bluuebunny/crossref_metadata_2025 huggingface dataset:
Glaucon’S Challenge and Thrasymacheanism
Authors: Reeve C D C
Published: November 2023

Plato‘s brothers, Glaucon and Adeimantus, spend roughly ten Stephanus pages—which, even in a long dialogue like the Republic , is a lot—trying to tell Socrates what they want him to do as regards justice. It has proved extremely difficult, none the less, to say what their message—’Glaucon’s challenge’ as it is often called—actually is and to identify its provenance. In this paper I take up matters afresh, looking away from the text to the secondary literature only very selectively. In Section I I go through what Glaucon and Adeimantus say, distinguishing four different, but I think consistent and mutually illuminating, formulations of the challenge they pose. In Section 2 I look more specifically at what they think is wrong with common conceptions and defences of justice. In Section 3 I examine the relationship between their views and those of Thrasymachus. In Sections 4 and 5 I consider Thrasymachus’ own account of justice and assess its coherence. In Section 6 I turn to the larger question of the philosophical significance of Thrasy -macheanism and the difficulty of responding successfully to it.
Alteration and Aristotle’s Theory of Change in Physics 6
Authors: Murphy Damian
Published: November 2023

In Physics 5 and 6 Aristotle outlines a theory of change. A key feature of this account is the claim that every change is infinitely temporally divisible into subchanges. So, for example, suppose a billiard ball moves from one end of the table to the other in a period of time. After part of the time it will have moved part of the way down the table, and for each smaller part of the time it will have travelled a smaller portion of the length of the table. Aristotle explicitly claims that this theory applies to all types of change and not merely to change of place (and change of size). Many modern critics believe that this is not Aristotle’s considered opinion.1 They claim that for Aristotle changes of quality are often not infinitely temporally divisible into subchanges because there are only, for example, finitely many shades of colour. My aim in this paper is to show that Aristotle thought that all alterations (changes in quality) were infinitely temporally divisible. In practice I shall follow Aristotle in focusing on changes of colour.
Automatic Action in Plotinus
Authors: Wilberding James
Published: November 2023

Several Plotinus scholars have recently called attention to a kind of action in the sensible world, which one could call ‘spontaneous’ or ‘automatic’ action, that is supposed to result automatically from the contemplation of the intelligible. Such action is meant to be opposed to actions that result from reason, calculation, and planning, and has been put to work to provide a way for Plotinus’ sage to act, and in particular to act morally , without compromising his contemplation. This opposition is found most markedly when he compares the non-deliberative manner in which the World-Soul(as well as Nature and the heavenly bodies) acts with the deliberative manner in which we normally act. ‘Automatic action’ is thus a term I am using to describe this kind of spontaneous and non deliberative action. A theory of automatic action can easily close the gap between the contemplative man and the practical man by allowing for action without deliberation. This is helpful because it is the deliberative element in action that would seem to be incompatible with contemplation. Deliberating about the world—anddeliberation is always about the world, since it is about what can be otherwise—forces one’s rational soul to look away from the intelligible.
Origin and maintenance of clausal embedding complexity
Authors: Karlsson Fred
Published: November 2023

There are many well-known parameters of grammatical complexity: number of terms (e.g. cases or genders) in a grammatical subsystem; more or less intricate elaboration of phrases by premodification and postmodification; restricted versus repeatable nominalization processes; number of affixes in word forms; simplex versus iterative compound formation; number and depth of embedding of clauses in sentences, etc.
Introduction
Authors: Green Ronald M , Aine Donovan , Jauss Steven A
Published: November 2023

In September 1960 Dartmouth College and Dartmouth Medical School hosted a landmark conference on ‘‘Great Issues of Conscience in Modern Medicine.’’ That conference helped set the agenda for the emergence of the modern field of bioethics. As Albert R. Jonson records in The Birth of Bioethics, the conference ‘‘was an impressive occasion: men of science, joined by a few humanists, reflected in public about the troubling issues they saw hidden within the wonderful inventions of modern science.
What is it Like to Be a Bird? Wikler and Brock on the Ethics of Population Health
Authors: Eya∗ Nir
Published: November 2023

Suppose that I were a bird: a very special bird, who takes an interest in the ethics of healthcare, and who can see through the walls of healthcare clinics. I could peek at anearby clinic, perhaps in the Dartmouth Medical School (near which this conference is taking place), and watch, through the wall, health- care providers treating a single patient. I could raise ethical questions about what I see.
‘Philosophy states only what everyone admits’
Authors: Kenny Anthony
Published: November 2023

In philosophy we do not draw conclusions. ‘But it must be like this! ‘ is not a philosophical proposition. Philosophy only states what everyone admits. This is one of Wittgenstein ‘s most important statements about the nature of philosophy. Commentators seem reluctant to take it at its face value. Peter Hacker comments on the first sentence: ‘It does not mean that there are no arguments in philosophy, or that no definitive conclusions can be drawn from them, e.g. that solipsism and idealism are incoherent, or that a private language is unintelligible. ‘¹ Garth Hallett comments on the third sentence: ‘[T]o appear plausible this too must be recognized as prescriptive, not descriptive. The trouble is that even the concluding words may have to be read ‘ ‘which everyone ought to admit ‘ ‘. ‘²
Empedocles and His Ancientreaders on Desire and Pleasure
Authors: Wolfsdorf David
Published: November 2023

