bluuebunny/crossref_metadata_2025 huggingface dataset:
Enigmatic Foot Marks on the Serpentinite Shabtis of King Senkamanisken
Authors: Howley Kathryn
Published: December 2024

The 1,277 faience and serpentinite shabtis of the Middle Napatan period Kushite king Senkamanisken (c. 640–620 BCE) are famed as the greatest number of shabtis known from a single tomb in either Egypt or Nubia. A peculiarity and as-yet unexplained feature of the corpus is that approximately two-thirds of the serpentinite figurines are inscribed on their base with signs based on Egyptian hieroglyphic characters. Previous discussion of the foot marks has tentatively suggested (among other interpretations) a magical explanation for the practice, but analyses have remained superficial and struggle to find patterns between hundreds of handmade figurines, while failing to put the foot marks in the context of other similar marking systems in wide use in Egypt.
This paper is based on a thorough stylistic analysis of the extant serpentinite Senkamanisken shabtis in Boston, Khartoum, and London. I argue that particular foot marks are linked with certain stylistic features, and that the most likely explanation for the marks is therefore that they are craftsman or workshop marks. Moreover, when the practice of foot marks is put into the context of other nontextual marking systems used in Egypt, it seems likely that Senkama- nisken’s shabtis were imported from Egypt and not locally manufactured in Nubia. This has important consequences for our understanding of trade and contact between Egypt and Nubia during the mid-first millennium BCE.
يشتهر 1277 تمثال أوشابتي من القيشاني والسربنتينيت للملك الكوشي سنكامانسكن (حوالي 640-620 قبل الميلاد) من العصر النبتي الأوسط باعتبارها أكبر عدد معروف لتماثيل أوشابتي من مقبرة واحدة في مصر أو النوبة. من بين الخصائص المستغربة والسمات التي لم يتم تفسيرها حتى الآن لهذه المجموعة من التماثيل الصغيرة أن ما يقرب من ثلثي هذه التماثيل المصنوعة من صخر السربنتينيت نُقشت على قاعدتها علامات مستمدة من العلامات الهيروغليفية المصرية. اقترحت الدراسات السابقة بشأن علامات القدم مبدئ ًيا (ضمن تفسيرات أخرى) تفس ًيرا سحريًا لهذه الممارسة، ومع ذلك فقد ظلت هذه التفسيرات سطحية وتسعى جاهدة لإيجاد أنماط مشابهة بين مئات التماثيل الصغيرة المصنوعة
يدويًا، وقد فشلت في وضع علامات القدم في سياق النظم المماثلة الأخرى لوضع العلامات المستخدمة على نطاق واسع في مصر القديمة. يعتمد هذا المقال على تحليل نمطي شامل لتماثيل أوشابتي الملك سنكامانسكن المصنوعة من صخر السربنتينيت والموجودة في بوسطن والخرطوم ولندن. أزعم في هذا المقال أن علامات قدم معينة ترتبط بسمات أسلوبية معينة، وأن التفسير الأرجح لهذه العلامات هو أنها علامات حرفيين أو ورش عمل. علاوة على ذلك فعندما يتم وضع ممارسة علامات القدم في سياق نظم وضع العلامات غير النصية الأخرى المستخدمة في مصر، يبدو على الأرجح أن تماثيل أوشابتي الملك سنكامانسكن قد تم استيرادها من مصر ولم تُصنع محل ًيا في النوبة. ولهذا عواقب مهمة تتعلق
بفهمنا للتجارة والاتصال بين مصر والنوبة في منتصف الألفية الأولى قبل الميلاد.
Polygamy in the Middle Kingdom
Authors: McCorquodale Kim
Published: December 2024

This paper examines potential instances of polygamy amongst the high officials during the Middle Kingdom Period, by examining evidence from their tombs. Iconographic and inscriptional material offers the ability to document several men who had more than one wife at the same time. Due to the introduction of the term mAat xrw, “justified,” we can more easily distinguish between deceased and living wives and determine those men who were married to more than one wife at the same time. Originally, polygamy was only practised by ruling kings but in the late Old Kingdom, a small number of high officials seem to have practised polygamy. The early Middle Kingdom provincial governors built and decorated large tombs in the provinces, some of them leaving evidence of concurrent wives. Some of the possible reasons some of the highest officials were polygamists during the Middle Kingdom are also discussed.
يتناول هذا المقال الحالات المحتملة لتعدد الزوجات بين كبار المسؤولين خلال عصر الدولة الوسطى من خلال دراسة الأدلة المتاحة في مقابرهم. تسجل الآثار التي تحمل مناظر وكتابات العديد من الرجال الذين كان من المحتمل لديهم أكثر من زوجة في نفس الوقت. فبفضل إدخال لقب «ماعت خرو» (صادقة الصوت أو المبرأة) يمكننا التمييز بسهولة أكبر بين الزوجات المتوفيات والأحياء والتعرف على الرجال الذين كانوا متزوجين من أكثر من امرأة في نفس الوقت. كان تعدد الزوجات في الأصل ممارسة تقتصر على الملوك الحاكمين، ولكن في أواخر عصر الدولة القديمة يبدو أن عد ادا قلي الا من كبار المسؤولين قد مارسوا تعدد الزوجات. قام حكام الأقاليم في أوائل عصر الدولة الوسطى ببناء وزخرفة مقابر كبيرة لهم في الأقاليم، نجد في بعض هذه المقابر أدلة على وجود زوجات متزامنات لرجل واحد. يناقش المقال أي اضا بعض الأسباب المحتملة لقيام بعض كبار
المسؤولين بممارسة تعدد الزوجات في عصر الدولة الوسطى.
Portrait Shabti for a Libyan General of the Saite Dynasty
Authors: Thompson David
Published: December 2024

