bluuebunny/crossref_metadata_2025 huggingface dataset:
Physical and chemical characteristics of Socah Estuary, Bangkalan
Authors: Jayanthi O W , Kartika A G D , Nuzula N I , Syaifullah M
Published: October 2023

Dominating the hydrodynamic influence of seawater and the entry of freshwater runoff from the land causes the estuary to have dynamic physical and chemical composition characteristics. The estuary area has fluctuating ecosystem changes caused by the many activities in the estuary. This study aims to determine the physical and chemical properties of the Socah River Estuary. Data were retrieved in situ at 4 station points 3 times a row. Physical and chemical parameters were measured three times. The analysis shows that each station’s temperature value is 28.5 – 30.3°C, the transparency value is 12,5cm – 30cm, the turbidity value is 13 – 25 NTU, and the TSS value is 13 mg/L – 16 mg/L. While the chemical parameters of the estuary showed the salinity concentration was between 20-22 ppt, the pH value was 6.8-7.5; the DO concentration was 2,7 mg/L - 4 mg/L, and CO2 concentration was 0,8 ppm – 2,4 ppm. Variations of water quality characteristics at each station were analyzed using Principal Component Analysis (PCA). The PCA obtained two main analysis components; 75,5% of the total variance is related to CO2, temperature, TSS, and transparency parameters.
Characteristics of North Pacific water masses in the Bali Sea
Authors: Khalishah P V , Naulita Y , Hernawan U
Published: October 2023

The Bali Sea is the trajectory of Indonesian Throughflow (ITF)’s water mass which originates from the North Pacific (NP) Ocean before exiting through Lombok Strait. Therefore, the NP water masses have an impact on the characteristics of the water mass in this area. The study aims to describe the stratification and structure of water masses and calculate the contribution of North Pacific Subtropical Water (NPSW) and North Pacific Intermediate Water (NPIW) using Optimum Multiparameter (OMP) analysis. Stratification of the Bali Sea consists of mixed, thermocline, and deep layers. There were found remnants of NPSW and NPIW inside the thermocline layer, deeper than their origin in the NP Ocean. The core layer of NPSW has an S-max value of 34,6 psu at 120-170m depth, while NPIW has an S-min value of 34,3 psu at the deeper layer, 260-280m depth. The NPIW more dominant presence in the Bali Sea with 80% contribution at a depth of 200-215 meters, while NPSW contribution is 70% at a depth of 110-130 meters. NPSW’s contribution decreases from east to west and vice versa the NPIW.
The phenomenon of Harmful Algae Blooms (HABs) based on literature study in Indonesia Sea Waters from 2005-2021
Authors: Samudra S H , Ghofari M A , Ismet M S , Fikri R A N , Sudrajat J C S , Azalia F , Sardi F D , Rifqi M , Maysaroh S , Febridelita A , Setyaningsih W A
Published: October 2023

Phytoplankton plays a vital role as a significant component of the food chain and primary production in the marine environment. However, the blooming of certain phytoplankton can have a detrimental impact on aquatic ecosystems. Toxins produced by these algae can be harmful to humans and animals. This study aims to map the spatial and temporal distribution of harmful phytoplankton in the sea waters of Indonesia. The study uses literature published from 2005 to 2021 about harmful algae blooms in Indonesia. This literature is then analyzed by reviewing existing literature from reputable repositories, with the keyword harmful algae blooms in Indonesia, and visualized using R. The study results show two phyla of phytoplankton most commonly found in the waters of the Indonesian Sea, namely Ochrophyta and Myzozoa. Seventeen genera were identified as potentially harmful phytoplankton (Chaetoceros, Coscinodiscus, Pyrodinium, Nitzschia, Skeletonema, Thalassiosira, Trichodesmium, Alexandrium, Rhizosolenia, Pseudo-Nietzsche, Ceratium, Dinophysis, Noctiluca, Protoperidinium, Prorocentrum, Anabaena, and Oscillatoria), with ten of them known to be potentially toxic (Nitzschia, Cochlodinium, Trichodesmium, Alexandrium, Dinophysis, Pyrodinium, Protoperidinium, Prorocentrum, Oscillatoria, and Anabaena). The most affected areas by harmful algae blooms (HABs) in Indonesia are in western Indonesia, especially the southern part of Sumatra, Lampung, and DKI Jakarta. The analysis of the causes of HABs shows that excess nutrients, as well as domestic and anthropogenic wastes, are the leading causes of the HABs phenomenon in Indonesia.
A cost benefit analysis of blue swimming crab gillnet fishery in Pangkajene Island, South Sulawesi
Authors: Welis M , Satria M B , Nugroho K C , Setioko W
Published: October 2023

Blue swimming crabs (Portunus pelagicus) are an important capture of the gillnet fisheries practiced around Pangkajene waters. The fisheries have been monitored by the Indonesian Blue Swimming Crab Association (APRI) by deploying enumerators who collect some data on the volume and size of crabs captured by fishermen. Information on the economic aspect of the fisheries, i.e., the business feasibility, has not been studied. The method in this study is observation and interviews. Based on monitoring data for 5 fishing units, the financial performance of the crab fisheries was evaluated. The fishing units were selected on the basis of records on eligible crabs. The available data collected from June 25th to July 5th, 2022, were processed and analyzed for calculations of business profit/loss analysis, benefit-cost ratio (B/C), break even point (BEP), and payback period (PP). The results showed that the blue swimming crab-catching business using net fishing gear is, on average feasible and profitable fishing gear with a Benefit Cost Ratio value of 1.36. Based on the calculation of the pay pack, the average period is 1, which means that fishermen only need one year to return the total capital. It is concluded that the crab fishing business is generally feasible financially.
Vertical and horizontal distribution model of lead (Pb) in Padelegan Waters, Pademawu District, Pamekasan Regency
Authors: Hariyanti A , Kartika A G D , Jayanthi O W , Wicaksono A , Nuzula N I , Efendy M
Published: October 2023