A: What are Plato, Speusippus, and Menedemus up to?… What weighty thought, what line of argument are they now investigating? …B: I can tell you about these fellows for sure, since at the Panathenaea I saw a group of youngsters in the exercise-grounds of the Academy and heard them speaking, indescribable, astonishing! They were propounding definitions about nature and separating into categories the forms of life of animals, the nature of trees, and the classes of vegetables. And in particular, they were investigating to what genus one should assign the pumpkin…One of the boys said it was a round vegetable; another that it was a grass; another that it was a tree.
Aristotle on Speusippus on Eudoxus on Pleasure
Authors: Warren James
Published: November 2023

Aristotle’s account in the Nicomachean Ethics of the role of pleasure in the good life and the effsects of pleasure on both character development and action is complex and difficult. Part of this difficulty is generated by Aristotle’s characteristic dialectical approach to the questions he is interested in asking. He raises possibilities, gathers alternative views, and suggests counter-arguments without always making immediately clear his own precise view. By working on the topic of pleasure in this way, Aristotle makes it clear that he is reacting to and offering his own commentary on an earlier debate on the nature and value of pleasure, with its own series of dialectical moves and counter-moves. In Aristotle’s presentation of the matter in the Nicomachean Ethics, three major philosophical rivals are invoked as participants in the debate: Eudoxus, Speusippus, and Plato.
Who gets lung cancer?
Authors: Falk Stephen , Williams Chris
Published: November 2023

At least 90% of lung cancers are related to smoking. Historically some occupations and chemicals increase the risk. Why exactly some smokers get cancer whereas others do not is unknown. Lung cancer affects over 3000 non-smokers a year in the UK.
Clinical trials
Authors: Falk Stephen , Williams Chris
Published: November 2023

Trials are necessary to show that new approaches in medicine are safe and benefit patients. Clinical trials exist because progress in medicine is slow. Many of our current treatments are only in practice because patients took part in trials. Taking part in trials offers patients access to the most up-to-date care and treatments.
Magna Moralia 1187a29–b–20 : The Early Reception of Aristotle’s Notion of Voluntary Action
Authors: Eliasson Erik
Published: November 2023

While traditionally included in the Aristotelian corpus, the Magna Moralia is generally regarded (for linguistic reasons, among others) as not written by Aristotle. Rather, it is thought to be a writing of one of his di ect disciples, or ‘a post-Aristotelian epitome’.

As the Magna Moralia clearly attempts to cover approximately the same ground as the Nicomachean and Eudemian Ethics, it is natural to analyse the extent to which the Magna Moralia develops Aristotle’s accounts. I shall analyse one such aspect in detail, namely the argument at MM 1187a29b20, within the account of how virtue and vice are voluntary and depend on us.This argument has not been given the attention it deserves in previous scholarship.
Simplicius on the Reality of Relations and Relational Change
Authors: Harari Orna
Published: November 2023

The ancient commentators’ approach to Aristotle’s account of relatives in Categories 7 is shaped by the conception that prevailed in later antiquity, in which relatives are composites of a substrate, i.e. an attribute that belongs to the other categories, and a relation. Simplicius shares this conception with the other commentators, but he formulates it in different terms.
Synthesis and purification of RNA substrates
Authors: Chabot Benoit
Published: November 2023

In recent years, the purification of RNA molecules from different organisms and cell types has been crucial to the analysis of gene expression and RNA processing events. Likewise, the rapid development of in vitro RNA maturation systems has relied extensively on the ability to synthesize and purify RNA substrates. Generating pure, undegraded RNA is thus critical to in vivo and in vitro analyses of RNA processing. For the most part, procedures used to obtain intact and pure RNA are relatively simple and have been described in detail in a variety of publications and technical books. This chapter does not attempt to provide a comprehensive coverage of all these procedures. Instead, it describes a few of the most rapid, convenient, and economical ways to prepare RNA for direct analysis or for use as substrates in in vitro systems of RNA processing. Researchers who work with RNA are always very much concerned about RNase contamination and thus take great pains to establish an RNase-free microenvironment. However, in most cases problems with RNase contamination can be avoided by taking the following simple precautions:
Overview of the steroid receptor superfamily of gene regulatory proteins
Authors: O’Malley Bert W , Tsai Ming-Jer
Published: November 2023

Over the past two decades, a great deal of evidence has accumulated in favour of the hypothesis that steroid hormones act at the level of nuclear DNA to regulate gene expression (1-4). The earliest studies were qualitative and involved experiments which showed that steroid hormones caused: (1) accumulation of new species of hybridizable RNAs that did not exist before stimulation; (2) stimulation of synthesis of new specific proteins; (3) a corresponding increase in the cellular levels of specific messenger RNAs (mRNAs); and (4) stimulation of the rate of transcription of select endogenous nuclear genes (5). At this point, the early 1970s, the primary pathway for steroid hormone action was defined as follows: steroid→ (steroid-receptor) → (steroid-receptor-DNA) → mRNA → protein → functional response (6). Steroid was thought to enter cells by passive diffusion and to activate receptors in either the cytoplasm or nucleus. The activated receptor was predicted to bind at the regulatory region of target genes and to stimulate transcription, and subsequently protein synthesis. Although initially controversial, this pathway has been generally accepted for the past 15 years (5-13).
In Vitro Sv40 Dna Replication
Authors: Kenny Mark K
Published: November 2023

