bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis, characterization, genotoxicity assessment and antibacterial applications of Zanthoxylum armatum silver nanoparticles (ZASNPs) with antibiotic efficacy enhancement potential
Authors: Quadri Nikita , Setty Manganahalli Manjunath , Awasthi Anshumali , Nayak Usha , Singh Minakshi , Sharma Sharad
Published: November 2024

A visual summary of our study, merging herbal knowledge with nanotechnology to combat antibiotic resistance. Silver nanoparticles from Zanthoxylum armatum DC. show effective bactericidal activity and enhance antibiotic efficacy.
Polyurethane foam acidolysis with carboxylic acids: acid structure dictates N-containing product distribution and kinetics
Authors: Westman Zach , Perikala Manasa , Wu Xinyi , Richardson Kelsey , Letko Christopher S. , Vlcek Vojtech , Christopher Phillip , Abu-Omar Mahdi M.
Published: November 2024

Spectroscopic characterization and kinetic studies elucidate the influence of dicarboxylic acid (DCA) structure on the formation of amide/imide products during chemical recycling of a flexible polyurethane foam (PUF).
M12L24 nanospheres as supramolecular templates for the controlled synthesis of Ir-nanoclusters and their use in the chemo-selective hydrogenation of nitro styrene
Authors: Metz Lotte L. , Ham Rens , Bobylev Eduard O. , Brouwer Kelly J. H. , van Blaaderen Alfons , van de Poll Rim C. J. , Drozhzhin Victor R. , Hensen Emiel J. M. , Reek Joost N. H.
Published: November 2024

We report a supramolecular template strategy for the controlled preparation of ultrafine metal nanoclusters (<2 nm), and demonstrate the unique properties in reductive catalysis.
North Polar Spur: Gaseous plume(s) from star-forming regions ∼3–5 kpc from the Galactic Center?
Authors: Churazov Eugene , Khabibullin Ildar I. , Bykov Andrei M. , Chugai Nikolai N. , Sunyaev Rashid A. , Utrobin Victor P. , Zinchenko Igor I.
Published: November 2024

We argue that the North Polar Spur (NPS) and many less prominent structures are formed by gaseous metal-rich plumes associated with star-forming regions (SFRs). The SFRs located at the tangent to the 3−5 kpc rings might be particularly relevant to the NPS. A multi-temperature mixture of gaseous components and cosmic rays rises above the Galactic disk under the action of their initial momentum and buoyancy. Eventually, the plume velocity becomes equal to that of the ambient gas, which rotates with different angular speeds than the stars in the disk. As a result, the plumes acquire characteristic bent shapes. An ad hoc model of plumes’ trajectories shows an interesting resemblance to the morphology of structures seen in the radio continuum and X-rays.
Conduction Disorders after Rapid Deployment Aortic Valve Replacement Compared to Conventional Aortic Valve Replacement
Authors: Schlömicher Markus , Prümmer Katrin , Haldenwang Peter , Moustafine Vadim , Berres Dinah , Bechtel Matthias , Strauch Justus T.
Published: November 2024

Objectives We evaluated and compared early postprocedural and midterm incidence and evolution of atrioventricular and intraventricular conduction disorders following rapid deployment aortic valve replacement (RDAVR) and conventional aortic valve replacement (AVR).

Materials and Methods One hundred and forty-seven patients who underwent isolated rapid deployment AVR between 2017 and 2021 as well as 128 patients after conventional biological AVR in the same period were included in this study. ECGs recorded at baseline, discharge, and 12 months were retrospectively analyzed. Intrinsic rhythm, PQ interval, QRS duration, and atrioventricular and intraventricular conduction were evaluated and compared between both groups.

Results Patients in both groups had comparable Society of Thoracic surgeons risc (STS) scores (2.9 ± 1.6 vs. 3.1 ± 2.2, p = 0.32) and comparable baseline characteristics. The mean age was 73.4 ± 5.7 years in the RDAVR group and 74.2 ± 5.9 years in the AVR group, respectively. At baseline, the mean QRS width was 95.7 ± 25.5 ms in the RDAVR group, and 97.3 ± 23.5 ms in the AVR group, respectively (p = 0.590). At discharge, the mean QRS width in the RDAVR group was significantly increased with 117.4 ± 28.6 ms and a mean ΔQRS width of 21.7 ± 26.3 ms (p < 0.001) compared with baseline. No significant changes in QRS width were found in the AVR group with a mean value of 101.2 ± 24.1 ms and a mean ΔQRS width of 3.9 ± 23.9 ms at discharge (p = 0.193). The left bundle branch block (LBBB) was increased in the RDAVR group after 12 months (19.3% vs. 5.1%, p < 0.001). Permanent pacemaker implantation (PPI) rates were significantly higher in the RDAVR group after 12 months (hazard ratio (HR): 4.68; 95% CI: 2.23–7.43, p < 0.001). Mortality did not differ between both groups after 12 months (HR: 1.09; 95% CI: 0.46–1.83, p = 0.835)