Seawater quality is importantly used in salt production, but it could be contaminated due to input of anthropogenic wastewater. This study aims to understand the quality of the water and the content of Pb in seawater, which will be used as raw material for salt production. Descriptive research methods and purposive sampling methods were used for the research method and the determination of the sampling respectively. Sampling of seawater was carried out water sampler, followed by analysis of heavy metal Pb based on APHA 1998 using Atomic Absorption Spectrophotometry (AAS). The concentration of Pb on the surface ranged from 0.6332 to 1.0815 mg/L, in the water column from 0.5842 to 1.0516 mg/L, and in the bottom waters from 0.5571 to 0.9375 mg/L, according to the findings. The horizontal distribution of the Pb showed an increasing trend towards the sea with concentrations ranging from 0.6332 to 1.0815 mg/L. Meanwhile, the concentrations of Pb in surface waters increased vertically, ranging from 0.5571 to 1.0815 mg/L. The horizontal distribution is higher towards open sea, while vertical distribution is higher towards the water surface. Seawater in vicinity of study area is still probably used although caution must be observed regarding to the Pb content.
The proportion of the egg berried female crabs and the hatching time based on differences in the eggs colour of the blue swimming crab in the crab box apartment
Authors: Qomariyah L , Wicaksono R Z , Nugroho K C , Setioko W
Published: October 2023

Fishermen in Pagagan Village who get the egg-berried female (EBF) of blue swimming crabs can store them in the Crab Box Apartment that has been provided on the coast so that the crabs incubate their eggs. The placement of EBF crabs in the crab box apartment showed fishermen actively participating in sustainable crab management. The EBF crabs are quite varied, especially in egg colour (yellow, orange, brown, and grey). This study used descriptive analysis to identify the EBF crab’s hatching time based on the egg colour that is incubated in the crab apartment. The result showed that the EBF crabs with yellow eggs have an average hatching time of more than 7 days. The orange eggs are, on average 5 days, the brown eggs are about 3 days, and the grey eggs are only 1 day. These hatching time records can also improve the implementation of the crab box apartment, which is a way to minimize the presence of EBF crabs in the supply chain and increase compliance, which leads to sustainability.
Potential of processed barnacles shell as soil conditioner using mung bean plants (Vigna radiata L.) growth
Authors: Buntaro G A , Avicenna R A
Published: October 2023

Barnacles as periphyte animals often found clinging on the ship’s hull, being unutilized waste that presents in such abundance. Calcium carbonate in barnacle shells would increase the chance of degrading microbial community survival in the soil, indirectly increasing soil fertility. The processing of barnacle shells to be used as a calcium carbonate supplement involves harvesting, drying, powdering, sterilizing, and mixing it to the soil. We want to observe comparison of the performance of control group (K), processed barnacle shells (T), industrial 16-16-16 NPK (Nitrogen, Phosphate, Potassium) fertilizer (P), and the combination of processed barnacle shell with 16-16-16 NPK fertilizer (TP) supplementation to the soil as planting media by the daily temperature, pH, and moisture fluctuation, besides the measurement of the growth of mung bean plant, Vigna radiata L. (VIMA 5 variant) regarding their application to the soil. The growth of V. radiata L. is measured by epicotyl length, number of leaves, and total wet mass increase of each plant individual. Vigna radiata L. in the control group shows the best growth measured by parameters listed above. However, ANOVA analysis shows statistical significance on the correlation of types of soil treatment (K, T, P, or TP supplementation) to daily moisture fluctuation.
Potential fishing grounds of Skipjack tuna (Katsuwonus pelamis) in western water of Sumatera using remotely sensed data and maximum entropy model
Authors: Syah A F , Ni’am A K , Jatisworo D
Published: October 2023

The fishery of skipjack tuna (Katsuwonus pelamis) was collected from the vessel monitoring system (VMS) as well as satellite oceanographic data for salinity, chlorophyll-a (chl-a) concentrations, and sea surface temperature (SST) used to determine the effects of oceanographic factors on potential fishing grounds for skipjack tuna in the western water of Sumatera (WWS). Salinity, chl-a and SST data were downloaded from the INDESO project website. The relationship between these parameters and the potential skipjack fishing area was analyzed using a maximum entropy (maxent) model. The Maxent model demonstrated its potential to predict the spatial distribution of skipjack, expressed as the area under the 0.852 curve value. In addition, jackknife test results indicate that the spatial pattern of fishery potential was influenced mainly by chl-a (0.50), followed by salinity (0.43) and SST (0.10). The integration of multi-sensor remote sensing data and modelling methods provides an ingenious way to determine a potential skipjack catch in the western water of Sumatera.
Preliminary: biodiversity of plankton in Sawaibu Bay, Manokwari, Indonesia
Authors: Ayu I P , Iswantari A , Wulandari D Y , Pratiwi N T M , Sulaiman G S A , Subhan B , Arafat D , Rahmadya A , Himawan M R , Suhaemi
Published: October 2023