There are no inscriptions on the remains of Ankhwahibresaneith’s tomb complex at Saqqara, but his title and three generations of his family are named on the distinctive shabtis that were left in it by looters. This paper describes one of his shabtis, and identifies Ankhwahibresaneith as one of the elite Libyan warriors who served in the Egyptian armies of the 26th Dynasty, in this instance probably in that of Psamtik I.
لا توجد نقوش على بقايا مجمع مقبرة عنخ-واح-إيب-رع-سا-نيت في سقارة، ومع ذلك فإن لقبه وأسماء ثلاثة أجيال من عائلته مذكورة على تماثيل الأوشابتي المميزة التي تركها لصوص الآثار فيها. يصف هذا المقال واح ًدا من تماثيل الأوشابتي هذه ويتعرف على عنخ-واح-إيب-رع- سا-نيت بصفته أحد نخبة المحاربين الليبيين الذين خدموا في الجيوش المصرية في عصر الأسرة 62، وربما في جيش الملك بسماتيك الأول على

وجه التحديد
Front Matter
Authors: Editors
Published: December 2024

Table of Contents
Charles C. Van Siclen III
Authors: Scott Gerry D.
Published: December 2024

Obituary for Charles C. Van Siclen III
Review of Mohamed Abuel-Yazid, The Tomb of the Mayor of Athribis
Authors: Zhang Lingxin
Published: December 2024

Mohamed Abuel-Yazid. The Tomb of the Mayor of Athribis. Athribis-Studien 1 (Wiesbaden: Harrassowitz Verlag, 2023). ISBN 978-3-447-12071-5. Pp. xiii + 274, 54 black and white illustrations, and 81 color plates. €128.00
Review of Aleksandra Hallmann, Ancient Egyptian Clothing: Studies in Late Period Private Representations
Authors: Bianchi Robert Steven
Published: December 2024

Aleksandra Hallmann, Ancient Egyptian Clothing: Studies in Late Period Private Representations, 2 vols. Harvard Egyptological Studies 20 (Leiden/Boston: Brill, 2023). Vols. 1 and 2. ISBN 978-900451300. Pp. clvii + 1,219, 447 pages of illustrations, most of which are in color. $459.00
Review of Tara Prakash, Ancient Egyptian Prisoner Statues: Fragments of the Late Old Kingdom
Authors: Mourad Anna-Latifa
Published: December 2024

Tara Prakash. Ancient Egyptian Prisoner Statues: Fragments of the Late Old Kingdom. Material and Visual Culture of Ancient Egypt 8 (Columbus: Lockwood Press, 2022). ISBN 978- 1-948488-87-7. Pp. xvi + 219, 89 illustrations, online content. $99.00
Review of Nasser Rabbat, Writing Egypt: Al-Maqrizi and His Historical Project
Authors: Ducène Jean-Charles
Published: December 2024

Nasser Rabbat. Writing Egypt: Al-Maqrizi and His Historical Project (Edinburgh: Edinburgh University Press, 2023). ISBN 978-1-3995-0281-8. Pp. 337. $125.00
Review of Thomas Schneider, Language Contact in Ancient Egypt
Authors: Cooper Julien
Published: December 2024

Thomas Schneider. Language Contact in Ancient Egypt. Einführungen und Quellentexte zur Ägyptologie 16 (Münster: Lit Verlag, 2023). ISBN 978-3-643-91507-8. Pp. 248, 7 tables, 4 maps. €24.90
Efectos de la estabilidad laboral en la motivación de los trabajadores de la Dirección Distrital 13D01 Portoviejo Manabí MTOP
Authors: Cedeño Fernández Mauro L
Published: December 2024

Se tiene el objetivo de analizar los efectos de la estabilidad laboral en la motivación de los trabajadores de la Direccion Distrital 13D01 Portoviejo Manabí MTOP. La investigación presentó un diseño mixto, un tipo de estudio descriptivo, de campo y documental y se utilizó una encuesta aplicada a una muestra de 72 servidores. Los resultados indicaron que la falta de estabilidad laboral tiene un impacto directo en la motivación laboral, provocando los siguientes efectos: frustración, disminución de la productividad, aumento del ausentismo y alta rotación de personal. En conclusión, es preciso que se mejoren las políticas de estabilidad de la institución y se presenten programa de motivación.
Medios de vida y desarrollo local en el recinto San Vicente de Macul del cantón El Empalme: un análisis desde la teoría de capitales
Authors: Bajaña Vera Ludy Dayana , Torres Navarrete Rumania Alexandra , Cevallos Mayorga Kimberlyn Yomira , Berenice Jurley Kaiser Flores
Published: December 2024

El presente trabajo de investigación tiene como objetivo evaluar los medios de vida a través de la Teoría de capitales y cómo influyen en el desarrollo local del recinto San Vicente de Macul del cantón El Empalme, Se trabajó con una población de 75 familias, donde se encuestaron a los jefes de hogar  y se empleó la teoría de los capitales donde en el capital humano el mayor promedio de edad en 55,09%, 44,44% delas familias encuestadas poseen educación primaria y el 77% de los hombre que viven en las finca trabajan. En cuanto al capital social la etnia más representativa son los montubios con el 67,78%, y solo el 20% de los encuestados pertenecen a una asociación de productores. En el capital natural el área promedio total de fincas es de 8,84 ha, los principales cultivos son: cacao nacional, cacao CCN51, plátano, cítricos, café y maíz. Para el capital financiero el 63,89% tienen acceso a créditos, el 54,44% de los encuestados no posee deudas y al 65,01% si les alcanzan los ingresos para pagar sus deudas. Por último, el capital físico el 79,26% poseen escrituras, el 82% manifiestan que el camino de acceso a la finca es de lastre, el 81.1% poseen vehículo y el 66% poseen moto guadaña. La distancia de la finca al pueblo más cercano es de 30 minutos en promedio. En conclusión, la alta tasa de analfabetismo y la inseguridad requieren atención inmediata, con la alfabetización y la seguridad como pilares fundamentales para mejorar la calidad de vida de la comunidad.
Contribution of Hand Eye Coordination and Arm Muscle Strength to Volleyball Serving Ability
Authors: Nugraha Jaka Setia , Handayani Widya , Lestari Hikmah
Published: December 2024