Conclusion Patients after RDAVR showed significantly higher rates of LBBB and PPI after 12 months. However, higher mortality was not observed in the RDAVR group.
Multidisciplinary Expert Guidance for the Management of Severe Bleeding on Oral Anticoagulation: An Algorithm for Practicing Clinicians
Authors: Mithoowani Siraj , Bungard Tammy , Castellucci Lana , Crowther Mark , de Wit Kerstin , Dowlatshahi Dar , Forbes Nauzer , Lin Katie , Siegal Deborah M.
Published: November 2024

Bleeding complications associated with oral anticoagulant (OAC) frequently lead to emergency department visits and hospitalization. Short-term all-cause mortality after severe bleeding is substantial ranging from approximately 10% for gastrointestinal bleeding (the most frequent single site) to approximately 50% for intracranial bleeding. A protocol for multidisciplinary approach to bleeding is needed to (i) ensure rapid identification of patients at risk of adverse outcomes, (ii) optimize delivery of supportive measures, (iii) treat the source of bleeding, and (iv) administer anticoagulant reversal or hemostatic therapies judiciously for patients most likely to benefit. We convened a multidisciplinary panel of experts (emergency medicine, gastroenterology, general internal medicine, hematology, neurology, pharmacy, thrombosis) to review the literature and provide practical guidance including a corresponding algorithm for use at the point of care to assist clinicians in the management of patients with acute severe OAC-related bleeding.
Synthesis the C1–C15 Fragment of Incednine
Authors: Roulland Emmanuel , Cordeau Damien , Norsikian Stéphanie , Genta-Jouve Grégory
Published: November 2024

We report on our progress towards the synthesis of the exotic, delicate, and tense polyketidic macrolactam of incednine. This work constitutes a significant advancement towards the total synthesis of a family of molecules of biological and medicinal interest. Some of the key features of this synthesis required evolutions from the initially designed strategy, leading to the use of a Horner–Wadsworth–Emmons olefination to build the C2–C9 tetraene. For this purpose, a polyfunctionalized phosphonate was used that was obtained through an unprecedented Pd-catalyzed cross-coupling involving the zinc salt of diethyl methylphosphonate. The resulting desired C1–C15 fragment displays a carboxylic acid ester at C1 and a vinyl iodide at C15, both functions being ready for subsequent amide coupling with the C16–C23 fragment and final Suzuki cyclization, respectively.
A Photocatalytic C(sp)–B Bond Formation Employing SOMOphilic Alkynyl Sulfones and Nucleophilic Boryl Radicals
Authors: Arpa Enrique M. , Rivera-Chao Eva , Corpas Javier , Obradović Luka
Published: November 2024

Alkynylboron compounds are important scaffolds with broad applicability in organic synthesis. In contrast to polar or metal-catalyzed processes, here a radical approach is employed for the addition of nucleophilic boryl radicals to electrophilic SOMOphiles for the construction of the C(sp)–B bond. The reaction renders the corresponding alkynylated amine boranes with broad functional group compatibility. In addition, theoretical studies have been carried out by means of DFT to understand the reactivity and selectivity of the addition process.
Arthroscopic Management of an Extremely Rare Wrist Fracture-Dislocation Pattern
Authors: Corella Fernando , Ocampos Montserrat , Collado Carlos , Laredo Rafael
Published: November 2024

Background Axial dislocation involves the displacement of carpal bones along the longitudinal axis of the wrist joint. There are three major groups: (1) axial ulnar, (2) axial radial, and (3) combined. On the other hand, radiocarpal dislocation entails disruption of the articulation between the radius and carpal bones. There are two groups: (group 1) it is either a pure radiocarpal dislocation or a minor avulsion of the radial styloid and (group 2) a fracture-dislocations characterized by a significant radial styloid fragment.

Case Description The patient, a 66-year-old female involved in a car accident, underwent imaging studies and arthroscopic exploration, revealing a transcapitate perihamate translunate fracture-dislocation, associated with a radiocarpal dislocation type 1. Arthroscopic treatment was performed through common dorsal radiocarpal and midcarpal portals, along with the volar radial portal. Anatomical reduction of the joints and fractures was achieved under arthroscopic control, along with suturing of the volar radiocarpal ligaments.

Literature Review The simultaneous occurrence of axial dislocation and radiocarpal dislocation, as observed in our case, is exceedingly rare and lacks comprehensive documentation in the existing literature. Furthermore, the specific type of axial dislocation (transcapitate perihamate translunate) has not been previously reported.

Various treatment approaches, including closed reduction, open reduction, and external fixation, have been described for these types of complex pathologies, but few reports describe their arthroscopy management.

Clinical Relevance This case report describes a rare occurrence of axial ulnar dislocation associated with radiocarpal dislocation of the wrist, which is exceptionally uncommon and not reported previously in the literature. This arthroscopic approach yielded excellent results, avoiding the need for multiple open approaches to address several fractures and ligament injuries.
Mind the Gap: The Journey of Skull Base Specialties Toward Gender Parity
Authors: Patel Shrey , Gall Emily , Kosarchuk Jacob , Toh Elizabeth H. , Soneru Christian , Noonan Kathryn
Published: November 2024

Background There are increased efforts to promote gender diversity in skull base specialties.