As a biological parameter of the aquatic ecosystem, plankton has various species and forms a specific community for each water. Plankton can characterize the water’s condition through its species richness. Both phytoplankton and zooplankton were observed in this research to determine the biodiversity. Plankton samples were collected using a plankton net from the surface water of Sawaibu Bay, Manokwari City, West Papua Province, Indonesia. Morphological identification is applied to approximate the plankton genera and count the diversity indices. Classes of Cyanophyceae, Bacillariophyceae, Dinophyceae, Chrysophyceae, Protozoa, and Crustaceae were found in Sawaibu Bay. Phytoplankton from the Bacillariophyceae group (30-90 x 102 cell/m3) and zooplankton from the Crustacean group (1.51-38.6 x 102 ind/m3) were high in abundance. Both phytoplankton and zooplankton’s evenness, dominance, and diversity index varied between stations. The biodiversity approach could be a snapshot of the aquatic ecosystem state.
The cavity perturbation method for evaluating hematocrit via dielectric properties
Authors: Kamel Abdulla A , Alawajji Raad A , Kannarpady Ganesh K
Published: October 2023

The physical parameters of human blood (complex permittivity and conductivity) at microwave frequencies have been investigated to assess the hematocrit (HCT). The cavity perturbation method based on a rectangular cavity operated in TE101 mode at frequency 4.212 GHz has been utilized to measure the permittivity of blood with different hematocrit % at a range of temperatures. According to the results, the dielectric constant, loss factor, and conductivity appeared to be influenced by HCT level. Though the dielectric constant is the only parameter that shows clear linear regression decreasing behavior with a correlation value around (R2 = 0.93). For thirty healthy donors the dielectric constant decreases from (65.61 ± 1.4 to 44.64 ± 4.0) and from (65.3 ± 1.2 to 48.3 ± 1.88) for men and women, respectively, with increasing hematocrit percentage from 20% HCT up to 95% HCT. The temperature dependence of the dielectric constant is also examined in the temperature range 27 °C–50 °C and the results display a slight decrease in dielectric constant with elevation temperature. The temperature-dependence dielectric constant of water and blood samples were fitted to an empirical polynomial with temperature. A comparison of estimated HCT using the cavity technique based on dielectric properties shows a very good agreement with commercially standard HCT measurement methods. Finally, the cavity technique can be applied to measure the hematocrit up to high values based on the dielectric constant with high precision, simplicity, and low cost compared with traditional techniques.
Time optimal quantum state transfer in a fully-connected quantum computer
Authors: Jameson Casey , Basyildiz Bora , Moore Daniel , Clark Kyle , Gong Zhexuan
Published: October 2023

The speed limit of quantum state transfer (QST) in a system of interacting particles is not only important for quantum information processing, but also directly linked to Lieb–Robinson-type bounds that are crucial for understanding various aspects of quantum many-body physics. For strongly long-range interacting systems such as a fully-connected quantum computer, such a speed limit is still unknown. Here we develop a new quantum brachistochrone method that can incorporate inequality constraints on the Hamiltonian. This method allows us to prove an exactly tight bound on the speed of QST on a subclass of Hamiltonians experimentally realizable by a fully-connected quantum computer.
Sliding mode controller design for unstable processes with dead time with a case study on continuous stirred tank reactor
Authors: Ali Mohammed Hasmat , Anwar Md Nishat
Published: October 2023

Unstable processes are difficult to control because one or more poles lie on the right-hand side of the s-plane. Control becomes further complicated by the presence of dead time in such systems. In this study, a sliding mode control (SMC) design is proposed for the control of unstable processes with dead time. To apply the SMC, a second order plus dead time (SOPDT) model of the unstable process is used, and a proportional-integral-derivative-acceleration type sliding surface is considered. The parameters of continuous and discontinuous control laws are obtained using the differential evolution optimization technique. The optimal control problem is solved by satisfying a new weighted bi-objective function constituting the performance index integral absolute error and control input total variation. The proposed control scheme has been satisfactorily extended to control unstable integrating and higher-order unstable processes with dead time by approximating them into the unstable SOPDT model. The efficacy of the suggested scheme has been evaluated on several benchmark unstable industrial chemical processes, including the continuous stirred tank reactor (CSTR). Further, this scheme has been compared with recently reported work, and the obtained results clearly demonstrate the effectiveness of the suggested controller.
Finding simplicity: unsupervised discovery of features, patterns, and order parameters via shift-invariant variational autoencoders
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Authors: Ziatdinov Maxim , Wong Chun Yin (Tommy) , Kalinin Sergei V
Published: October 2023