Simian virus 40 (SV40) has served as an excellent model for various cellular processes including transformation, transcription, RNA processing, and DNA replication (1). Replication of the genome of this small DNA tumour virus very closely resembles the replication of cellular DNA. SV40 has a 5 kb circular duplex genome which exists in a chromatin structure indistinguishable from that of the cell. Replication initiates at a single 64 bp core origin of replication and proceeds bidirectionally in a semi-conservative manner. SV40 uses only a single viral protein for its replication, the large T antigen, albeit it serves several functions. All of the other replication proteins are provided by the host cell. There is a species specificity to SV40 DNA replication. It will replicate in primate cells but not in rodent cells.
Purification and assay of PLC-δ
Authors: Homma Yoshimi , Emori Yasufumi
Published: November 2023

In contrast to what is known about the PLC-β and PLC-γ subfamilies, the activation mechanism of PLC-δ remains unclear. Neither receptors nor transducers that couple to PLC-δ members have been identified. The PLC-δ subfamily contains so far four members: PLC-δ1, -δ2, -δ3, and -δ4. PLC-δ1 and PLC-δ2 can be purified from either rat or bovine brains (4—7). PLC-δ3 is known only at the cDNA level (8). PLC-δ4 cDNA and protein have been reported very recently (9). Structural analyses demonstrate that the molecular structure of PLC-δ contains three characteristic regions: the X and Y regions, which both show sequence similarity to the other PLC isoforms and are essential for enzymatic activity; a region which contains two EF hand-like motifs; and the pleckstrin homology (PH) region (Figure 1).
Analysis ofRNA:protein and RNA:RNA contacts between ribosomes and functional ligands using site-directed cross-linking techniques
Authors: Rinke-Appel Jutta , Brimacombe Richard
Published: November 2023

Cross-linking methods have been widely applied for the investigation of contacts or neighbourhoods of the individual components of a variety of biological systems. The ribosome is particularly well-suited to this type of approach; while on the one hand the ribosomal particles are too large and complex to allow a structural determination by X-ray crystallographic techniques, on the other hand it is this very complexity which makes the ribosome-with its numerous different components and functional ligands-an ideal substrate for cross-linking studies.
Cloning transcription factors by sequence similarity
Authors: Ashworth Alan
Published: November 2023

Knowledge of the primary structure of different classes of transcription factors has revealed the modular nature of these proteins. Functional domains, such as DNA binding motifs, are often highly conserved between different transcription factors. The sequence conservation of these domains can be taken advantage of to isolate clones related to a particular transcription factor. In some cases, these gene families may have more than 500 members (1).
Identification of target genes for a transcription factor by genomic binding-site cloning
Authors: Inoue Satoshi , Kondo, Shigeru , Muramatsu Masami
Published: November 2023

Whereas a great number of genes or cDNAs are isolated by molecular cloning, relatively few genes are known with respect to their function. In order to gain more insight into the life processes of higher eukaryotes, including humans, a greater understanding of gene function is of prime importance.
Analysis of cloned factors
Authors: White Roger , Parker Malcolm
Published: November 2023

The analysis of a cloned transcription factor and the characterization of its functional properties is carried out primarily by the identification and map ping of domains within the protein using deletion and point mutagenesis. This is accomplished by expression of either the factor itself, or altered forms of the protein, in vitro and in vivo in different cell types. The aim of this chapter is to describe some of the approaches and methods used in this analysis. Methods will also be described by which the cloned factor itself, or fragments of the factor, may be overexpressed with the aim of producing large amounts of the protein for biochemical and structural studies. Finally a number of assay systems will be described which may be used to measure the transcriptional activity of the cloned factor and its ability to interact with different components of the cell, in particular other proteins and DNA.
Surface plasmon resonance
Authors: Van Der Merwe P Anton
Published: November 2023

Since the development almost a decade ago (1, 2) of the first biosensor based on surface plasmon resonance (SPR), the use of this technique has increased steadily. Although there are several SPR-based systems (3-5), by far the most widely used one is the BlAcore (1, 2), produced by BlAcore AB, which has developed into a range of instruments (Table 1). By December 1998 over 1200 publications had reported results obtained using the BlAcore. It is likely that it would be even more widely used were it not for its high cost and the pitfalls associated with obtaining accurate quantitative data (5-8). The latter has discouraged many investigators and led to the perception that the technique may be flawed. This is unjustified because the pitfalls are common to many binding techniques and, once understood, they are easily avoided (4, 8, 9). Furthermore, the BlAcore offers particular advantages for analysing weak macromolecular interactions, allowing measurements that are not possible using any other technique (4, 10). This chapter aims to provide guidance to users of SPR, with an emphasis on avoiding pitfalls. No attempt is made to describe the routine operation and maintenance of the BlAcore, as this is comprehensively described in the BlAcore instrument manual (see Section 9.3). Although written for BlAcore users, the general principles will be applicable to experiments on any SPR instrument.
Introduction to macromolecular visualization
Authors: Martz Eric , Driscoll Timothy
Published: November 2023