Aims/Objectives This study seeks to evaluate changes within neurotology, rhinology, and skull base neurosurgery (SBNS) over the past decade.

Methods Information regarding fellows training in the past 10 years, current faculty members and fellowship directors, and grants and awards were extracted from the American Neurotology Society, American Rhinologic Society, and North American Skull Base Society Web sites, tabulated, and summarized. Chi-square analysis compared the proportional makeup of female fellows within related fields.

Results In the past decade in neurotology, men constituted 89 of 128 (69.53%) fellows, 132 of 170 (77.64%) faculty members, and 25 of 29 (86.2%) fellowship directors. Within rhinology, men constituted 211 of 279 (75.63%) fellows, 113 of 141 (80.14%) faculty members, and 32 of 35 (91.4%) fellowship directors. In SBNS programs, men constituted 94 of 105 (90%) fellows, 120 of 133 (90%) faculty members, and 43 of 44 (97.73%) fellowship directors. In neurotology fellowships, the proportion of women increased (12%, p = 0.06) from 2012–2017 to 2018–2022. Similarly, SBNS and rhinology had statistically insignificant increases of 4.28% (p = 0.86) and 8.70% (p = 0.87).

Conclusion The representation of women is consistent across all three skull base specialties. Although the overall number of women in each field is increasing, it changes slowly.

Significance The gender makeup across all three skull base specialties is similar.
Vascular Labeling of Extracranial Head and Neck Vessels Using Silicone Dye Injection: An Effective Method for Cadaver-Based Facial Surgery Training
Authors: Tiwari Raja , Dhingra Renu , Lalwani Sanjeev , Singhal Maneesh
Published: November 2024

Background Silicone dye injection is a well-described technique for studying vascular anatomy. Plastic surgeons routinely participate in cadaveric workshops and are involved in the preparation of vascular-labeled cadavers. However, sparse literature is available on dye studies of extracranial head and neck vessels, even with anatomists, and the preparation of these cadavers is a daunting task.

Materials and Methods In this study, we describe a straightforward technique of silicone dye injection for extracranial head and neck vasculature and its application for filler injection training and other plastic surgical procedure demonstrations on cadavers. We used six soft-embalmed cadavers. The common carotid arteries and internal jugular veins were cannulated with infant feeding tubes. The vessels that could lead to dye extravasation into intracranial vessels and upper limbs were ligated. The vasculature was irrigated with water and then injected with color-coded silicone dyes (red: arterial; blue: venous). The solvent-to-catalyst ratios were varied to identify the ideal combination. Injected specimens were dissected 24 hours later to identify the staining quality.

Results A clear demarcation of the extracranial head and neck vasculature in all cadavers was seen. The best solvent-to-catalyst ratio was identified in cadavers with the best staining of both large and small-sized blood vessels (<1 mm) with no dye spillage from arteries to the veins.

Conclusion Silicone dye injection with the described technique can give excellent and predictable results. The technique also uses less quantity of dye, and the intracranial structures are spared, which can be used for other studies; hence, there is more economical utilization of cadavers.
Treatment of Chronic Scapholunate Dissociation with FCR Tenodesis: A Systematic Review of the Results of MBT and 3LT Technique
Authors: Goeminne Sofie , Stroobants Eline , van Beek Nathalie
Published: November 2024

A systematic literature review was performed to assess the results of modified Brunelli tenodesis modified Brunelli technique (MBT) and three-ligament tenodesis (3LT) in the treatment of chronic scapholunate (SL) ligament injuries reported between 1998 and 2001. This review describes the surgical techniques, clinical outcomes, radiological evaluations, and complication rates among 600 patients. Following adherence to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, 15 studies were included (289 MBT and 311 3LT procedures). A heterogeneity in surgical technique was noted. An average pain reduction of 3 points on the visual analog score and a flexion–extension arch compatible with most daily activities were found. Radiographic follow-up showed medium-term improvements, but loss of reduction was observed in the long term. Secondary degeneration was seen in 15% of cases. Radiographic decay did not correlate with clinical outcomes. The overall complication rate was 9%. This review underscores the satisfactory clinical outcome of both procedures. Nonetheless, both interventions pose risks of complications and/or degeneration in the long term.
A Case Report on Ellis–van Creveld Syndrome: Clinical, Embryological, Anesthetic, and Surgical Implications
Authors: Mohan Monusha , Sabapathy S. Raja
Published: November 2024

Postaxial polydactyly (PAP) in the form of rudimentary soft tissue masses is quite common. Management involves ligation or surgical excision. Rarely do literature discussions cover complex variants in which the extra finger is fully developed. Ellis–van Creveld syndrome (EVC) or chondroectodermal dysplasia is a rare disorder characterized by PAP. When chondral dysplasia encompasses PAP, dwarfism, and genu valgum, ectodermal dysplasia involves nails and teeth. We describe two EVC cases. When one had cardiac malformations, the other had dental anomalies. One of them underwent genu valgum correction and removal of the additional finger. The hand surgery proved complex due to fusion of its metacarpal with the fifth metacarpal. Pediatric Outcomes Data Collection Instrument (PODCI) scores at 1.5 and 2.5 years after hand and knee surgeries were excellent. A multidisciplinary approach is essential to achieve comprehensive care. Additional embryological research is necessary to elucidate the clinical manifestations described in this report.
Chinese and Indian Inequality in a Comparative and Global Context
Authors: Vakulabharanam Vamsi
Published: November 2024