The aim of the research is to find out whether there is a contribution between the eyes and arms and arm muscle strength on the ability of the upper body in the sport of volleyball among students at SMA 08 Oku. Correlation research method with quantitative enhancement. The samples are X.1 and Data collection techniques are tests and documentation. The data analysis techniques are normality test, multiple linear correlation, T test and F test. The results of the correlation research for X1 and Y produced a figure of 0.892, while X2 and Y produced a figure of 0.892. For the F test, Fcount (86.470) > Ftable (3.555) and the significant p-value < 0.05, namely 0.000. So it is concluded that Ho is rejected, this means that push-ups and wrist flexibility affect the volleyball serve.
The Influence of Learning Methods and Learning Motivation on the Learning Outcomes of Basketball
Authors: Prasetya Agung , Wardiah Dessy , Junaidi Ilham Arvan
Published: December 2024

The aim of this study was to investigate the impact of learning methods and motivation on basketball performance outcomes among eighth-grade students at SMP Negeri 07 Mukomuko. The research employed a quasi-experimental design to evaluate student motivation using descriptive and qualitative analysis, while basketball performance was assessed through quantitative analysis. The study population included 109 students enrolled in basketball classes at SMP Negeri 07 Mukomuko. The sample was 43 students. Data on learning motivation were gathered through questionnaires, and skill tests were used to evaluate learning outcomes. Data analysis was conducted using two-way analysis of variance (ANOVA) and the Tukey test. Prior to performing variance analysis, prerequisite tests were conducted to check for normality using the Lilliefors test and variance homogeneity using the Bartlett test, with a significance level set at α = 0.05. The results state that the inquiry teaching learning method is more effective in improving basketball playing skills than the peer teaching learning method. The group with a high level of motivation had better basketball playing skills compared to the group with a low level of motivation. There is an interaction between learning methods and learning motivation on improving basketball playing skills.
The Impact of Arm Muscle Explosive Strength and Hand-Eye Coordination on Smash Performance Among Players at the Tulung Selapan Badminton Union Club
Authors: Antoni Antoni , Lanos Muhsana El Cintami , Rizhardi Rury
Published: December 2024

This study aims to evaluate the impact of arm muscle explosive strength and hand-eye coordination on smash performance among players at the Tulung Selapan Badminton Union Club. The research employs a quantitative method with a correlational approach. The study population and sample consist of 20 participants from the Tulung Selapan Badminton Union Club. Data collection was carried out using tests, and data analysis was performed through simple and multiple regression tests using the F-test formula. The findings of this study are 1) Arm muscle explosive strength has a significant impact on smash performance; 2) Hand-eye coordination also significantly affects smash performance; 3) Both arm muscle explosive strength and hand-eye coordination together have a significant impact on smash performance.
Estilos de aprendizaje Visual, Auditivo y Kinestésico: ¿mito o realidad? Implicaciones para la práctica docente
Authors: Arellano Gualle Patricia del Carmen , Saldaña Sigcha Mayra Jeanneth , Azuero Granda Ángel Benigno , Zavala Verdezoto Jesús Amado , Zavala Camargo Priscila Lisbeth
Published: December 2024

El presente estudio tiene como objetivo analizar la persistencia de los estilos de aprendizaje VAK en el ámbito educativo, específicamente en la Unidad Educativa Liceo Naval Quito. Se cuestionó la persistencia del mito o realidad de los estilos de aprendizaje VAK en el ámbito educativo. A través de un análisis de las prácticas docentes, se evidencia la necesidad de revisar y actualizar las concepciones sobre el aprendizaje. A diferencia de la perspectiva de los estilos de aprendizaje VAK, autores como Hart (1983) y Ribeiro (2000, 2019) proponen una visión más integral del aprendizaje, considerando las capacidades auditivas, visuales y kinestésicas como canales de información que utilizamos de manera flexible según las demandas de cada tarea. Esta perspectiva se alinea con los hallazgos de Pashler et al. (2009), quienes demostraron que los estilos de aprendizaje son construcciones poco estables y varían según el contexto, cuestionando así la utilidad del modelo VAK en la práctica educativa. Los resultados obtenidos ponen de manifiesto la importancia de basar las prácticas pedagógicas en evidencia científica sólida. En este sentido, se propone generar un cambio de enfoque neuropedagogico hacia el uso de canales de información, que permite una enseñanza más personalizada y efectiva, al considerar la diversidad de los estudiantes y las múltiples formas en que aprenden. Este cambio busca desmitificar las creencias erróneas sobre los estilos de aprendizaje y fomentar un ambiente educativo más inclusivo y efectivo.
ChemPhoto Screenshots: Appearance of Structures and Browsing Large Collections
Authors: Apodaca Richard L.
Published: December 2024

Chemical structure imaging software solves the problem of how to easily create large numbers of readable chemical structures in a variety of formats automatically. ChemPhoto was recently introduced as what appears to be the first chemical structure imaging application. With development of the ChemPhoto user interface now in full-swing, it’s possible to show some screenshots.
measr 1.0.0
Authors: Thompson Jake
Published: December 2024

I am thrilled to announce the release of measr 1.0.0. The goal of measr is to provide a user-friendly interface for estimating and evaluating diagnostic classification models (DCMs; also called cognitive diagnostic models [CDMs]). This is a major release to mark the conclusion of the initial development work that was funded by the Institute of Education Sciences. Importantly, this does not mean that measr is going dormant!
What I'm reading (July 2024)
Authors: Turner Stephen
Published: December 2024