The ability to view a macromolecule in three dimensions is a great asset to science students and researchers alike. A decade ago, the primary method for examining 3D molecular structures was stereoscopic viewing, which often required training or special glasses. Now a number of excellent computer tools, many of them free, are available for rendering molecular structures in 3D, interacting with them, and customizing their appearance. Some are stand-alone programs like WebLab ViewerPro and DeepView Swiss-Pdb Viewer. Others are browser plug-ins like Chime. Still others, like Protein Explorer, a browser-based package using the Chime plug-in, can work entirely over the Web. This Chapter explains which of these programs to use for your particular objectives. However, the scope of this Chapter is limited-it does not cover some other freeware visualization packages with very strong features, including Cn3D, DINO, MAGE, PyMOL, and VMD (find links in the World Index, see the WebLinks box below).
Invasive Hemodynamic and Vasoreactivity Testing with Inhaled Iloprost in Children with Pulmonary Arterial Hypertension Associated with Congenital Heart Defects
Authors: Li Qiangqiang , He Yuan , Zhang Chen , Gu Hong
Published: November 2023

Objective:

Invasive hemodynamic evaluation and acute vasoreactivity testing are recommended in the diagnosis of pulmonary arterial hypertension (PAH), but their clinical role in children with PAH associated with congenital heart defects (CHD) is unclear. This study aims to investigate acute hemodynamic responses to inhaled iloprost, and its role in prognosis in children with PAH-CHD.

Methods:

A retrospective analysis was conducted on 83 pediatric patients with PAH-CHD in whom invasive hemodynamics were evaluated before and after a single inhaled dose of iloprost at a single center between 2010 and 2022. Details of the CHD corrective operation, medical treatment, and outcome for each patient were obtained via medical records or telephone contact. A composite endpoint of all-cause death, admission for worsening heart failure during follow-up, and event-free survival was defined, and risk factors associated with this composite endpoint were analyzed.

Results:

The patient age was (11.3 ± 4.6) years, and 60 (72.3%) were female. Fifty-nine (71.1%) patients were diagnosed with Eisenmenger syndrome. After iloprost inhalation, mean pulmonary artery pressure decreased from (78.2 ± 11.5) to (72.3 ± 13.2) mmHg (P < 0.001), and pulmonary vascular resistance index (PVRI) decreased from (18.0 ± 7.9) to (14.5 ± 8.1) WU·m2 (P < 0.001). A total of 38 (45.8%) patients had a positive response, defined as a PVRI decrease >25% with stable systemic pressure. Thirty-seven (44.6%) patients underwent a corrective CHD operation at a median of 24 d after hemodynamic evaluation. Nine patients died, and 15 met the composite endpoint during a follow-up period of 5.4 (3.8, 8.8) years. Five-year event-free survival estimates were 96.7% (95% confidence interval: 90.3%–100%) in patients with a positive response, and 82.8% (95% confidence interval: 71.7%–94.5%) in patients with a non-positive response (log-rank P = 0.012). A positive PVRI response and higher pulmonary arterial oxygen saturation after iloprost inhalation, lower baseline brain natriuretic peptide, and PAH-targeted therapy at follow-up were significantly associated with a favorable clinical outcome. A positive acute vasoreactivity testing response and PAH-targeted therapy at follow-up were independent predictors of outcome in multivariate Cox analysis.

Conclusions:

Acute inhalation of iloprost can lead to a significant decrease in hemodynamic parameters. Responsiveness to inhaled iloprost is associated with better outcomes and can be a valuable predictor of outcomes.
Treatment of Internal Mammary Nodes is Associated With Improved Overall Survival in Breast Cancer
Authors: Shaikh Parvez Memet , Mulherkar Ria , Khasawneh Mohammad T. , Clump David , Hazard-Jenkins Hannah , Hafez Maria , Vargo John A.
Published: November 2023

Introduction:

The role of internal mammary nodal irradiation (IMNI) as a component of regional nodal radiotherapy is a controversial issue in breast radiation oncology with conflicting results presented in recent landmark trials. We thus created a meta-analysis of available data to better ascertain the potential benefit of IMNI. We hypothesize that with the increased power available within a meta-analysis, IMNI will prove to improve overall survival (OS) in breast cancer.

Methods:

Literature search was conducted for prospective studies comparing IMNI to no IMNI. Primary endpoint was OS and secondary endpoints included local recurrence, regional recurrence, disease-free survival (DFS), breast cancer mortality (BCM), distant metastasis-free survival (DMFS), grade 2+ skin toxicity, cardiac events, and pneumonitis events. Subgroup analyses were performed for tumor location (medial/central vs. lateral), and nodal status (pN+ vs. pN0). Fixed-effect model was used if there was no heterogeneity, random-effects model otherwise.

Results:

Four studies with a total of 5258 patients (IMNI: n=2592; control: n=2666) were included in the study. Pooled results showed IMNI significantly improved OS for all-comers (hazard ratio [HR]=0.89; 95% CI 0.81-0.97; P=0.008), as well as subgroups of pN+ with medial/central tumor location (HR=0.84; 95% CI 0.73-0.96; P=0.01) and pN+ with lateral tumor location (HR=0.87; 95% CI 0.77-0.99; P=0.04). There was no significant difference in OS for subgroups of pN0 and medial/central tumor location. There was no difference in local recurrence, but regional recurrence was significantly improved (P=0.04). Endpoints of DFS (HR 0.91, 95% CI 0.84-0.99 P=0.03), BCM (HR 0.87, 95% CI 0.77-0.98, P=0.03), and DMFS (HR=0.87; 95% CI, 0.78-0.98; P=0.02) were all improved with IMNI. Grade 2+ skin toxicity, cardiac events and pneumonitis events were not significantly different between patient in the IMNI and no IMNI groups.