In this introductory chapter, the rationale for comparing Chinese and Indian inequalities is presented. After indicating the trajectories of China and India along the growth and inequality dimensions, it is argued that these trajectories are remarkably similar despite significant differences in their respective domestic institutions. To make sense of this phenomenon, an alternative framework is presented. First, the chapter discusses the blind spots in the theoretical frameworks of Kuznets and Piketty in shedding light on within-country inequalities, arguing that this book, among other things, offers an alternative framework drawing from the experiences of China and India. Second, the chapter outlines this alternative framework—that it is of a non-deterministic kind that brings together changes in global capitalism and national/regional political economies that explain different configurations of growth and inequality across space and time.
Class and Inequality Patterns in Post-Revolutionary China during the Mao Period (1949–1976)
Authors: Vakulabharanam Vamsi
Published: November 2024

By all known accounts, on the eve of the formation of the People’s Republic of China (PRC) in 1949, economic inequality levels in the predominantly rural-based society were quite high. Additionally, there was significant spatial/regional inequality, such as the intra-urban inequality between coastal and inland provinces. The PRC government interventions significantly altered the patterns of inequality in China. Given the paucity of data for this period, nothing definitive can be said regarding how the national  levels of inequality changed over time, although changes in the patterns can be discussed with some confidence, and the direction was toward reducing inequality with varying degrees of success. In this short chapter, a summary is presented of these various patterns of and changes in economic inequality during the Mao period.
Indian Inequality (1951–1983)
Authors: Vakulabharanam Vamsi
Published: November 2024

Immediately after Indian independence, the Indian economy was quite unequal. Understanding three post-independence dynamics are crucial. First, incorporating the peasantry and urban working poor into the independence struggle from the 1920s went with the promise of creating an egalitarian India with broad-based development. Second, the actions of the existing dominant classes that tried to decisively protect their own interests after independence. Third, there was a tussle among different dominant classes that pushed the state in different directions. This complex dialectic produced a deep puzzle with which this chapter engages. On the one hand, the dominant classes were accorded significant protection right from independence. The bottom 40% in rural as well as urban areas did not witness much improvement until the 1970s (the poverty rate was nearly constant until then). Yet, inequality levels witnessed a decline. This chapter provides an answer to this puzzle.
Comparing Class and Inequality in China and India
Authors: Vakulabharanam Vamsi
Published: November 2024

This chapter first presents a quantitative comparison of growth and inequality trends in China and India. It proceeds to explain the differences in output growth and inequality levels in terms of the different class dynamics and history. It then locates these class dynamics in terms of different regimes of accumulation or different economic systems that these countries adopted (e.g., during the 1950–80 period). The comparative framework has three dimensions: class analyses of growth and distribution in these two economies, comparison of sectoral and macro dynamics, and the growth and evolution of inequality dynamics located in a larger world system. The chapter delves into the comparative literature of China–India (from economics and political economy literature) and arrives at a synthesis of concepts that are helpful in analyzing inequality dynamics between these two countries. The underlying patterns of inequality in these two economies are remarkably similar, especially after 1980s.
China, India, and their Changing Place in the Global Economy
Authors: Vakulabharanam Vamsi
Published: November 2024

This chapter does four things. First, it analyzes the growth of China and India and its impact of reducing the between-country inequality component of global inequality. Second, it looks at the increased inequality in China and India and shows how this has increased the within-country inequality component of global inequality. Third, this rise in the within-country component has led to an externalization (markets, capital) of China and India to continents like Africa or Latin America or the emerging Asia. Finally, the chapter speculates on the impact of these transformations on the existing world order to ask whether China or India is becoming imperialist. At this moment, China and India occupy a position of an unfavorable relation of exchange with the advanced capitalist world, and an extractivist relationship with the poorer world.
Of Pots and Plato’s Aesthetics
Authors: Fine Jonathan
Published: November 2024

What role should examples play in aesthetic inquiry? This essay brings a neglected early episode in the history of aesthetics to bear on this question. Asked 'What is beauty?' in Plato's Hippias Major, Hippias first cites a beautiful maiden. Surprisingly, before refuting this answer, Socrates asks about other examples: a beautiful mare, lyre, and pot (chytra). These widely ignored examples, I show, work to contest an association between beauty and aristocratic class. By beginning the inquiry in this way, Plato emphasizes the need to critique and not rely on cultural examples that incline reflection on beauty.
Analytical performance of a point-of-care CBC hematology analyzer, including a 5-part differential: A prospective study to evaluate a microfluidic flow cytometry–based analyzer in waived settings
Authors: Emerson Jane F , Wang Hao , Siddiqi Imran N
Published: November 2024

Objectives

A microfluidic flow cytometer–based point-of-care (POC) analyzer was validated against an in-laboratory hematology analyzer (Sysmex XN Automated Hematology System). Concordance on a full complete blood cell count (CBC) with 5-part differential, as performed by operators with no prior clinical laboratory experience, was evaluated.