This post expands on a few of the papers I posted in this Twitter thread. I highlight a few in the deep dive at the top, then link to a few other papers of note later on. Subscribe to Paired Ends to get summaries like this in your e-mail as soon as I write them.
The Art and Science of Chemical Structure Diagrams - ChemWriter as Chemically-Aware Vector Graphics System
Authors: Apodaca Richard L.
Published: December 2024

Of the many problems to be solved when building software to view and manipulate 2D chemical structures, one of the trickiest is getting all features to scale proportionally. This problem is widespread because it can seldom be predicted at which resolution a chemical structure will be viewed. This article describes some ways in which this problem was addressed in the Web-based chemical structure editor ChemWriter.
Weekly Recap (Sep 2024, part 4)
Authors: Turner Stephen
Published: December 2024

This week’s recap highlights a new nf-core workflow for multi-omics trait association studies, a new tool for linking genotype to phenotype (G2P) by directly sequencing alleles from CRISPR base editing experiments, the SplitsTree app for interactive analysis and visualization using phylogenetic trees and networks, mapping cellular interactions from spatially resolved transcriptomics data, a study of marine microbial diversity and bioprospecting
The Witness
Authors: Apodaca Richard L.
Published: December 2024

The following is a work of fiction. Any resemblance to real persons, places, or events may or may not be coincidental.

What he’d witnessed had shaken him. The burden he now carried weighed on his shoulders and tinged the undersides of his expressionless eyes. “Halford, right?” The man looked up at me and blinked. “Yes, he said.” He was seated on the chair in front of my desk, right foot resting on his left knee.
What I'm reading (July 2024, part 2)
Authors: Turner Stephen
Published: December 2024

This post expands on a few of the papers I posted in this Twitter thread. I highlight a few in the deep dive at the top, then link to a few other papers of note later on. Subscribe to Paired Ends to get summaries like this delivered to your e-mail as soon as I write them. Subscribe now You might remember me from Getting Genetics Done where I blogged about genetics, statistics, and bioinformatics from 2008-2017.
Building Chempedia: The Human Element
Authors: Apodaca Richard L.
Published: December 2024

The study of chemistry is an inherently social activity. From the papers we use and cite, to the conferences we attend, to the informal discussions we engage in daily, being a chemist means interacting with your fellow chemists. Yet strangely, most chemical information systems either totally ignore this central fact, or provide only the most meager of tools to harness it to its full potential.
What I'm reading (Aug 2024, part 4)
Authors: Turner Stephen
Published: December 2024

Here are a few papers that caught my attention recently. I summarize a few in the deep dive at the top, then link to a few other papers of note later on. Subscribe to Paired Ends to get periodic summaries like this delivered to your e-mail.
SMILES Reading Performance: RDKit vs ChemCore
Authors: Apodaca Richard L.
Published: December 2024

The Rust homepage cites “blazingly fast” performance as an important reason to consider the language, and top-tier performance is often cited by developers as a reason they chose Rust. So far, this blog has emphasized Rust’s many other compelling features. This article breaks from that focus to examine performance. Specifically, it compares the speed with which RDKit (Python/C++) and ChemCore (Rust only) can read SMILES.
Weekly Recap (Dec 2024, part 2)
Authors: Turner Stephen
Published: December 2024

This week’s recap highlights a new way to turn Nextflow pipelines into web apps, DRAGEN for fast and accurate variant calling, machine-guided design of cell-type-targeting cis-regulatory elements, a Nextflow pipeline for identifying and classifying protein kinases, a new language model for single cell perturbations that integrates knowledge from literature, GeneCards, etc., and a new method for scalable protein design in a relaxed sequence
Weekly Recap (Oct 2024, part 3)
Authors: Turner Stephen
Published: December 2024

This week’s recap highlights a new Nextflow workflow for calculating polygenic scores with adjustments for genetic ancestry, a paper demonstrating that whole exome plus imputation on more samples is more powerful than whole genome sequencing for finding more trait associated variants, a new deep-learning-based splice site predictor that improves spliced alignments, a new method for accurate community profiling of large metagenomic datasets, and
Clock Yourself
Authors: Apodaca Richard L.
Published: December 2024

Fear of falling (FOF) is a major concern among the elderly. Depending on the source, between 21% and 85% of those living in care communities experience FOF. The condition is insidious due to its reinforcing mental and physical aspects. Fear of falling leads to reduced physical activity, which leads to weaker muscles and joints, and degraded coordination. These follow-on effects increase fall risk, setting up a feedback loop.
Reading CTfiles with CTcore
Authors: Apodaca Richard L.
Published: December 2024

CTfile is a widely-used family of file formats in cheminformatics and computational chemistry. CTfiles are most commonly processed through a cheminformatics toolkit. But sometimes that kind of power is overkill. You might, for example, want to pull out just certain pieces of information from a file without the overhead of building high-level data structures. In other situations, a toolkit does too little.
Weekly Recap (Nov 2024, part 2)
Authors: Turner Stephen
Published: December 2024

This week’s recap highlights an AI agent for automated multi-omic analysis (AutoBA), rapid species-level metagenome profiling and containment (sylph), a review on genome-wide association analysis beyond SNPs, private information leakage from scRNA-seq count matrices, and a method to “unlearn” viral knowledge in protein language models as a means to develop safe PLM-based variant effect analysis (PROEDIT). Others that caught my attention include
ChemWriter 1.3.1
Authors: Apodaca Richard L.
Published: December 2024