Recent advances in scanning tunneling and transmission electron microscopies (STM and STEM) have allowed routine generation of large volumes of imaging data containing information on the structure and functionality of materials. The experimental data sets contain signatures of long-range phenomena such as physical order parameter fields, polarization, and strain gradients in STEM, or standing electronic waves and carrier-mediated exchange interactions in STM, all superimposed onto scanning system distortions and gradual changes of contrast due to drift and/or mis-tilt effects. Correspondingly, while the human eye can readily identify certain patterns in the images such as lattice periodicities, repeating structural elements, or microstructures, their automatic extraction and classification are highly non-trivial and universal pathways to accomplish such analyses are absent. We pose that the most distinctive elements of the patterns observed in STM and (S)TEM images are similarity and (almost-) periodicity, behaviors stemming directly from the parsimony of elementary atomic structures, superimposed on the gradual changes reflective of order parameter distributions. However, the discovery of these elements via global Fourier methods is non-trivial due to variability and lack of ideal discrete translation symmetry. To address this problem, we explore the shift-invariant variational autoencoders (shift-VAEs) that allow disentangling characteristic repeating features in the images, their variations, and shifts that inevitably occur when randomly sampling the image space. Shift-VAEs balance the uncertainty in the position of the object of interest with the uncertainty in shape reconstruction. This approach is illustrated for model 1D data, and further extended to synthetic and experimental STM and STEM 2D data. We further introduce an approach for training shift-VAEs that allows finding the latent variables that comport to known physical behavior. In this specific case, the condition is that the latent variable maps should be smooth on the length scale of the atomic lattice (as expected for physical order parameters), but other conditions can be imposed. The opportunities and limitations of the shift VAE analysis for pattern discovery are elucidated.
Transmission at different scales
Authors: Wayne Marta L. , Bolker Benjamin M.
Published: October 2023

This chapter details the various ways disease can be transmitted between organisms. Respiratory viruses such as influenza are airborne; some pathogens such as HIV and hepatitis can be transmitted through bodily fluids; some infectious diseases, such as cholera, can survive in water; and still other pathogens have evolved to use other organisms, especially blood-sucking insects and mites, as vectors to travel from one host to another. The concepts of the encounter and compatibility filters describe the competition between hosts and pathogens to enhance or reduce the pathogen’s ability to move into new hosts (the encounter filter) and replicate within them (the compatibility filter). Mathematical models help understand how pathogens spread both among hosts and within individual hosts’ bodies. Virulence, resistance, and tolerance describe the pathogen and host factors that determine how badly pathogens will compromise an infected host’s health.
Writing the constitution
Authors: Loughlin Martin
Published: October 2023

This chapter reviews how scholars have written about the unwritten constitution. Claiming that an Anglo-Saxon state of liberty pre-dated the Norman conquest, some explain constitutional development through continuous antagonism between liberty and authority that eventually led to intense conflicts during the 17th century. These conflicts were subsequently transcended by adopting as a new legitimizing principle the ambiguous concept of the supremacy of the Crown-in-Parliament. Thereafter, constitutional scholars like Blackstone, Dicey, and Bagehot examined how this principle is tempered by conventional understandings. Since the 20th century, the authority of these understandings has been eroded following the rise of democracy and extension of government powers, generating pressure for the official codification of constitutional rules.
Parliamentary government
Authors: Loughlin Martin
Published: October 2023

This chapter examines the evolving role of Parliament in the British system of government. Formed by royal will, Parliament became an established institution due to monarchical necessity and, following the civil war, when it exerted its authority over the monarch, a system of parliamentary government was instituted. With the expansion of the franchise, the Commons acquired primacy over the Lords and with the growth of big government Parliament has ceded legislative initiative to the executive. Party mechanisms now control governmental operations, leaving Parliament with responsibility for holding government to account.
Whither the constitution?
Authors: Loughlin Martin
Published: October 2023

This chapter discusses the continuing trajectory of constitutional development. The British constitution blends all three of the Weberian sources of legitimacy: charismatic, traditional, and rational. What has been distinctive is the extent to which governmental power has been made accountable to the people through political practice rather than legal reconstitution. But these practices are now losing their authority and with this the traditional idea of a constitution is unable any longer to provide a coherent account of the nature of British government. The judiciary has been incrementally seeking to set in place a modern arrangement expressed as a framework of fundamental law, but the political tensions this gives rise to leaves the constitution in an unsettled state.
From France
Authors: Andrew Dudley
Published: October 2023

This chapter explores the origins of French cinema. It starts with the Lumière brothers, who became the epicentre of a global image exchange due to their compact, multifunctional cinématographe. Meanwhile Georges Méliès spearheaded the world’s first dedicated production studio, dipping into a repertoire of magic shows, music hall turns, and science fiction. At Gaumont studios, Alice Guy is the first influential woman in world cinema adapting and honing a narrative style. Staid dramas and adaptations of classics during La Belle Époque seem pretentious and banal compared to the comedies and especially the serials of Feuillade that excited the masses and the avant-garde alike. After World War I, experimental films became a niche mode financed by patrons of Paris’ modern art and dance scene while a flagging industry still produced several magnificent silent masterpieces just before 1930.
A legacy, disputed and renewed
Authors: Andrew Dudley
Published: October 2023

