylococcus, which is also the most common etiological agent of the postoperative endophthalmitis. The bacterial ocular surface load is influenced by age, climate, associated diseases, topical and systemic medication. The use of povidone-iodine alone or in association with levofloxacin eyedrops as prophylactic method is effective in reducing the conjunctival bacterial contamination and consequently decreases the incidence of postoperative endophthalmitis. Conclusions: Based on the current pieces of evidence, adequate treatment of the bacterial ocular surface contamination prior to cataract surgery seems to be effective in preventing endophthalmitis after cataract surgery. Abbreviations: EU = European Union, Spp. = Species, HIV = Human Immunodeficiency Virus
Hyperglycemia and Correlated High Levels of Inflammation Have a Positive Relationship with the Severity of Coronavirus Disease 2019

Objective Coronavirus disease 2019 (COVID-19) is a considerable global public health threat. This study sought to investigate whether blood glucose (BG) levels or comorbid diabetes are associated with inflammatory status and disease severity in patients with COVID-19. Methods In this retrospective cohort study, the clinical and biochemical characteristics of COVID-19 patients with or without diabetes were compared. The relationship among severity of COVID-19, inflammatory status, and diabetes or hyperglycemia was analyzed. The severity of COVID-19 in all patients was determined according to the diagnostic and treatment guidelines issued by the Chinese National Health Committee (7th edition). Results Four hundred and sixty-one patients were enrolled in our study, and 71.58% of patients with diabetes and 13.03% of patients without diabetes had hyperglycemia. Compared with patients without diabetes (n = 366), patients with diabetes (n = 95) had a higher leucocyte count, neutrophil count, neutrophil to lymphocyte ratio (NLR), and erythrocyte sedimentation rate (ESR). There was no association between severity of COVID-19 and known diabetes adjusted for age, sex, body mass index (BMI), known hypertension, and coronary heart disease. The leucocyte count, NLR, and C-reactive protein (CRP) level increased with increasing BG level. Hyperglycemia was an independent predictor of critical (OR 4.00, 95% CI 1.72-9.30) or severe (OR 3.55, 95% CI 1.47-8.58) COVID-19, and of increased inflammatory levels (high leucocyte count (OR 4.26, 95% CI 1.65-10.97), NLR (OR 2.76, 95% CI 1.24-6.10), and CRP level (OR 2.49, 95% CI 1.19-5.23)), after adjustment for age, sex, BMI, severity of illness, and known diabetes. Conclusion Hyperglycemia was positively correlated with higher inflammation levels and more severe illness, and it is a risk factor for the increased severity of COVID-19. The initial measurement of plasma glucose levels after hospitalization may help identify a subset of patients who are predisposed to a worse clinical course.
Corneal Application of R9-SOCS1-KIR Peptide Alleviates Endotoxin-Induced Uveitis

Purpose Uveitis is an ocular inflammation that can affect individuals of all ages and is a major cause of blindness. We have tested the therapeutic efficacy of a cell penetrating peptide from the kinase inhibitory region of suppressor of cytokine signaling 1, denoted as R9-SOCS1-KIR. Methods We stimulated J774A.1 cells with lipopolysaccharide (LPS) in the presence of R9-SOCS1-KIR or its inactive control peptide. Effect on inflammatory pathways was followed by the nuclear translocation of nuclear factor κB p65 subunit and phosphorylated-p38. Synthesis of inflammatory markers induced by LPS was tested by reverse transcriptase polymerase chain reaction, Western blot analysis, and ELISA of cell supernatants. We monitored effects on the barrier properties of a differentiated ARPE-19 monolayer treated with LPS. We treated C57BL/6 mice topically with either R9-SOCS1-KIR or vehicle and injected their eyes intravitreally with LPS. Eyes were analyzed by fundoscopy, fluorescein angiography, optical coherence tomography, histology, Western blotting, multiplex enzyme-linked immunosorbent assay, and flow cytometry. Results Treatment with R9-SOCS1-KIR resulted in suppression of signaling through nuclear factor κB and p-p38 pathways. R9-SOCS1-KIR suppressed the expression of inflammatory genes, the secretion of inflammatory makers such as nitric oxide, and IL-1β induced by LPS. Increased permeability of retinal pigment epithelial cell monolayers was prevented. Corneal administration of R9-SOCS1-KIR blocked the acute inflammation observed in LPS-injected mouse eyes. Conclusions Treatment with R9-SOCS1-KIR alleviated the inflammatory responses in cell culture. Topical delivery of this peptide on mouse eyes protected against LPS-induced damage. Translational Relevance Topical delivery of R9-SOCS1-KIR peptide allows the patient to self-administer the drug, while preventing any systemic effects on unrelated organs.
The complete mitochondrial genome of Dicraeus orientalis Becker, 1911 (Diptera: Chloropidae)