ChemWriter 1.3.1 can now be downloaded. This version resolves an EditorApplet issue in which molfiles containing two or more atoms with exactly the same 2D coordinates were not displayed properly. Details are available on the Metamolecular Company Blog. ChemWriter is the 2D chemical structure editor designed for Web applications.
Weekly Recap (Nov 2024, part 3)
Authors: Turner Stephen
Published: December 2024

This week’s recap highlights pangenome graph construction with nf-core/pangenome, building pangenome graphs with PGGB, benchmarking algorithms for single-cell multi-omics prediction and integration, RNA foundation models, and a Nextflow pipeline for characterizing B cell receptor repertoires from non-targeted bulk RNA-seq data.
Non-linear models: A Case for Synaptic Plasticity
Authors: Castillo-Aguilar Matías
Published: December 2024

Introduction

The human brain is a show-off, really.
Ten Things That Surprised Me About Blogging
Authors: Apodaca Richard L.
Published: December 2024

Depth-First began with a single post on August 12th, 2006. One year and 193 posts later, I thought it would be interesting to reflect back on how my expectations about blogging diverged from reality. Many of my observations come from statistics compiled by Google Analytics. An investment in time to install and use analytics software more than pays for itself within a few weeks.
measr 0.3.1
Authors: Thompson Jake
Published: December 2024

I’m stoked to announce the release of measr 0.3.1. The goal of measr is to provide applied researchers and psychometricians with a user friendly interface for estimating and evaluating diagnostic classification models (DCMs). This update is a minor release to introduce a couple of enhancements to model and prior specifications.
Demystifying Java Applets, Part 1 - Cross-Browser, Standards-Compliant, Pure HTML Deployment Using the Object Tag
Authors: Apodaca Richard L.
Published: December 2024

Update June 10, 2009

:

The information in this article, while accurate, has been superseded by Applet-Fu, a small JavaScript library that simplifies the use of the applet deploy technique described here.

A 2006 survey on java.net posed a simple question to developers: What’s wrong with applets?
Inciteful+Zotero to find relevant literature
Authors: Turner Stephen
Published: December 2024

I am in the middle of writing a review / perspectives paper. One that I’m confident will be exciting once we get it published. Some sections of the review cover subject matter at the outer periphery of my expertise.
Weekly Recap (Sep 2024, part 5)
Authors: Turner Stephen
Published: December 2024

This week’s recap highlights a Nextflow pipeline for eQTL detection, an end-to-end pipeline for spatial transcriptomics (visium) data analysis, a method for identification of perturbed cell types in single cell RNA-seq data, a method for guide assignment in single-cell CRISPR screens, a tool for on-target/off-target analysis of gene editing outcomes, and “digital microbes” for collaborative team science on emerging microbes.
Graphs from Scratch in Python
Authors: Apodaca Richard L.
Published: December 2024

Graphs are central to many areas of programming, so it’s not surprising to find many general-purpose graph libraries. But these ready-made solutions sometimes lack the focus needed to solve specific problem well. Having hit this problem several times, I recently proposed a solution in the form of a minimal graph API with a Rust implementation.
What I'm reading (Aug 2024, part 1)
Authors: Turner Stephen
Published: December 2024

It’s been a big week in the genomics+bioinformatics space. This post expands on a few of the recent papers I posted in a Twitter thread. I highlight a few in the deep dive at the top, then link to a few other papers of note later on. Subscribe (free!) to Paired Ends to get summaries like this delivered to your e-mail as soon as I write them.
Building Chempedia - Start Simple, Then Iterate
Authors: Apodaca Richard L.
Published: December 2024

As a medium for building software, the Web offers unparalleled adaptability. With nothing to download or install, users of Web applications automatically see the newest version - always. This may sound like a small thing, and technically it is. But it dramatically increases the effectiveness with which software can be created.
Weekly Recap (Oct 2024, part 1)
Authors: Turner Stephen
Published: December 2024

This week’s recap highlights a new multispecies codon optimization method, personalized pangenome references with vg, a commentary on the wild west of spike-in normalization, a new pipeline for comprehensive and scalable polygenic scoring across ancestrally diverse populations, a paper showing deep learning / transformer-based methods don’t outperform simple linear models for predicting gene expression after genetic perturbations, and finally, a
Screencast: Drawing Structures Quickly With ChemWriter
Authors: Apodaca Richard L.
Published: December 2024

[Video Scrubbed] This short video shows how to use ChemWriter to draw structures quickly with keyboard shortcuts.
Thinking of Starting an Anonymous Science Blog? Five Reasons to Think Again
Authors: Apodaca Richard L.
Published: December 2024

You can find them in nearly every scientific discipline: the anonymous science blog. For a variety of reasons, their authors have decided not to reveal their identities, as is their right. Styles range from the absolutely analytical to the cynically sarcastic. I have nothing against anonymous science blogs. Some of the most interesting writing I’ve seen has been posted to them.
Better Structure Drawing With ChemWriter 1.3.0
Authors: Apodaca Richard L.
Published: December 2024

ChemWriter 1.3.0 has been released and is ready for download. This version makes it possible to change the mouse cursor hover radius for more accurate drawing. It also adds a setting to disable heteroatom keyboard shortcut events occurring away from a molecule node, reducing the possibility of an off-atom label being inadvertently drawn. For details, see the Metamolecular Company Blog.
Create Your Own PubChem Datasets - Exporting Results As SD Files
Authors: Apodaca Richard L.
Published: December 2024

Recently, I needed to create a subset of the PubChem database in Structure Data File (SD File) format. Although it’s far from obvious how to do this, the capability does exist. In this article, I’ll give a step-by-step procedure for creating custom datasets in SD File format from arbitrary PubChem structure queries.
Parsing SD Files with Ruby and Rubidium
Authors: Apodaca Richard L.
Published: December 2024