This chapter covers the legacy of French cinema since the New Wave. Paradoxically, this national cinema is most celebrated for its disenchantment with a national synthesis. Unruly filmmakers often challenge the good taste and high-mindedness of French culture, especially in works labelled “extreme cinema” where violence and eroticism become corrosive. French art cinema has increasingly profited from outsiders, such as Abdellatif Kechiche who drew on his Tunisian background to produce La Graine et le mulet (2007). Once in the industry he further disrupted norms in Blue is the Warmest Color. Today several female directors bring a new sensibility to issues not just of gender but of race and ethnicity. Healthy for French society, this also expands cinema’s capabilities and ambitions. The chapter clarifies that French national cinema can never be stable nor achieve a synthesis, ethnic or otherwise; so it needs to be constantly refreshed. It does so most distinctively in filmmakers with New Wave roots, such as Claire Denis, Arnaud Desplechin, and Olivier Assayas, whose Clouds of Sils Maria (2014) demonstrates that genuine cinema is not a spectacle but a search for the truth following traces of the real. Genuine cinema still can surprise us.
What is imagination?
Authors: Gosetti-Ferencei Jennifer
Published: October 2023

This chapter introduces the history of the concept of imagination within philosophy, the human sciences, and literary theory. It shows how imagination allows escape from ordinary life while also illuminating possibilities with which we can engage reality. While imagination has been revered for its expansion of human life and its contributions to human achievement, imagination has also been blamed for disrupting our grasp or perception of reality. In this context, this chapter explains how imagination both departs from reality and affords the expression of new ideas and their subsequent integration into the world we experience. It demonstrates how we can best understand imagining as operating in multiple modes: inner imaging, pretence, hypothetical or counterfactual thinking, concrete imagining, and creativity.
Imagination in human evolution
Authors: Gosetti-Ferencei Jennifer
Published: October 2023

This chapter explores the influence of imagination in human evolution and its role in the emergence of human culture. It explains how approaching imagination as an evolved dimension of human consciousness requires complementing philosophical understanding with insights from other disciplines. Human cognitive evolution saw the emergence of people’s capacity for ‘seeing-as’ alongside inner representation and hypothetical thinking. From a modern perspective, prehistoric artefacts such as cave paintings, sculptures, and toys appear to express the raw vitality of early human imagination. The chapter highlights how imagination has allowed human beings to amplify, transform, and expressively reflect on their experiences of living while also enabling a symbolic humanization of the world.
Creativity from invention to wonder
Authors: Gosetti-Ferencei Jennifer
Published: October 2023

This chapter considers creativity as a means of negotiating reality through imagination, demonstrating how multiple modes of imagining are involved in creative thought and practice, and how creativity has in recent decades been recognized as drawing on fundamental processes of cognition. While ordinary cognition may involve creative resources, the exquisite or special creativity that can emerge in artistic, playful, and inventive thinking may diverge from ordinary cognitive habits. Drawing on aesthetic theory, this chapter discusses how cognitive play allows diversion from habitual paths of thinking while what Keats called negative capability and what art theorists describe as defamiliarization can foster wonder and tolerance for the not yet fully understood, making way for new ideas. This chapter engages examples from the mathematician and inventor Archimedes, poets Wordsworth, Yeats, and Ovid, painters Breughel and da Vinci, the Nazca geoglyphs, the music of Stravinsky, and jazz. In conclusion this chapter considers the contribution of creativity to human innovation and human happiness.
JEasyTFM: an open-source software package for the analysis of large 2D TFM data within ImageJ
Authors: Carl Philippe , Rondé Philippe
Published: October 2023

Motivation

Cells adhering to the extracellular matrix can sense and respond to a wide variety of chemical and physical features of the adhesive surface. Traction force microscopy (TFM) allows determining the tensile forces exerted by the cells on their substrate with high resolution.

Results

To allow broad access of this techniques to cell biology laboratories we developed JeasyTFM, an open-source ImageJ package able to process multi-color and multi-position time-lapse pictures thus suitable for the automatic analysis of large TFM data.

Availability and implementation

JEasyTFM is implemented as an ImageJ plugin and available at: http://questpharma.u-strasbg.fr/JEasyTFM.html.
An automated model annotation system (AMAS) for SBML models
Authors: Shin Woosub , Gennari John H , Hellerstein Joseph L , Sauro Herbert M
Published: October 2023

Motivation

Annotations of biochemical models provide details of chemical species, documentation of chemical reactions, and other essential information. Unfortunately, the vast majority of biochemical models have few, if any, annotations, or the annotations provide insufficient detail to understand the limitations of the model. The quality and quantity of annotations can be improved by developing tools that recommend annotations. For example, recommender tools have been developed for annotations of genes. Although annotating genes is conceptually similar to annotating biochemical models, there are important technical differences that make it difficult to directly apply this prior work.

Results

We present AMAS, a system that predicts annotations for elements of models represented in the Systems Biology Markup Language (SBML) community standard. We provide a general framework for predicting model annotations for a query element based on a database of annotated reference elements and a match score function that calculates the similarity between the query element and reference elements. The framework is instantiated to specific element types (e.g. species, reactions) by specifying the reference database (e.g. ChEBI for species) and the match score function (e.g. string similarity). We analyze the computational efficiency and prediction quality of AMAS for species and reactions in BiGG and BioModels and find that it has subsecond response times and accuracy between 80% and 95% depending on specifics of what is predicted. We have incorporated AMAS into an open-source, pip-installable Python package that can run as a command-line tool that predicts and adds annotations to species and reactions to an SBML model.