Methods

We prospectively collected 376 venous blood specimens (376) from individuals with self-reported medical conditions and from apparently healthy individuals. Forty-six additional remnant specimens were acquired to ensure coverage of analytic measuring ranges. Parallel testing was performed, with up to 7 hours between testing on the POC and Sysmex XN analyzers.

Results

Regression analysis resulted in r values of 0.998 to 0.932 for all parameters of a 5-part differential CBC other than basophils (0.709). The mean percentage bias from the reference method, inclusive of the upper and lower reporting limits, was less than 2% for parameters other than lymphocytes (–6.4%), monocytes (25.9%), eosinophils (12.2%), and basophils (–15%). Overall agreement on abnormal flagging was 93.3%.

Conclusions

The Cito CBC microflow cytometer (CytoChip Inc) provides a CBC with a 5-part differential with accuracy, precision, and abnormal flagging equivalent to a moderate-complexity hematology analyzer. It has the key features required of a POC device that can be operated in a waived setting: minimum space requirements, rapid results, single-action measurement (no sample processing or dilution), ease of use, and minimal blood volume.
Evaluation of barcode-assisted medication preparation technology for liquid medication doses
Authors: Deyhim Niaz , Adeola Mobolaji , Bhakta Sunny B
Published: November 2024

Purpose

The purpose of this study was to evaluate the outcomes associated with barcode-assisted medication preparation (BCMP) technology and practice workflows for oral syringe dose preparation in a health-system pharmacy department.

Methods

This evaluative study was conducted at a flagship quaternary academic medical center. An electronic medical record (EMR)–integrated BCMP workflow was implemented in the central pharmacy operational area to enhance the safety of oral syringe dose preparation. The primary endpoints assessed compliance with BCMP implementation and the rate at which potential preparation errors were identified. The secondary endpoints evaluated operational markers of dose preparation batching, information technology enhancement needs, and medication waste avoidance.

Results

A 95% rate of compliance with the BCMP workflow was observed over 2 years. The composite near-miss detection rate improved from year 1 to year 2 of implementation (0.89% vs 0.94%). The composite rate was influenced by increased yearly compliance with BCMP (93.8% vs 95.3%). A total of 176,679 preparations were reviewed in the 2-year period, including 81,240 in year 1 and 89,638 in year 2. The rate at which orders were rejected by pharmacists decreased over time (0.26% in year 1 vs 0.24% in year 2). Of the 1,005 wrong ingredient warnings, only 4 were overridden; in all other instances, the order was rejected at pharmacist checking due to use of an incorrect product in the preparation history. Wrong ingredient warnings led to canceled preparations in 96.1% of alert instances.

Conclusion

EMR-integrated BCMP technology aligned with safety efforts in the oral syringe dose preparation process reduced potential waste of medications and allowed insight into operational performance and volume indicators.
Evaluating pediatric antimicrobial dosing of β-lactam antibiotics for upper respiratory tract infections in emergency and primary care settings
Authors: Blower Noah , Draper Heather M , McAlpine Tara , Dumkow Lisa E
Published: November 2024

Purpose

Pediatric prescribing is often weight and indication specific and has been associated with high rates of error. The aim of this study was to evaluate outpatient β-lactam suspension dosing practices for pediatric upper respiratory tract infections (URIs), to characterize the rate of error and to describe common error types.

Methods

This retrospective cohort study was conducted at a community health system with 2 emergency departments and 20 outpatient family medicine practices. Pediatric patients treated from these settings with oral suspension formulations of amoxicillin, amoxicillin/clavulanate, cefdinir, or cephalexin for streptococcal pharyngitis or otitis media between June 1, 2020, and May 31, 2023, were eligible for inclusion. Doses were evaluated against indication-specific best-practice guidelines and assessed for guideline concordance.

Results

Of the 200 patients evaluated, 100 were treated for streptococcal pharyngitis and 100 were treated for otitis media. Of the prescribed β-lactam doses, 32% were discordant with best-practice guideline recommendations. Dosing errors were more common for pharyngitis than for otitis media (47% vs 17%; P < 0.001). Overdosing was the most frequently observed error in pharyngitis prescriptions (93.6% of errors) and most commonly occurred in patients weighing more than the 20-kg weight associated with the dosing maximum (80.9% of overdosing errors). All patients receiving an inappropriate dose for otitis media were underdosed.