Reading SD files is a bread-and-butter cheminformatics operation. At a minimum, a cheminformatics toolkit needs to parse the individual entries of an SD file, and provide access to the embedded molfile and data hash for each. Recent articles have introduced Rubidium, a Ruby cheminformatics scripting environment. The Rubidium team now announces the release of Rubidium-0.1.1, which, among other features, introduces the ability to parse SD files.
Weekly Recap (Oct 2024, part 4)
Authors: Turner Stephen
Published: December 2024

This week’s recap highlights protein design with RoseTTAFold, surveillance with wastewater sequencing, T2T human genomes, Vitessce for visualization of multimodal spatial single-cell data, and Taxometer for taxonomic classification of metagenomics contigs.
Nextflow Summit Barcelona 2024
Authors: Turner Stephen
Published: December 2024

I just returned from a week in Barcelona where I attended the Nextflow Summit and nf-core hackathon, and I can hardly contain my excitement for the near term future of bioinformatics, computational biology, and open science in general.
Paired Ends Podcast
Authors: Turner Stephen
Published: December 2024

This is an experiment... ignore this post
Build a Python CLI with Click+Cookiecutter
Authors: Turner Stephen
Published: December 2024

In the spirit of Learning in Public, I wanted an excuse to explore (1)

click

for creating command line interfaces, (2)

Cookiecutter

project templates, and (3) modern tools in the Python packaging ecosystem. If you’re primarily an R developer like me, I recently wrote about resources for getting better at Python for R users.
Building an original and internationally standardized public health system in the Kingdom of Yugoslavia
Authors: Dugac Željko
Published: December 2024

This paper analyzes the key processes involved in establishing the public health system in the Kingdom of Serbs, Croats, and Slovenes (later the Kingdom of Yugoslavia), drawing upon existing scholarly studies and relevant archival sources. In the aftermath of World War I, the nascent state was confronted with numerous public health challenges. The establishment of the Ministry of Public Health marked the beginning of efforts to address these issues, as the Ministry assumed responsibilities over healthcare, medicine, veterinary medicine, pharmacy, and military health. This initiative included the enactment of necessary legal regulations, the creation of social medical institutions, and the regulation of medical personnel training, thereby laying the groundwork for a new approach to public health. The Ministry spearheaded reforms in the organization of health services, encompassing the establishment of new healthcare institutions, the creation of an innovative educational system, and the implementation of health programs and competencies designed to address both crisis situations and ongoing healthcare needs. Concurrently, the Ministry launched various preventive and social programs, as well as comprehensive health education initiatives, aimed at enhancing public awareness of hygiene and healthy behaviors. Additionally, significant efforts were made to establish enduring conditions for the integration of new scientific knowledge into daily life. All these programs were unified by a common ideological principle that posited that medicine, healthcare, and scientific advancements must serve the broader society, ensuring equal access for all community members. These initiatives were undertaken under the auspices of the Hygiene Department of the Ministry of Public Health, led by Dr. Andrija Štampar, an internationally recognized public health expert. The development of this public health system was further supported by professional and financial assistance from international organizations, including the Health Organization of the League of Nations and the Rockefeller Foundation. This collaborative effort resulted in the creation of a public health system that was both original and internationally standardized.
Does financial technology reduce inflation: Lessons learnt from Sumatra
Authors: Syariful Anam , Silahul Mu'min , Kartiko Nafis
Published: December 2024

The purpose of this paper is to investigate the impact of financial technology (Fintech) on the inflation rate. The contribution reflects in the creation of a new index for Fintech, involving several indicators using principal component analysis. The data utilized belong to a panel dataset pertaining to the 10 provinces of the island of Sumatra, Indonesia, spanning from January 2020 to June 2023. The pooled mean group (PMG) estimation method is employed in order to test the relationship between Fintech and the inflation rate. The research findings of the study indicate that Fintech is capable of reducing inflation in the long run. Therefore, this research study implies the necessity to intensify the use of Fintech for the purpose of creating an efficient economic environment and promoting economic stability.
Investigating Aptitude in Learning Programming Language Using Machine Learning and Natural Language Processing
Authors: Iqbal Muhammad Faisal , Zafar Adeel , Khalil Umer , Ishaq Afia
Published: December 2024

This study investigates the relationship between prerequisite courses and skill acquisition in programming education. It proposes a case study examining cognitive, natural language, and mathematical aptitude indicators as predictors of programming performance. Analyzing data from 1238 undergraduate students at Riphah International University, the research employs Machine Learning models to predict outcomes, achieving high R2 scores and low Mean Squared Error rates. A zero-shot text classification model identifies required aptitude skills: 62% cognitive, 24% natural language, and 14% mathematical. These skills are mapped to predicted programming course scores, offering a new approach to understanding programming language aptitude. The study aims to bridge the gap between prerequisite courses and subsequent skill development, contributing valuable insights to computing education curriculum design.
Protective effect of nano-extract of Lepidium meyenii on some func-tional parameters and epididymal tissue in male albino rats treated with the Oxymetholone
Authors: Alrushdy Maryam Ahmed Ali , Obeid Ashwaq Kadhem
Published: December 2024