Availability and implementation

Our project is hosted at https://github.com/sys-bio/AMAS, where we provide examples, documentation, and source code files. Our source code is licensed under the MIT open-source license.
The open abdomen in trauma, acute care, and vascular and endovascular surgery: comprehensive, expert, narrative review
Authors: Roberts Derek J , Leppäniemi Ari , Tolonen Matti , Mentula Panu , Björck Martin , Kirkpatrick Andrew W , Sugrue Michael , Pereira Bruno M , Petersson Ulf , Coccolini Federico , Latifi Rifat
Published: October 2023

Background

The open abdomen is an innovation that greatly improved surgical understanding of damage control, temporary abdominal closure, staged abdominal reconstruction, viscera and enteric fistula care, and abdominal wall reconstruction. This article provides an evidence-informed, expert, comprehensive narrative review of the open abdomen in trauma, acute care, and vascular and endovascular surgery.

Methods

A group of 12 international trauma, acute care, and vascular and endovascular surgery experts were invited to review current literature and important concepts surrounding the open abdomen.

Results

The open abdomen may be classified using validated systems developed by a working group in 2009 and modified by the World Society of the Abdominal Compartment Syndrome—The Abdominal Compartment Society in 2013. It may be indicated in major trauma, intra-abdominal sepsis, vascular surgical emergencies, and severe acute pancreatitis; to facilitate second look laparotomy or avoid or treat abdominal compartment syndrome; and when the abdominal wall cannot be safely closed. Temporary abdominal closure and staged abdominal reconstruction methods include a mesh/sheet, transabdominal wall dynamic fascial traction, negative pressure wound therapy, and hybrid negative pressure wound therapy and dynamic fascial traction. This last method likely has the highest primary fascial closure rates. Direct peritoneal resuscitation is currently an experimental strategy developed to improve primary fascial closure rates and reduce complications in those with an open abdomen. Primary fascial closure rates may be improved by early return to the operating room; limiting use of crystalloid fluids during the surgical interval; and preventing and/or treating intra-abdominal hypertension, enteric fistulae, and intra-abdominal collections after surgery. The majority of failures of primary fascial closure and enteroatmospheric fistula formation may be prevented using effective temporary abdominal closure techniques, providing appropriate resuscitation fluids and nutritional support, and closing the abdomen as early as possible.

Conclusion

Subsequent stages of the innovation of the open abdomen will likely involve the design and conduct of prospective studies to evaluate appropriate indications for its use and effectiveness and safety of the above components of open abdomen management.
Patient-reported outcome measures and surgery for Crohn’s disease: systematic review
Authors: Kim Whei J , Iskandarani Mohamad , Manzo Carlo A , Pellino Gianluca , Gallostra Marc Martí , Tekkis Paris P , Celentano Valerio , Kontovounisios Christos
Published: October 2023

Background/Aims

Crohn’s disease is an inflammatory bowel disease with up to 50 per cent of patients requiring surgery within 10 years of diagnosis. Patient-reported outcome measures (PROMs) are vital to monitor and assess patient health-related quality of life (HRQoL). This systematic review aims to evaluate PROMs within studies for perioperative Crohn's disease patients.

Methods

Articles from MEDLINE, Embase, Emcare and CINAHL databases were searched to find studies relating to the assessment of HRQoL in perioperative Crohn's disease patients using PROMs and patient-reported experience measures (PREMs) from 1st January 2015 to 22nd October 2023. Bias was assessed using the ROBINS-I tool was used for non-randomized interventional studies and the Cochrane RoB2 tool was used for randomized trials.

Results

1714 journal articles were filtered down to eight studies. Six studies focused on ileocaecal resection, one on perianal fistulas and one on the effects of cholecystectomy on patients with Crohn's disease. Within these articles, ten different PROM tools were identified (8 measures of HRQoL and 2 measures of functional outcome). Overall improvements in patient HRQoL pre- to postoperative for ileocaecal Crohn's disease were found in both paediatric and adult patients. Outcomes were comparable in patients in remission, with or without stoma, but were worse in patients with a stoma and active disease.

Conclusion

There are significant variations in how PROMs are used to evaluate perioperative Crohn's disease outcomes and a need for consensus on how tools are used. Routine assessments using an internationally accepted online platform can be used to monitor patients and support areas of treatment pathways that require further support to ensure high standards of care. They also enable future statistical comparisons in quantitative reviews and meta-analyses.
Lesion network mapping of eye-opening apraxia
Authors: Zarifkar Pardis , Shaff Nicholas A , Nersesjan Vardan , Mayer Andrew R , Ryman Sephira , Kondziella Daniel
Published: October 2023

Apraxia of eyelid opening (or eye-opening apraxia) is characterized by the inability to voluntarily open the eyes because of impaired supranuclear control. Here, we examined the neural substrates implicated in eye-opening apraxia through lesion network mapping. We analysed brain lesions from 27 eye-opening apraxia stroke patients and compared them with lesions from 20 aphasia and 45 hemiballismus patients serving as controls. Lesions were mapped onto a standard brain atlas using resting-state functional MRI data derived from 966 healthy adults in the Harvard Dataverse. Our analyses revealed that most eye-opening apraxia-associated lesions occurred in the right hemisphere, with subcortical or mixed cortical/subcortical involvement. Despite their anatomical heterogeneity, these lesions functionally converged on the bilateral dorsal anterior and posterior insula. The functional connectivity map for eye-opening apraxia was distinct from those for aphasia and hemiballismus. Hemiballismus lesions predominantly mapped onto the putamen, particularly the posterolateral region, while aphasia lesions were localized to language-processing regions, primarily within the frontal operculum. In summary, in patients with eye-opening apraxia, disruptions in the dorsal anterior and posterior insula may compromise their capacity to initiate the appropriate eyelid-opening response to relevant interoceptive and exteroceptive stimuli, implicating a complex interplay between salience detection and motor execution.
Molecular characteristics of circulating B cells and kidney cells at the single-cell level in special types of primary membranous nephropathy
Authors: Feng Xiaoqian , Chen Qilin , Zhong Jinjie , Yu Sijie , Wang Yue , Jiang Yaru , Wan Junli , Li Longfei , Jiang Huimin , Peng Liping , Wang Anshuo , Zhang Gaofu , Wang Mo , Yang Haiping , Li Qiu
Published: October 2023