Conclusion:

Inclusion of IMN irradiation improves OS, DFS, BCM, and DMFS in breast cancer. Largest effect on OS was noted in the subgroup of patients with pN+ and medial/central tumor location.
Sex-Specific Differences in Clinical Outcomes in Patients With Coronary Bifurcation Lesions
Authors: Hosseinpour Alireza , Attar Armin , Agrawal Ankit , Malik Aaqib H. , Sood Akshit , Patel Nainesh C. , Aronow Wilbert S. , Frishman William H. , Gupta Rahul
Published: November 2023

Coronary bifurcation lesions are frequent challenging findings during percutaneous coronary intervention (PCI). Contemporary evidence has explored the potential sex-specific differences in patients undergoing PCI. In the present meta-analysis, we compared clinical outcomes of patients undergoing bifurcation PCI between women and men. Using the random-effects method, we compared the clinical outcomes of patients with a coronary bifurcation lesion following PCI between women and men. The results were reported using relative risk (RR) and 95% confidence interval (CI). Baseline comorbidities and mean age were compared between the 2 studied groups. Four observational studies comprising 30,684 patients (8898 women and 21,786 men) were included in the meta-analysis. Women were significantly older than men with a relatively higher prevalence of baseline comorbidities. After using adjusted data from 2 out of 4 available studies, performing PCI for bifurcation lesions in women was not associated with an increased risk of mortality (RR 1.33, 95% CI, 0.78–2.29), myocardial infarction (RR 1.22, 95% CI, 0.41–3.61), target lesion revascularization (RR 1.06, 95% CI, 0.40–2.81), stent thrombosis (RR 0.99, 95% CI, 0.09–10.52), and stroke (RR 1.19, 95% CI, 0.64–2.22). Women were at higher risk of major bleeding compared to male counterparts (RR 2.23, 95% CI, 1.73–2.89). The present study showed no difference in the risk of adverse clinical outcomes except the risk of bleeding between genders with coronary bifurcation lesions. Future studies with adjustment of age and baseline comorbidities are needed to confirm these findings.
Requirements for the successful set-up of an international, multicentre, multilanguage, noninterventional patient-reported outcomes pain study
Authors: Weinmann Claudia , Komann Marcus , Liedgens Hiltrud , Pogatzki-Zahn Esther M. , Fletcher Dominique , Meissner Winfried
Published: November 2023

BACKGROUND

For setting up and implementing an international follow-up survey study in different countries, many prerequisites are necessary: obtaining permission or licenses to use the tools/questionnaires selected, translating the questionnaires according to a standardised translation process, implementing the survey technically, recruiting, training and monitoring the data collecting study sites, obtaining ethics approvals and data protection clearance, developing the study and training materials, and registering the study.

OBJECTIVE

Within the IMI-PainCare project (Improving the care of patients suffering from acute or chronic pain), we needed to conduct a large noninterventional patient survey – PROMPT NIT-1 – aiming to find out which PROMs (patient-reported outcome measures) work best for postoperative pain assessment. Planning and implementing this international multicentre, multilanguage, follow-up study was complex and time consuming. Consequently, experiences from its successful implementation may help future study coordinators.

DESIGN

The NIT-1 surveys consisted of several established tools. We planned to include 4000 patients, and to collect data at seven time points: baseline, postoperative days (POD) 1, 3 and 7 and follow-up on postoperative months (POM) 1, 3 and 6.

SETTING

Eighteen hospitals, mostly primary care, across Europe collected data for our study. First patient in was in August 2019, last patient out in June 2022.

PATIENTS

Adult patients of both sexes who had undergone one of four defined surgical procedures answered our surveys; total knee arthroplasty (TKA), breast surgery, endometriosis surgery and sternotomy.

MAIN OUTCOMES

Results from the study related to the primary and secondary outcomes are not part of this publication and will be presented separately. This publication describes only the technical, administrative and coordinating implementation.

RESULTS

Although the COVID-19 pandemic affected patient inclusion, and some preparations took longer than foreseen, 18 hospitals across Europe included 3303 patients. We were able to attain sufficient case numbers, and follow-up rates were very good.

CONCLUSION

The setting up and implementation of a large, international, multilanguage data collection is challenging and ambitious but feasible if it is well planned, if sufficient resources (project management and technical/IT expertise, qualified staff, funding, commitment) are available and if the timeframe for preparing the study is generously calculated.