Due to the widespread use of the Oxymetholone and its widespread health problems, it was necessary to search for an alternative medicine treatment that reduces the harm of the Oxymetholone. Objectives from this study is determine the protective effect of the nano-extract of the Lepidium meyenii on the damage caused by the Oxymetholone in male rats. the experimental animals (28) were randomly divided into four groups, with 7 animals for each group The duration of the experiment was 55 days. The animal dosed daily, as follows: control group (G1): The animals were dosed with normal saline,Positive control group (G2): animals dosed orally with Oxymetholone (5 mg/kg B.w.),Group three (G3): Animals were dosed orally with the nano-extract of Lepidium meyenii ( 100 mg/kg B.w.),Group four (G4): It included animals dosed orally with the nano-extract of Lepidium meyenii (100 mg/kg B.w.) four hours before oral dosing with the Oxymetholone ( 5 mg/kg B.w.). The level of (GSH, SOD and number of sperm in epididymal tail) decreased in the Oxymetholone group and rose and was within the normal level in G3, G4.The histological sections of the epididymal in G2 It was noted that there were interstitial spaces between the epididymal tubules, and few sperm in the tubule cavities. With a lack of smooth muscle surrounding the tubules.Also showed in G3 and G4 the normal structure of the epididymis appears with regular epididymal tubules, an increase in the number of sperm in the lumen of the epididymis and the presence of connective tissue between the tubules. Maca root nano-extract has been shown to be effective in inhibiting oxymetholone-induced damage to oxidative stress and epididymal tissue in male rats.
Response of different genetic groups of sheep to nutritional flushing in their reproductive performance
Authors: Hussein Mohammed Ali Jawad  , Ali Ahmed Alou Al-Qutbi  , Hafedh Mossa Ali Altaei
Published: December 2024

This research aims to find out the response of different groups of sheep to Nutritional Flushing and analyse the impact of this response on their reproductive performance, where 60 sheep of different ages were used in the experiment, 3 different groups of sheep breeds were selected (Naimi, Awasi karakul bat, Awasi Hamdani bat) and 3 control groups of the same breeds with 10 sheep per group agencies : the first treatment: - control group Pure Naimi sheep / 10 head, the second treatment: - control group Awasi bat + karakul / 10 heads, the third treatment: - control group sheep bat Awassi + Hamdani / 10 heads, the fourth treatment: - Nutritional Flushing group Pure Naimi sheep / 10 Ras, the fifth transaction: - Nutritional Flushing group al-mudrab Awasi + Karakul Sheep / 10 Ras, the sixth transaction: Nutritional Flushing group al-mudrab Awasi + Hamdani sheep / 10 Ras. The experimental groups were given a Nutritional Flushing of 3% of the animal's weight, concentrated feed six weeks before the fertilization process and six weeks before the birth process, with the provision of hay and free jet threshing as needed, in addition to water and mineral salts, the results of the experiment showed a moral superiority (P<0.05) in the fertility and fertilization rates, the percentage of births and the percentage of pregnancy and the ratio of twins and fertility, and we conclude that the treatment with Nutritional Flushing for the three groups of sheep (Naimi, Awasi mudrab The use of a Nutritional Flushing for the three sheep groups at a concentration of 3 % of the animal's weight six weeks before the fertilization process and six weeks before the birth process, with the provision of hay and free jet threshing as needed, in addition to water and mineral salts, has given the best results compared to natural feeding(control group).
Farmers' use of phone applications in accessing information for maize production in Kwara state, Nigeria
Authors: Olatinwo Latifat Kehinde , Yusuf Olayinka Jelili , Wahab Munir Jamiu
Published: December 2024

This study assessed the farmers' use of phone applications to access information for maise production in Kwara State. Data for the study were analysed using descriptive statistics, likert scale, and Pearson Product Moment Correlation (PPMC). A simple random sampling was used to select 120 maise farmers from 6 villages in both Omupo and Ajase-Ipo districts. The study revealed that 83.3% of the maise farmers were males with an average of 37.6, and 83.3% were married, with an average of 12 years of schooling. The average household size was 7 persons while the number of years of experience was 11 years. The study also revealed that the most common way of accessing information was through voice calls, radio, and WhatsApp, with all the respondents choosing both of these sources. The study also showed that poor internet networks on field/farm sites, with a mean score of 2.59 were the most glaring effect of the use of phones to access information on maise production, while the high cost of mobile smart/android phones with a mean score of 2.58 was one of the mitigating factors. The major constraint of using phone features/applications to access information was that smartphones use a bunch of data bundles and cost implications with a mean score of 2.61. The results of the hypothesis showed a significant relationship between socioeconomic characteristics and farmers' use of phone applications in accessing information for maise production. Data subscriptions on customised phones can also be made affordable for farmers.
Role of exopolysacharide bacteria in improving the tolerance of Zea mays (L.) Seedlings to drought stress
Authors: Karrar . K . Hashim  , Khalid A. Hussein  , Najeh H. Kadhum
Published: December 2024

In this study, 20 Bacillus and 20 Pseudomonas bacteria were isolated from arid and semiarid soil samples. Bacillus and Pseudomonas bacteria are soil-dwelling bacteria that can promote plant growth. They are known to produce exopolysaccharides (EPS), which can help plants retain water and tolerate drought stress. The isolates were morphologically and microscopically characterized and tested for their ability to produce exopolysaccharides. The isolates that were most capable of producing exopolysaccharides were used as biofertilizer to improve drought tolerance of maize seedlings. The seedlings were irrigated every 24, 48, or 72 h. The results showed that biofertilizers containing the most EPS-producing Bacillus and Pseudomonas isolates, B. subtillus, B. brevibacillus, P. putida, P. fluorescens, significantly improved the transpiration rate, stress tolerance index, drought tolerance, chlorophyll stability and membrane damage index of maize seedlings.
The physiological effects of orlistat and efficiency extract of cinnamon on body weight and lipid profile in obese male rats
Authors: Benan Aad abed  , Wafaa Kadhim Jasim  , Tuqa Sabbar Rahi
Published: December 2024