Conclusion

Outpatient pediatric dosing errors for URI indications are common among both emergency medicine and family medicine prescribers. Patients weighing over the weight corresponding to the dosing maximum are at highest risk for error. Antimicrobial stewardship interventions targeting the point of prescribing are urgently needed to provide safe dosing practices for pediatric patients.
Determination of ultrafine particle number emission factors from building materials in standardized conditions
Authors: Concha-Lozano Nicolas , Muller Yan , Favreau Philippe , Suarez Guillaume
Published: November 2024

When comparing the particle emissivity for different materials and/or mechanical activities, a serious methodological issue emerges due to the dynamic nature of solid aerosols. Particle size distribution and concentration depend on initial particle emission that constantly evolves due to aerodynamic collisions. In this context, we propose a methodological approach and an experimental setup that enables to assess the release of fine/ultra-fine particles maintaining a steady-state inhalable mass concentration, here chosen at the Swiss occupational exposure level value for biopersistent granular particles (OEL: 10 mg/m3) in a controlled ventilation chamber. As a case study, this methodological protocol was tested in the occupational exposure scenario in which a series of insulating materials based on silica aerogel and conventional mortar and concrete were subjected to handling or sawing. Once the OEL was reached, the particle size distribution and morphology of the aerosols were characterized using direct reading instruments (scanning mobility sizer, aerosol photometer) and electron microscopy (SEM and TEM) analyses. As a main result, the presence of silica aerogel in the mortar did not modify the emission profile for submicronic particles during sawing in comparison to the bulk mortar. Emission factors for ultra-fine particles were found to be 88 × 106 and 81 × 106 particles/µg of inhalable dust for the aerogel mortar and bulk mortar, respectively. For concrete sawing, the number concentration of submicronic particles at the OEL is one order of magnitude greater. The aerogel-glass-wool handling generated similar particle number concentration at the OEL with ultra-fine particle emission factors of 647 × 106 particles/µg of inhalable dust, in comparison to 758 × 106 particles/µg of inhalable dust during dry concrete sawing. In conclusion, the methodology introduced in this work provides standardized particle emission factors for comparing materials and activities, while establishing a link between particle number emissions and occupational exposure limits.
Vegetative and reproductive morphology of Othniophyton elongatum (MacGinitie) gen. et comb. nov., an extinct angiosperm of possible caryophyllalean affinity from the Eocene of Colorado and Utah, USA
Authors: Manchester Steven R , Judd Walter S , Correa-Narvaez Julian E
Published: November 2024

Background and Aims

Eocene foliage formerly attributed to the extant araliaceous genus Oreopanax was found attached to twigs bearing inflorescences and infructescences unlike those of Araliaceae. Using newly observable characters of phyllotaxy, vegetative and floral buds, infructescences and seeds, we sought to reassess the affinities of this strange angiosperm.

Methods

Fossils were studied from the Parachute Creek Member of the Green River Formation from near Bonanza, Utah and Douglas Pass, Colorado (~47 Mya). Macrofossil impression remains were investigated by low-angle reflected light, and subtle details of the vegetative and floral buds, stamens, mature fruits and seeds were revealed by optical shadow effect microscopy, documenting previously obscure topographic surface features.

Key Results

Othniophyton elongatum (MacGinitie) Manchester, Judd, Correa-Narvaez gen. et comb. nov. has simple, short-petiolate, elongate, entire-margined leaves with thick midveins, pinnate, brochidodromous secondaries, common intersecondary veins and finely reticulate higher-order venation. Inflorescences are small axillary cymes; flower buds are subglobose and pedicellate, in bract axils. The flowers are actinomorphic, bisexual, with approximately five imbricate perianth parts, ~24 stamens with elongate anthers and short filaments, arising from a hypanthium. The whorl of stamens persists to fruiting stage. The ovary is superior, with probable basal placentation and five stigmatic arms. Fruits are pedicellate berries with a cup-shaped hypanthium and contain ~15 lensoidal reniform seeds, each with a curved embryo and ornamented with concentric ridges. The combined characters refute the prior placement in Araliaceae and rule out affinities with most extant clades of angiosperms.

Conclusions

The distinctive combination of observed features does not coincide with any extant family. Among extant orders of Eudicots, the fossil seems to conform most closely to the order Caryophyllales, but key differences remain. This example indicates that the vegetation of ~47 Mya included some taxa that cannot readily be placed in modern families and genera.
Masting ontogeny: the largest masting benefits accrue to the largest trees
Authors: Szymkowiak Jakub , Hacket-Pain Andrew , Kelly Dave , Foest Jessie J , Kondrat Katarzyna , Thomas Peter A , Lageard Jonathan G A , Gratzer Georg , Pesendorfer Mario B , Bogdziewicz Michał
Published: November 2024

Background and Aims

Both plants and animals display considerable variation in their phenotypic traits as they grow. This variation helps organisms to adapt to specific challenges at different stages of development. Masting, the variable and synchronized seed production across years by a population of plants, is a common reproductive strategy in perennial plants that can enhance reproductive efficiency through increasing pollination efficiency and decreasing seed predation. Masting represents a population-level phenomenon generated from individual plant behaviours. While the developmental trajectory of individual plants influences their masting behaviour, the translation of such changes into benefits derived from masting remains unexplored.

Methods and Key Results

We used 43 years of seed production monitoring in European beech (Fagus sylvatica) to address that gap. The largest improvements in reproductive efficiency from masting happen in the largest trees. Masting leads to a 48-fold reduction in seed predation in large trees compared with 28-fold in small trees. Masting yields a 6-fold increase in pollination efficiency in large trees compared with 2.5-fold in small trees. Paradoxically, although the largest trees show the biggest reproductive efficiency benefits from masting, large trees mast less strongly than small trees.