Abstract Dicraeus orientalis feeds on the seeds of Poaceae. The complete mitochondrial genome of D. orientalis was sequenced and annotated as the first representative of the family Chloropidae. The full length of mitogenome was 16,188 bp, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). The nucleotide composition was highly A + T biased, accounting for 79.1% of the whole mitogenome. All PCGs start with ATN codons except COI, which end with TAN or incomplete stop codon. ML analysis revealed that Carnoidea was closely related to Ephydroidea and the phylogenetic relationship within Acalyptratae was Tephritoidea + ((Carnoidea + Ephydroidea) + Opomyzoidea).
Mitochondrial genome of Aphis gossypii Glover cucumber biotype (Hemiptera: Aphididae)

Abstract The complete mitochondrial genome of Aphis gossypii Glover cucumber biotype was sequenced using traditional PCR amplification coupled with Sanger sequencing. The genome is 15,870 bp long, with 83.7% AT content (MW048625). The genome encodes 37 typical mitochondrial genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, a repeat region of 784 bp, and a control region of 627 bp. The base composition of the genome is A (45.4%), T (38.3%), C (10.5%), and G (5.8%). An analysis of two biotypes A. gossypii mitogenomes identified 77 single nucleotide polymorphisms and 1 insertion and deletion.
Monocyte CD169 expression in COVID‐19 patients upon intensive care unit admission

During the second surge of COVID‐19 in France (fall 2020), we assessed the expression of monocyte CD169 (i.e., Siglec‐1, one of the numerous IFN‐stimulated genes) upon admission to intensive care units of 45 patients with RT‐PCR‐confirmed SARS‐CoV2 pulmonary infection. Overall, CD169 expression was strongly induced on circulating monocytes of COVID‐19 patients compared with healthy donors and patients with bacterial sepsis. Beyond its contribution at the emergency department, CD169 testing may be also helpful for patients' triage at the ICU to rapidly reinforce suspicion of COVID‐19 etiology in patients with acute respiratory failure awaiting for PCR results for definitive diagnosis.
The complete mitochondrial genome of Yuukianura szeptyckii Deharveng & Weiner 1984 (Collembola: Neanuridae)

Abstract The complete mitochondrial genome of Yuukianura szeptyckii Deharveng & Weiner 1984 was sequenced, assembled, and annotated. The mitochondrial genome of Y. szeptyckii has a length of 15,771 bp and contains 13 protein-coding genes (PCGs), 22 transfer (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. Y. szeptyckii was closely clustered with the following species of Neanuridae: Bilobella aurantiaca and Friesea grisea.
A phase 1 study of NY-ESO-1 vaccine + anti-CTLA4 antibody Ipilimumab (IPI) in patients with unresectable or metastatic melanoma