The purpose of the current study was to examine the adverse effects of orlistat used alone and in combination with cinnamon with regard to weight gain, body weight percentage, and alterations in the lipid profile in male rats that were obese. Have been selected There were two groups of adult male rats.  First experience (induction obesity) for six weeks to induce obesity into (Control group : 10 rats received only rats normal diet without fat as a daily dose) and (High fat diet group : 30 rats received only fed with high-fat diet contain  Plate with soy fat and introduce as daily dose) , After this period (six weeks) weight gain and second main groups to ensure the induction , Second experience for six weeks , The treatment period lasted from week 6 to week 12 after confirming the induction of obesity daily oral dosing with the fallowing groups) Control group : 10 rats received only rats normal diet without fat as a daily dose , High fat diet group : 30 rats after induction of obesity divided into the  following:-A) Group high fat diet with orlistat 10 rats (10 mg/kg/day). B) Group high fat diet with cinnamon  10 rats (100 mg/kg BW). C) Group high fat diet with orlistat (10 mg/kg/day ) and cinnamon (100 mg/kg BW) 10 rats. The findings show that Weight gain were increase in a significant value (P<0.05) in fat group comparatively to control group and orlistat group , cinnamon group , combination  mix group While cholesterol , Triglycerides , LDL-c and VLDL-c were increase in a significant value (P<0.05) while showed a significant (P<0.05) decrease in HDL-c in fat group comparatively to control group and orlistat group , cinnamon group , combination mix group , Conclusions In addition to its ability to inhibit pancreatic lipase, orlistat can also be used to control weight because it indirectly reduces appetite by raising glucagon, IDE, and dopamine levels and by inhibiting the glutamate neurotransmitter. Meanwhile, cinnamon improves blood sugar levels and glycaemic targets.
طبيعة ومصادر القانون الجنائي الدولي وقواعده ومفهوم وأنواع الجرائم الدولية
Authors: م. حيدر مهدي بنية
Published: December 2024

يعدّ القانون الجنائي الدولي من أبرز فروع القانون الدولي العام الذي يعنى بمحاسبة الأفراد على الجرائم التي ترتكب على مستوى عالمي، والتي تهدد السلم والأمن الدوليين ويستند هذا النوع من القانون إلى مفهوم العدالة الدولية، حيث لا تقتصر المساءلة الجنائية على الحدود الوطنية بل تمتد لتشمل الأفراد مهما كانت جنسياتهم أو مواقعهم الجغرافية.
يتسم القانون الجنائي الدولي بطبيعة خاصة تُميّزه عن غيره من فروع القانون، إذ يهدف إلى ضمان حقوق الإنسان وحمايتها من الانتهاكات الجسيمة مثل الإبادة الجماعية، الجرائم ضد الإنسانية، وجرائم الحرب. وقد ظهرت الحاجة إليه نتيجة لتزايد الجرائم التي تتجاوز الحدود الوطنية، مثل الجرائم المرتبطة بالحروب والنزاعات المسلحة.
من ناحية أخرى، يُستمد القانون الجنائي الدولي من مجموعة من المصادر التي تضم المعاهدات والاتفاقيات الدولية، والعرف الدوِلي، بالإضافة إلى المبادئ العامة للقانون المعترف بها دولياً. ولعل المحكمة الجنائية الدولية، التي تم إنشاؤها بموجب "نظام روما الأساسي"، تمثل أبرز الأدوات القانونية التي تُطبَّق على المستوى الدولي لمقاضاة الأفراد المسؤولين عن ارتكاب هذه الجرائم.
ويتضمن القانون الجنائي الدولي مجموعة من القواعد التي تهدف إلى تحديد المسؤولية الجنائية للأفراد وفرض العقوبات المناسبة، فضلاً عن الإجراءات التي يتم من خلالها التحقيق والمحاكمة. وتقوم هذه القواعد على مبادئ أساسية مثل عدم قابلية العفو، والقاعدة التي تقتضي بأن "لا جريمة ولا عقوبة إلا بنص"، وأيضاً مبدأ الولاية القضائية الدولية.
من خلال البحث نتناول في هذا المطلب الطبيعة القانونية لمصادر القانون الجنائي الدولي في الفرع الاول ومن ثم نتناول أنواع الجرائم الدولية في الفرع الثاني.
الجريمة البيئية
Authors: مسلم طالب جالي الزيادي
Published: December 2024

بالنظر لأهمية بيان جريمة التلوث البيئي لما لهذه الجريمة من أثر كبير على حياة الكائنات الحية ومن ضمنها الإنسان كما أن التلوث البيئي من الموضوعات التي أصبحت محل اهتمام الباحثين في المجالات القانونية، لدى اختيار جزئية معينة تتعلق بال التلوث البيئي وهي أركان التلوث البيئي، حيث يعد موضوع أركان جريمة التلوث البيئي من الموضوعات مفصلية والمهمة حيث انه أهميتها تبرز في بيان طبيعة الجريمة في كونها جريمة وقتها أن يتحقق كيان القانوني بمجرد تيان السلوك أو امتناع المنهي عنه، أم أنها جريمة مستمرة يتدخل الجاني بإرادته ويجعل الفعل متتابعة عنها، حيث يقبل رها المادي بطبيعته الاستمرار فترة من الزمن أبناء على إرادة الجاني ، تبانا البيان أركان الجريمة البيئة أهمية في تحديد بدء تقادم والخاص القضائي وتحديد بدأ سريان القانون البيئي ، وقد تم اعتماد أكثر من منهج في دراسة موضوعات البحث منها المنهج التحليلي و المقارن
How to Maximize Minimum Number of Colour Classes for Edge Colouring Using Families of Disjoint Sets Colouring Technique
Authors: Satti Mansoor
Published: December 2024

In this paper we use families of disjoint sets colouring technique, to introduce some results of edge colouring for minimum and maximum number of colour classes, and introduce a results explains how to find different values of minimum colour classes, and how to maximize minimum number of colour classes for edge colouring, when maximum degree of vertex is fixed, here we prove a result as a method for finding minimum number of colour classes for edge colouring. Families of disjoint sets colouring technique, as generalization technique deal even with graph of multiple edges, and here graph of multiple edges given as application of some examples and results.