TRIAL REGISTRATION

clinicaltrials.gov (ID NCT03834922).
Small-aperture intraocular lens implantation in a patient with cataract and keratoconus
Authors: Ezzeldin Mona , Steinberg Johannes , Frings Andreas , Linke Stephan
Published: November 2023

A case of small-aperture intraocular lens (IOL) implantation in a patient with nuclear cataract and keratoconus is presented. The patient had femtosecond laser–assisted cataract surgery (FLACS) with implantation of a small-aperture lens into the right eye. Two weeks later, the left eye had FLACS with implantation of an aspheric lens inducing zero spherical aberrations. A small aperture IOL was implanted in the right eye due to the irregular cornea and an aspheric nontoric, monofocal IOL with an asphericity of zero was implanted in the left eye.
Bilateral transient myopia induced by oral acetazolamide in the early postoperative period after phacoemulsification
Authors: Kalina Paul H. , Kalina Andrew G.
Published: November 2023

A 62-year-old man with bilateral pseudophakia experienced transient myopia and diminished distant vision after administration of oral acetazolamide following his second cataract surgery. Neither eye demonstrated elevated intraocular pressure, closed angles, or choroidal detachments. The idiosyncratic myopic shift resolved within a few days without intervention and vision improved. This unique presentation and its role in understanding the mechanism of action underlying acetazolamide-induced myopia were examined.
Three-Dimensional Navigation-Assisted Open Reduction and Internal Fixation of a Subcondylar and Ramus Fracture on a Maxillary Oligodontia Patient
Authors: NG Kwan-Lok B. , Liu Tsung-Hsien , Lee Su-Shin
Published: November 2023

Treatment of condylar fractures in patients with edentulous mandibles or no-occlusion reference is particularly challenging due to the absence of important anatomical structures and landmark for occlusion analysis. In this case, a 69-year-old female maxillary oligodontia victim suffered from a traumatic accident with a right facial contusion, resulting in a right-side subcondylar and mandibular ramus fracture with right ramus height loss. In the preoperative planning, the 3-dimensionalimage of the left-side mandible was highlighted by the navigation software. A mirror image of the left-side mandible was made and superimposed on the right side of the face. Surgical intervention with an endoscope and 3-dimensional navigation-assisted open reduction and internal fixation of the right-side subcondylar and ramus fracture was performed. The patient recovered well with no restriction in mandibular movement, no limitation in mouth opening, and a satisfied esthetic outcome.
Marixanthotalea marina gen. nov., sp. nov., a bacterium in the family Flavobacteriaceae isolated from seawater
Authors: Fu Zi-Yue , Xue Hua-Peng , He Wei , Ma Guang-Yuan , Zhang Ai Hua , Zhang Dao-Feng , Li Wen-Jun
Published: November 2023

A Gram-stain-negative, yellow-pigmented, non-motile, rod-shaped, catalase-positive, strictly aerobic marine bacterium, designated XHP0103T, was isolated from seawater collected from the southern Yellow Sea, PR China (34° 45′ 53″ N 119° 25′ 30″ E). Strain XHP0103T grew optimally at 28 °C, pH 7.5 and in 1.0–3.0 % (w/v) sea salt. MK-6 was the major respiratory quinone. The major cellular fatty acids (>10%) were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The polar lipid profile contained phosphatidylethanolamine, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. Results of 16S rRNA gene sequence analysis indicated that strain XHP0103T displayed highest sequence similarity to

Aestuariibaculum marinum

IP7T (94.1 %). However, the phylogenetic trees based on 16S rRNA gene sequences suggested that strain XHP0103T clustered with

Tamlana crocina

HST1-43T (93.4 % sequence similarity) and

Aestuariivivens insulae

AH-MY3T (93.5 %). Genome sequencing revealed that strain XHP0103T comprised 3 134 388 bp with 2770 protein-coding genes, and the DNA G+C content was 35.5 %. The average nucleotide identity and digital DNA–DNA hybridization values between strain XHP0103T and

T. crocina

HST1-43T were 73.6 and 17.3 %, respectively. Based on phylogenetic, phenotypic, genomic and chemotaxonomic evidence, strain XHP0103T represents a novel genus in the family

Flavobacteriaceae

, for which the name Marixanthotalea marina gen. nov., sp. nov. is proposed. The type strain is XHP0103T (=MCCC 1K06060T=JCM 34682T).
Taxonomic descriptions of Aeromicrobium duanguangcaii sp. nov., Aeromicrobium wangtongii sp. nov. and Aeromicrobium senzhongii sp. nov.
Authors: Ye Lin , Zhang Gui , Yang Jing , Yang Caixin , Liu Yue , Pu Ji , Huang Yuyuan , Zhang Sihui , Jin Dong , Lu Shan , Liu Liyun , Xu Jianguo
Published: November 2023

Six Gram-stain-positive, facultative anaerobic, nonmotile and rod-shaped strains, designated zg-Y50T, zg-Y1362, zg-Y1379T, zg-Y869, zg-629T and zg-Y636, were isolated from the intestinal contents of Marmota himalayana in Qinghai Province, PR China. Strains zg-Y50T, zg-Y1379T and zg-629T exhibited the highest 16S rRNA gene sequence similarities of 99.2, 98.9 and 98.8 % to

Aeromicrobium choanae

9 H-4T,

Aeromicrobium ginsengisoli

JCM 14732T and

Aeromicrobium flavum

TYLN1T, respectively. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene and genomic sequences, respectively, revealed that the six strains formed three distinct clades within the genus

Aeromicrobium

. The genome sizes of strains zg-Y50T, zg-Y1379T and zg-629T were 3.1–3.7 Mb, with DNA G+C contents of 69.6–70.4 mol%. Average nucleotide identity and digital DNA–DNA hybridization values between each novel strain and available members of the genus