ABSTRACT Ipilimumab (IPI) can enhance immunity to the cancer-testis antigen NY-ESO-1. A clinical trial was designed to assess safety, immunogenicity, and clinical responses with IPI + NY-ESO-1 vaccines and effects on the tumor microenvironment (TME). Patients with measurable NY-ESO-1+ tumors were enrolled among three arms: A) IPI + NY-ESO-1 protein + poly-ICLC (pICLC) + incomplete Freund’s adjuvant (IFA); B) IPI + NY-ESO-1 overlapping long peptides (OLP) + pICLC + IFA; and C) IPI + NY-ESO-1 OLP + pICLC. Clinical responses were assessed by irRC. T cell and Ab responses were assessed by ex vivo IFN-gamma ELIspot and ELISA. Tumor biopsies pre- and post-treatment were evaluated for immune infiltrates. Eight patients were enrolled: 5, 2, and 1 in Arms A-C, respectively. There were no DLTs. Best clinical responses were SD (4) and PD (4). T-cell and antibody (Ab) responses to NY-ESO-1 were detected in 6 (75%) and 7 (88%) patients, respectively, and were associated with SD. The breadth of Ab responses was greater for patients with SD than PD (p = .036). For five patients evaluable in the TME, treatment was associated with increases in proliferating (Ki67+) CD8+ T cells and decreases in RORγt+ CD4+ T cells. T cell densities increased for those with SD. Detection of T cell responses to NY-ESO-1 ex vivo in most patients suggests that IPI may have enhanced those responses. Proliferating intratumoral CD8+ T cells increased after vaccination plus IPI suggesting favorable impact of IPI plus NY-ESO-1 vaccines on the TME. List of Abbreviations: Ab = antibody; CTCAE = NCI Common Terminology Criteria for Adverse Events; DHFR/DHRP = dihydrofolate reductase; DLT = Dose-limiting toxicity; ELISA = enzyme-linked immunosorbent assay; IFA = incomplete Freund’s adjuvant (Montanide ISA-51); IFNγ = Interferon gamma; IPI = Ipilimumab; irRC = immune-related response criteria; mIFH = multispectral immunofluorescence histology; OLP = NY-ESO-1 overlapping long peptides; PBMC = peripheral blood mononuclear cells; PD = Progressive disease; pICLC = poly-ICLC (Hiltonol), a TLR3/MDA-5 agonist; RLT = Regimen-limiting Toxicity; ROI = regions of interest; RT = room temperature; SAE = serious adverse event; SD = stable disease; TEAE = treatment-emergent adverse events; TLR = toll-like receptor; TME = tumor microenvironment; TRAE = treatment-related adverse events.
Loncomelos koprulense (Asparagaceae), a new species from southern Turkey

Abstract A new species, Loncomelos koprulense (Asparagaceae), is described and illustrated from southern Turkey. It is a very rare endemic species growing on small semi-rocky escarpments within the Köprülü Kanyon in the province of Antalya. Morphologically for its hairy leaves, L. koprulense shows some relationships with L. malatyanum and L. tardum, species localized in Anatolia too. The chromosome number of the new species is 2n = 2x = 22. Geographical distribution map for L. koprulense, L. malatyanum and L. tardum is provided.
Exons and introns exhibit transcriptional strand asymmetry of dinucleotide distribution, damage formation and DNA repair

Abstract Recent cancer sequencing efforts have uncovered asymmetry in DNA damage induced mutagenesis between the transcribed and non-transcribed strands of genes. Here, we investigate the major type of damage induced by ultraviolet (UV) radiation, the cyclobutane pyrimidine dimers (CPDs), which are formed primarily in TT dinucleotides. We reveal that a transcriptional asymmetry already exists at the level of TT dinucleotide frequency and therefore also in CPD damage formation. This asymmetry is conserved in vertebrates and invertebrates and is completely reversed between introns and exons. We show the asymmetry in introns is linked to the transcription process itself, and is also found in enhancer elements. In contrast, the asymmetry in exons is not correlated to transcription, and is associated with codon usage preferences. Reanalysis of nucleotide excision repair, normalizing repair to the underlying TT frequencies, we show repair of CPDs is more efficient in exons compared to introns, contributing to the maintenance and integrity of coding regions. Our results highlight the importance of considering the primary sequence of the DNA in determining DNA damage sensitivity and mutagenic potential.
Comparative Study Among Ketamine, Fentanyl, and Ropivacaine, as Pre-incisional Analgesic Given by Surgical Site Infiltration, in Cases Posted for Elective Lower Segment Cesarean Section Under General Anesthesia