Conclusions

Apparently suboptimal allocation of effort across years by large plants may be a consequence of anatomical constraints or bet-hedging. Ontogenetic shifts in individual masting behaviour and associated variable benefits have implications for the reproductive potential of plant populations as their age distribution changes, with applications in plant conservation and management.
LUKB: preparing local UK Biobank data for analysis
Authors: Li Xiangnan , Huang Yaqi , Wang Shuming , Hao Meng , Li Yi , Zhang Hui , Hu Zixin
Published: November 2024

Motivation

The UK Biobank data holds immense potential for human health research. However, the complex data preparation and interpretation processes often act as barriers for researchers, diverting them from their core research questions.

Results

We developed LUKB, an R Shiny-based web tool that simplifies UK Biobank data preparation by automating these preprocessing tasks. LUKB reduces preprocessing time and integrates functions for initial data exploration, allowing researchers to dedicate more time to their scientific endeavors. Detailed deployment and usage can be found in the Supplementary Data.

Availability and implementation

LUKB is freely available at https://github.com/HaiGenBuShang/LUKB.
BindCompare: a novel integrated protein–nucleic acid binding analysis platform
Authors: Mahableshwarkar Pranav , Shum Jasmine , Ray Mukulika , Larschan Erica
Published: November 2024

Advanced genomic technologies have generated thousands of protein–nucleic acid binding datasets that have the potential to identify testable gene regulatory network (GRNs) models governed by combinatorial associations between factors. Transcription factors (TFs), and RNA binding proteins (RBPs) are nucleic-acid binding proteins regulating gene expression and are key drivers of GRN function. However, the combinatorial mechanisms by which the interactions between specific TFs and RBPs regulate gene expression remain largely unknown. To identify possible combinations of TFs and RBPs that may function together, developing a tool that compares and contrasts the interactions of multiple TFs and RBPs with nucleic acids to identify their common and unique targets is necessary. Therefore, we introduce BindCompare, a user-friendly tool that can be run locally to predict new combinatorial relationships between TFs and RBPs. BindCompare can analyze data from any organism with known annotated genome information and outputs files with detailed genomic locations and gene information for targets for downstream analysis. Overall, BindCompare is a new tool that identifies TFs and RBPs that co-bind to the same DNA and/or RNA loci, generating testable hypotheses about their combinatorial regulation of target genes.

Availability and implementation

BindCompare is an open-source package that is available on the Python Packaging Index (PyPI, https://pypi.org/project/bindcompare/) with the source code available on GitHub (https://github.com/pranavmahabs/bindcompare). Complete documentation for the package can be found at both links.
PRONA: an R-package for Patient Reported Outcomes Network Analysis
Authors: Bergsneider Brandon H , Celiku Orieta
Published: November 2024

Network analysis (NA) has recently emerged as a new paradigm by which to model the symptom patterns of patients with complex illnesses such as cancer. NA uses graph theory-based methods to capture the interplay between symptoms and identify which symptoms may be most impactful to patient quality of life and are therefore most critical to treat/prevent. Despite NA’s increasing popularity in research settings, its clinical applicability is hindered by the lack of a unified platform that consolidates all the software tools needed to perform NA, and by the lack of methods for capturing heterogeneity across patient cohorts. Addressing these limitations, we present PRONA, an R-package for Patient Reported Outcomes Network Analysis. PRONA not only consolidates previous NA tools into a unified, easy-to-use analysis pipeline, but also augments the traditional approach with functionality for performing unsupervised discovery of patient subgroups with distinct symptom patterns.

Availability and implementation

PRONA is implemented in R. Source code, installation, and use instructions are available on GitHub at https://github.com/bbergsneider/PRONA.
PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature
Authors: Tian Shubo , Chen Qingyu , Comeau Donald C , Wilbur W John , Lu Zhiyong
Published: November 2024

Over 55% of author names in PubMed are ambiguous: the same name is shared by different individual researchers. This poses significant challenges on precise literature retrieval for author name queries, a common behavior in biomedical literature search. In response, we present a comprehensive dataset of disambiguated authors. Specifically, we complement the automatic PubMed Computed Authors algorithm with the latest ORCID data for improved accuracy. As a result, the enhanced algorithm achieves high performance in author name disambiguation, and subsequently our dataset contains more than 21 million disambiguated authors for over 35 million PubMed articles and is incrementally updated on a weekly basis. More importantly, we make the dataset publicly available for the community such that it can be utilized in a wide variety of potential applications beyond assisting PubMed’s author name queries. Finally, we propose a set of guidelines for best practices of authors pertaining to use of their names.