Aeromicrobium

were all below species thresholds. All novel strains contained MK-9 (H4) as the major menaquinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the polar lipids. The predominant fatty acid of the six isolates was C18 : 1
 ω9c. The cell-wall peptidoglycan contained ʟʟ-diaminopimelic acid as the diagnostic diamino acid. Based on the results from this polyphasic taxonomic study, three novel species in the genus

Aeromicrobium

are proposed, namely, Aeromicrobium duanguangcaii sp. nov. (zg-Y50T=GDMCC 1.2981T=KCTC 49764T), Aeromicrobium wangtongii sp. nov. (zg-Y1379T=GDMCC 1.2982T=KCTC 49765T) and Aeromicrobium senzhongii sp. nov. (zg-629T=CGMCC 1.17414T=JCM 33888T).
Trinickia violacea sp. nov. and Trinickia terrae sp. nov., isolated from forest soil
Authors: Gao Zeng-hong , Guo Xiu-yin , Liu Yi-zhi , Zhang Qiu-mei , Tong Xin-jie , Qiu Li-hong
Published: November 2023

Two Gram-stain negative, aerobic and rod-shaped bacterial strains, DHOD12T and 7GSK02T, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOD12T grew at 4–42 °C (optimum, 28–33 °C), pH 4.0–8.5 (optimum, pH 5.5–6.5) and in the presence of 0–1.5 % (w/v; optimum, 0–0.5 %)NaCl; while strain 7GSK02T grew at 12–42 °C (optimum, 28–33 °C), pH 4.0–8.5 (optimum, pH 5.0–6.0) and in the presence of 0–0.5 % (w/v; optimum, 0 %) NaCl. Strains DHOD12T and 7GSK02T had the highest 16S rRNA sequence similarities of 98.0 and 98.3 % with the same species Trinickia mobilis DHG64T, respectively, and 98.4 % between themselves. In the 16S rRNA phylogeny, they formed a clade that was sister to a major cluster consisting of all described

Trinickia

species. Phylogenomic analyses with the UBCG and PhyloPhlAn methods consistently showed that strains DHOD12T and 7GSK02T formed a clade with T. mobilis DHG64T that was a sister of a cluster containing the remainder of the

Trinickia

species. The DNA G+C contents of strains DHOD12T and 7GSK02T were 63.1 and 64.6 mol%, respectively. Digital DNA–DNA hybridization and average nucleotide identity values of strains DHOD12T, 7GSK02T and their closely related strains were in the ranges of 21.6–31.4 % and 77.1–86.9 %, respectively. These two strains had the same major respiratory quinone, ubiquinone-8, and both had C16 : 0, C17 : 0 cyclo and summed feature 8 (C18 : 1
 ω7c/C18 : 1
 ω6c) as their major fatty acids. Their major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Genomic analysis indicated that the two strains could have the potential to degrade aromatic compounds like other

Trinickia

species. On the basis of phenotypic and phylogenetic results, strains DHOD12T and 7GSK02T represent two novel species of the genus

Trinickia

, for which the names Trinickia violacea sp. nov. (type strain DHOD12T=LMG 30258T=CGMCC 1.15436T) and Trinickia terrae sp. nov. (type strain 7GSK02T=CGMCC 1.15432T=KCTC 62468T) are proposed.
Fatty acid metabolism in neutrophils promotes lung damage and bacterial replication during tuberculosis
Authors: Sankar Poornima , Ramos Ramon Bossardi , Corro Jamie , Saqib Mohd , Nafiz Tanvir Noor , Bhargavi Gunapati , Ojha Anil K , Cai Yi , Subbian Selvakumar , Mishra Bibhuti B.
Published: November 2023

Mycobacterium tuberculosis(Mtb) infection triggers a significant influx of neutrophils to the lungs, which is linked to tuberculosis (TB) severity. The mechanism by which Mtb infection induces neutrophillic inflammation remains unclear. Using a clinically relevant and hypervirulent Mtb strain from the W-Beijing family, HN878, we found that genes related to both glycolysis and fatty acid metabolism are upregulated in the lung neutrophils of susceptible mice. Similar effects in gene expression were observed in rabbits, and humans with pulmonary TB compared to healthy controls. Inhibiting glycolysis with 2-deoxy D-glucose (2-DG) exacerbated disease pathology, while fatty acid oxidation (FAO) inhibitor Etomoxir (ETO) improved outcomes by reducing weight loss, immunopathology, and bacterial replication within neutrophils in genetically susceptible mice. Notably, ETO reduced neutrophil production in the bone marrow and their recruitment to the lungs. ETO specifically restrained the recruitment of Ly6Glow/dimimmature neutrophil population, which is elevated during disease progression and harbors the bulk of bacilli. In a transwell setup, we demonstrated that ETO dose-dependently inhibited neutrophil chemotaxis towards infected macrophages. In summary, our research highlights the crucial role of fatty acid metabolism in regulating neutrophilic inflammation during TB and provides a rationale for targeting immunometabolism of neutrophils for potential TB treatment.
Activity in the reticulospinal tract scales with handgrip force in humans
Authors: Danielson Tyler L. , Gould Layla , DeFreitas Jason M. , MacLennan Rob J. , Ekstrand Chelsea , Borowsky Ron , Farthing Jonathan P. , Andrushko Justin W.
Published: November 2023

Introduction

The neural pathways that contribute to force production in humans are currently poorly understood, as the relative roles of the corticospinal tract and brainstem pathways, such as the reticulospinal tract (RST), vary substantially across species. Using functional magnetic resonance imaging (fMRI) we aimed to measure activation in the pontine reticular nuclei during different submaximal handgrip contractions to determine the potential role of the RST in force modulation.