Background

Although primary membranous nephropathy (pMN) associated with podocyte autoantibodies (POS) is becoming well-known, the molecular characteristics of the specific type of pMN that is negative for podocyte autoantibodies (NEG) is still unclear.

Methods

We performed single-cell transcriptome sequencing and single-cell B cell receptor sequencing on circulating CD19+ cells and kidney cells of a NEG paediatric patient with pMN. The single-cell datasets of POS patients and healthy control individuals were included for integrative analysis.

Results

The gene expression characteristics and clonal expansion of naïve and memory B cells in the NEG patient changed significantly. We found that a group of CD38+ naïve B cells expanded in the NEG patient, which had the functional characteristics of cell activation. In addition, the conversion between immunoglobulin M (IgM)/IgD and IgG1 in the NEG patient was increased. Parietal epithelial cells (PECs) and podocytes shared similar signature genes (WT1, CLIC5), and new candidate marker genes for PECs, such as NID2, CAV1 and THY1, might contribute to the definition of cell subsets. PECs might have undergone significant changes in the disease, mainly manifested by changes in the expression of CCN2, PLAAT4 and SEPTIN2. The scores of gene sets related to extracellular matrix, cell adhesion and calcium channel in podocytes of the NEG patient was significantly increased. The gene expression of sodium transporter in a group of proximal tubule cells in the disease was significantly increased, especially SLC5A12, which might be related to the oedema of patients.

Conclusions

Our research demonstrated the cell type–specific molecular features in the circulation and kidney of the NEG pMN patient.
Should we enlarge the indication for kidney biopsy in patients with diabetes? The pro part
Authors: Gesualdo Loreto , Fiorentino Marco , Conserva Francesca , Pontrelli Paola
Published: October 2023

Diabetic nephropathy (DN) and non-diabetic renal diseases (NDRD) represent intricate challenges in diagnosis and treatment within the context of the global diabetes epidemic. As the prevalence of diabetes continues to escalate, effective management of renal complications becomes paramount. Recent advancements in comprehending the multifaceted nature of renal damage, fueled by insights from histopathological investigations, offer unprecedented prospects for refining diagnostic strategies and customizing therapeutic interventions. Renal biopsies have emerged as indispensable tools for unraveling the diverse phenotypes of renal damage in diabetes. The pioneering study by Mazzucco identified three classes of renal damage in type 2 diabetes patients: classical diabetic glomerulosclerosis (DN), vascular and ischemic glomerular changes (NDRD), and other glomerulonephritides in the presence (DN + NDRD, mixed forms) or absence of DN (NDRD). The prevalence of these classes varies widely in published studies, influenced by factors such as ethnicity, geography and selection criteria for renal biopsy. Moreover, the international Renal Pathology Society consensus classification system has stratified the classical diabetic nephropathy into progressive categories of renal impairment, a breakthrough that aids in prognostication. Histopathological scrutiny, particularly the intricate correlation between glomerular and tubulointerstitial lesions, contributes profoundly to enhancing our grasp of the phenotype's heterogeneity. This amplified comprehension holds the potential to steer personalized treatment strategies. Cutting-edge interventions, encompassing sodium-glucose cotransporter 2 inhibitors, mineralocorticoid receptor antagonists and anti-endothelin receptor agents, are broadening the arsenal against renal injury in diabetes. When combined with the profound insights garnered from histopathological, omics, imaging and clinical data, these therapeutic avenues promise a transformative shift towards precision-driven care paradigms. Collaborative efforts uniting researchers, clinicians and patients are indispensable for propelling our knowledge of diabetic renal damage and ameliorating patient outcomes. The fusion of histopathological, omics and imaging findings into clinical decision-making harbors the potential to customize interventions and optimize care for individuals grappling with diabetes-associated renal complications. Furthermore, groundbreaking initiatives like the iBeat Study within the BEAt-DKD (Biomarker Enterprise to Attack Diabetic Kidney Disease) project (https://www.beat-dkd.eu/), elucidating distinct phenotypes of renal damage within diabetes, underscore the imperative necessity of integrating histopathological data into the broader framework of diabetic renal management.
Thiopurine Exposure During Pregnancy is Not Associated With Anemia in Infants Born to Mothers With IBD
Authors: Yeaman Fiona , Stritzke Amelie , Kuret Verena , Sharifi Nastaran , Seow Cynthia H , Metcalfe Amy , Leung Yvette
Published: October 2023

Background

Thiopurines are commonly used to treat inflammatory bowel disease (IBD). Thiopurines are considered safe throughout pregnancy. However, a published study suggested the risk of neonatal anemia was increased if exposed to thiopurines in utero. This prospective cohort study aimed to determine if there is an increased risk of cytopenia among infants born to pregnant people with IBD, exposed or unexposed to thiopurines, compared to infants born to those without IBD.