Availability and implementation

The PubMed Computed Authors dataset is publicly available for bulk download at: https://ftp.ncbi.nlm.nih.gov/pub/lu/ComputedAuthors/. Additionally, it is available for query through web API at: https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/authors/.
Anti-Müllerian hormone as a predictor of oocyte yield following controlled ovarian stimulation in the rhesus macaque
Authors: Jensen Jared V , Leung Philberta Y , Mishler Emily C , Burch Fernanda C , Piekarski Nadine , Bishop Cecily V , Hanna Carol B
Published: November 2024

Anti-Müllerian hormone (AMH) is widely used in the clinic as a biomarker for ovarian reserve and to predict ovarian response to gonadotropin stimulation. Patients with higher AMH levels tend to yield more oocytes and have better outcomes from assisted reproductive technology procedures. The goal of this study is to determine if AMH can be used to predict the outcome of controlled ovarian stimulation in rhesus macaques, which are commonly used in biomedical research, to refine animal use while maximizing oocyte yield. We hypothesized that pre-stimulation AMH values can be used to predict oocyte yield and quality. Regularly cycling adult macaques underwent controlled ovarian stimulation and baseline (pre-stimulation) plasma AMH levels were determined using an AMH-specific enzyme-linked immunoassay. Oocytes were collected by laparoscopic or ultrasound-guided aspiration, then counted and evaluated for quality and stage of meiosis. Sperm from established fertile males were used to inseminate the oocytes in vitro with fertilization success checked 14–16 h later. Females were grouped by oocyte yield: low ≤17; mid = 18–41; high ≥42. We found that high and mid yielders had significantly higher AMH than low yielders (p < 0.0001) and the percent of mature oocytes was greater in the high and mid yielders. There were no significant differences in oocyte quality or ova fertilization rate. These data suggest that AMH is a useful measure for controlled ovarian stimulation success in rhesus macaques and can be used to identify suitable animals for oocyte donation before entering them into a stimulation protocol.
The effects of bisphenol A and its analogs on steroidogenesis in MA-10 Leydig cells and KGN granulosa cells
Authors: Iskandarani Lama , Romanelli Sabrina , Hales Barbara F , Robaire Bernard
Published: November 2024

Bisphenols are a family of chemicals used in the manufacture of consumer products containing polycarbonate plastics and epoxy resins. Studies have shown that exposure to bisphenol A (BPA) may disrupt steroidogenesis and induce adverse effects on male and female reproduction, but little is known about BPA replacements. We determined the effects of six bisphenols on the steroidogenic function of MA-10 Leydig cells and KGN granulosa cells by measuring the levels of progesterone and estradiol produced by these cells as well as the expression of transcripts involved in steroid and cholesterol biosynthesis. MA-10 and KGN cells were exposed for 48 h to one of six bisphenols (0.01–50 μM): BPA, bisphenol F, bisphenol S, bisphenol AF, bisphenol M, or bisphenol TMC, under both basal and dibutyryl cAMP (Bu2cAMP)-stimulated conditions. In MA-10 cells, most bisphenols increased the Bu2cAMP-stimulated production of progesterone. In KGN cells, there was a general decrease in progesterone production, while estradiol levels were increased following exposure to many bisphenols. Quantitative real-time polymerase chain reaction analyses revealed that all six bisphenols (≥1 μM) upregulated the expression of STAR, a cholesterol transporter, in both cell lines after stimulation. Key transcripts directly involved in steroid and cholesterol biosynthesis were significantly altered in a cell line, chemical, and concentration-dependent manner. Thus, BPA and five of its analogs can disrupt steroid production in two steroidogenic cell lines and alter the levels of transcripts involved in this process. Importantly, BPA replacements do not appear to have fewer effects than BPA.
Spontaneous breaking of symmetry in overlapping cell instance segmentation using diffusion models
Authors: Kirkegaard Julius B
Published: November 2024

Instance segmentation is the task of assigning unique identifiers to individual objects in images. Solving this task requires breaking the inherent symmetry that semantically similar objects must result in distinct outputs. Deep learning algorithms bypass this break-of-symmetry by training specialized predictors or by utilizing intermediate label representations. However, many of these approaches break down when faced with overlapping labels that are ubiquitous in biomedical imaging, for instance for segmenting cell layers. Here, we discuss the reason for this failure and offer a novel approach for instance segmentation based on diffusion models that breaks this symmetry spontaneously. Our method outputs pixel-level instance segmentations matching the performance of models such as cellpose on the cellpose fluorescent cell dataset, while also permitting overlapping labels.
The impact of coarsening an exposure on partial identifiability in instrumental variable settings
Authors: Gabriel Erin E , Sachs Michael C , Sjölander Arvid
Published: November 2024

In instrumental variable (IV) settings, such as imperfect randomized trials and observational studies with Mendelian randomization, one may encounter a continuous exposure, the causal effect of which is not of true interest. Instead, scientific interest may lie in a coarsened version of this exposure. Although there is a lengthy literature on the impact of coarsening of an exposure with several works focusing specifically on IV settings, all methods proposed in this literature require parametric assumptions. Instead, just as in the standard IV setting, one can consider partial identification via bounds making no parametric assumptions. This was first pointed out in Alexander Balke’s PhD dissertation. We extend and clarify his work and derive novel bounds in several settings, including for a three-level IV, which will most likely be the case in Mendelian randomization. We demonstrate our findings in two real data examples, a randomized trial for peanut allergy in infants and a Mendelian randomization setting investigating the effect of homocysteine on cardiovascular disease.