Aim The aim of this study was to evaluate the effect of surgical site infiltration prior to giving incision, with ketamine, fentanyl, and ropivacaine, on perioperative hemodynamic parameters, pain, and any adverse outcomes. Methods The study was carried out on 68 patients divided into four groups of 17 each. After intubation, the study drug was infiltrated subcutaneously at the surgical site, seven min before incision, by the surgeon who was unaware of the injectate. Hemodynamic variables were monitored and recorded during the intraoperative period and postoperative period at one, two, four, six, eight, 12, and 24 hours. The level of sedation was assessed using the Ramsay sedation score (RSS). The fetal outcome was assessed by the APGAR (Appearance, Pulse, Grimace, Activity, and Respiration) score at one, five, and 10 minutes. Results The mean visual analog scale (VAS) scores were significantly (p < 0.05) lower in group A as compared to other groups for most of the postoperative period. Hemodynamic stability was also significantly better with group A as compared to other groups during the perioperative period. The fetal outcome was comparable between the study groups with the APGAR scores similar between the groups at 10 min. However, significantly lower APGAR values were seen in group C as compared to the other study groups, at one and five minutes. Conclusion Ketamine infiltration resulted in a better hemodynamic profile, a significantly longer duration of the postoperative pain-free interval, and more sedation in the postoperative anesthesia care unit (PACU). It did not affect the fetal wellbeing, as discernable from the APGAR scores.
Efficacy of Anti-inflammatory Treatment Versus Rescue Analgesia After Arthroscopic Partial Meniscectomy in Nonarthritic Knees: A 3-Arm Controlled Study

Background: There is currently no consensus regarding the appropriate treatment for postoperative pain after arthroscopic partial meniscectomy (APM). Prescribing a mild non–anti-inflammatory protocol of rescue analgesia may be sufficient to avoid the side effects of opioids or anti-inflammatories. Purpose/Hypothesis: The purpose was to compare the efficacy of pain reduction after APM in nonarthritic knees using betamethasone or celecoxib as anti-inflammatory analgesics versus acetaminophen or tramadol as rescue analgesics. The hypothesis was that there is no advantage for anti-inflammatories in achieving postoperative immediate pain relief after APM in nonarthritic knees compared with a simple nonopioid treatment. Study Design: Cohort study; Level of evidence, 2. Methods: This 3-arm controlled study evaluated postoperative pain levels and analgesic consumption in patients who underwent primary APM (under general anesthesia) at a single institution from December 2018 to December 2019. Patients were prospectively divided into 3 treatment groups: (1) betamethasone injection at the end of the procedure, (2) oral celecoxib prescription, or (3) neither treatment (control). All groups were instructed to take supplementary acetaminophen as needed. Patients were also allowed to take tramadol as needed to evaluate the need for opioids. At postoperative weeks 1, 2, and 3, patients completed the Knee injury and Osteoarthritis Outcome Score (KOOS) Pain subscale, and results were compared between time points and groups. Results: A total of 99 patients were included in the treatment groups: betamethasone group (32 patients), celecoxib group (30 patients), and control group (37 patients). At baseline, there were no statistically significant differences between the groups in age, sex, body mass index, level of activity, comorbidities, or surgical findings. KOOS Pain scores improved at every time point for all 3 groups (P < .001), and no differences in scores were observed among groups. The consumption of acetaminophen or tramadol as rescue analgesia throughout the follow-up period was negligible among groups. Conclusion: During the first 3 postoperative weeks after APM in nonarthritic knees, pain was efficiently controlled by betamethasone or celecoxib; however, pain was also efficiently controlled by minimal consumption of acetaminophen with negligible use of tramadol. Therefore, acetaminophen could be prescribed as an effective first-line postoperative analgesic after APM.