Methods

Pregnant IBD patients, with and without thiopurine exposure, and one cohort of control individuals were recruited over a 5-year period. Consenting individuals completed a questionnaire and infants had a complete blood cell count at the newborn heel prick. Anemia was defined as hemoglobin (Hb) < 140g/L. Descriptive statistics were used to characterize the study population. Fisher exact tests were used to examine differences in outcomes between groups, a P-value of < 0.05 was deemed significant.

Results

Three cohorts were recruited: 19 IBD patients on thiopurines, 50 IBD patients not on thiopurines, and 37 controls (total of 106). Neonatal median Hb was not different with 177g/L (IQR 38g/L) for the IBD thiopurine group, 180.5g/L (IQR 40g/L) for the IBD non-thiopurine group, and 181g/L (IQR 37g/L) for the controls. Nineteen infants (18%) were cytopenic with 12 (11%) anemic, 6 (5.6%) thrombocytopenic, and 1 (0.94%) lymphopenic. Thiopurine exposure was only in one, mildly anemic, infant.

Conclusions

These findings further support physicians and IBD patients contemplating pregnancy that current guidelines recommending thiopurine adherence do not lead to increased perinatal risk of anemia or cytopenia.
Automatic measurements of left ventricular volumes and ejection fraction by artificial intelligence: clinical validation in real time and large databases
Authors: Olaisen Sindre , Smistad Erik , Espeland Torvald , Hu Jieyu , Pasdeloup David , Østvik Andreas , Aakhus Svend , Rösner Assami , Malm Siri , Stylidis Michael , Holte Espen , Grenne Bjørnar , Løvstakken Lasse , Dalen Havard
Published: October 2023

Aims

Echocardiography is a cornerstone in cardiac imaging, and left ventricular (LV) ejection fraction (EF) is a key parameter for patient management. Recent advances in artificial intelligence (AI) have enabled fully automatic measurements of LV volumes and EF both during scanning and in stored recordings. The aim of this study was to evaluate the impact of implementing AI measurements on acquisition and processing time and test–retest reproducibility compared with standard clinical workflow, as well as to study the agreement with reference in large internal and external databases.

Methods and results

Fully automatic measurements of LV volumes and EF by a novel AI software were compared with manual measurements in the following clinical scenarios: (i) in real time use during scanning of 50 consecutive patients, (ii) in 40 subjects with repeated echocardiographic examinations and manual measurements by 4 readers, and (iii) in large internal and external research databases of 1881 and 849 subjects, respectively. Real-time AI measurements significantly reduced the total acquisition and processing time by 77% (median 5.3 min, P < 0.001) compared with standard clinical workflow. Test–retest reproducibility of AI measurements was superior in inter-observer scenarios and non-inferior in intra-observer scenarios. AI measurements showed good agreement with reference measurements both in real time and in large research databases.

Conclusion

The software reduced the time taken to perform and volumetrically analyse routine echocardiograms without a decrease in accuracy compared with experts.
Non-steroidal anti-inflammatory drugs and risk of pulmonary embolism in patients with inflammatory joint disease—results from the nationwide Norwegian Cardio-rheuma registry
Authors: Ikdahl Eirik , Rollefstad Silvia , Kazemi Amirhossein , Provan Sella A , Larsen Trine-Lise , Semb Anne Grete
Published: October 2023

Aims

Patients with inflammatory joint diseases (IJD), including rheumatoid arthritis (RA), psoriatic arthritis (PsA), and axial spondyloarthritis (axSpA) have increased rates of pulmonary embolism (PE). Non-steroidal anti-inflammatory drugs (NSAIDs) use is associated with PE in the general population. Our aim was to evaluate the association between NSAIDs use and PE in IJD patients.

Methods and results

Using individual-level registry data from the whole Norwegian population, including data from the Norwegian Patient Registry and the Norwegian Prescription Database, we: (1) evaluated PE risk in IJD compared to non-IJD individuals, (2) applied the self-controlled case series method to evaluate if PE risks were associated with use of traditional NSAIDs (tNSAIDs) and selective cox-2 inhibitors (coxibs). After a one-year wash-out period, we followed 4 660 475 adults, including 74 001 with IJD (RA: 39 050, PsA: 20 803, and axSpA: 18 591) for a median of 9.0 years. Crude PE incidence rates per 1000 patient years were 2.02 in IJD and 1.01 in non-IJD individuals. Age and sex adjusted hazard ratios for PE events were 1.57 for IJD patients compared to non-IJD. Incidence rate ratios (IRR) [95% confidence interval (CI)] for PE during tNSAIDs use were 0.78 (0.64–0.94, P = 0.010) in IJD and 1.68 (1.61–1.76, P < 0.001) in non-IJD. IRR (95% CI) for PE during coxibs use was 1.75 (1.10–2.79, P = 0.018) in IJD and 2.80 (2.47–3.18, P < 0.001) for non-IJD.

Conclusion

Pulmonary embolism rates appeared to be higher in IJD than among non-IJD subjects in our study. Traditional NSAIDs may protect against PE in IJD patients, while coxibs may associated with increased PE risk.