Methods

Thirteen neurologically intact participants (age: 28 ± 6 years) performed unilateral handgrip contractions at 25%, 50%, 75% of maximum voluntary contraction during brain scans. We quantified the magnitude of RST activation from the contralateral and ipsilateral sides in addition to the contralateral primary motor cortex during each of the three contraction intensities.

Results

A repeated measures ANOVA demonstrated a significant main effect of force (p= 0.012, ηp2= 0.307) for RST activation, independent of side (i.e., activation increased with force for both contralateral and ipsilateral nuclei). Further analyses of these data involved calculating the linear slope between the magnitude of activation and handgrip force for each ROI at the individual-level. One-samplet-tests on the slopes revealed significant group-level scaling for the RST bilaterally, but only the ipsilateral RST remained significant after correcting for multiple comparisons.

Conclusions

Here, we show evidence of task dependent activation in the RST pontine nuclei that was positively related to handgrip force. These data build on a growing body of literature that highlights the RST as a functionally relevant motor pathway for force modulation in humans.

New & Noteworthy

In this short report, we used a task-based fMRI paradigm to show that activity in the reticulospinal tract, but not the contralateral motor cortex, scales linearly with increasing force during a handgrip task. These findings directly support recently proposed hypotheses that the reticulospinal tract may play an important role in modulating force production in humans.
Revisiting Y-chromosome detection methods: R-CQ and KAMY efficiently identify Y chromosome sequences in Tephritidae insect pests
Authors: Rallis Dimitris , Tsoumani Konstantina T , Krsticevic Flavia , Papathanos Philippos Aris , Mathiopoulos Kostas D , Papanicolaou Alexie
Published: November 2023

Background

The repetitive and heterochromatic nature of Y chromosomes poses challenges for genome assembly methods which can lead to fragmented or misassembled scaffolds. While new sequencing technologies and assembly techniques becoming popular, tools for improving the generation of an accurate Y chromosome are limited, especially for species, such as insects, with a frequent occurrence of heterochromatic chromosomes.

Results

Two novel Y-detection methods are presented here, R-CQ and KAMY, that revisit the ratio-based Chromosome Quotient and kmer-based Y-Genome Scan methods, respectively. We benchmark R-CQ and KAMY methods against their predecessors, over their ability in identifying Y-derived regions in genome assemblies of two important insect pests of the Tephritidae genus: the olive fruit flyBactrocera oleaeand the Mediterranean fruit flyCeratitis capit ata.These species are characterised by different Y-chromosome morphologies and their genomes were sequenced with different methodologies. We also evaluated the efficiency and generic applicability of these methods using suitableDrosophila melanogastergenomic data, whose Y-chromosome is the best studied among insects. Furthermore, KAMY was assessed for the capability of identifying Y-derived transcripts in the absence of a reference-Y sequence and effectively identified the Tephritid maleness factorMoYin a set of mixed-sex transcriptomic data. Through our work, we describe a methodology for manually curating the computational results, through which the performance of different Y detection methods is determined, together with the size and quality of assembled Y sequences.

Conclusions

We find a variability in the performance of Y-detection methods, that is highly dependent on the sequencing approach used and on the sequence of the Y. Our benchmarking suggests an improved overall efficiency of KAMY and R-CQ compared to their predecessors, while our analysis highlights the importance for manually curating the algorithmic outputs towards describing the accuracy and quality of identified Y sequences. Based on our results, we provide some recommendations for future sequencing efforts in insects to best support downstream Y assembly steps.
Myogenic artifacts masquerade as neuroplasticity in the auditory frequency-following response (FFR)
Authors: Bidelman Gavin M. , Sisson Alexandria , Rizzi Rose , MacLean Jessica , Baer Kaitlin
Published: November 2023

The frequency-following response (FFR) is an evoked potential that provides a neural index of complex sound encoding in the brain. FFRs have been widely used to characterize speech and music processing, experience-dependent neuroplasticity (e.g., learning, musicianship), and biomarkers for hearing and language-based disorders that distort receptive communication abilities. It is widely assumed FFRs stem from a mixture of phase-locked neurogenic activity from brainstem and cortical structures along the hearing neuraxis. Here, we challenge this prevailing view by demonstrating upwards of ∼50% of the FFR can originate from a non-neural source: contamination from the postauricular muscle (PAM) vestigial startle reflex. We measured PAM, transient auditory brainstem responses (ABRs), and sustained frequency-following response (FFR) potentials reflecting myogenic (PAM) and neurogenic (ABR/FFR) responses in young, normal-hearing listeners with varying degrees of musical training. We first establish PAM artifact is present in all ears, varies with electrode proximity to the muscle, and can be experimentally manipulated by directing listeners’ eye gaze toward the ear of sound stimulation. We then show this muscular noise easily confounds auditory FFRs, spuriously amplifying responses by 3-4x fold with tandem PAM contraction and even explaining putative FFR enhancements observed in highly skilled musicians. Our findings expose a new and unrecognized myogenic source to the FFR that drives its large inter-subject variability and cast doubt on whether changes in the response typically attributed to neuroplasticity/pathology are solely of brain origin.