bluuebunny/crossref_metadata_2025_split huggingface dataset:
A case and review of FGF23-mediated hypophosphatemic osteomalacia in the absence of pathogenic PHEX variants
Authors: Park Yeung-Ae , Gong Joanna Y , Chiang Cherie , Trainer Alison H , Yates Christopher J 
Published: December 2024

Abstract
We report an atypical case of fibroblast growth factor-23 (FGF23)-mediated hypophosphatemic osteomalacia without a pathogenic variant (PV) of PHEX, who improved biochemically, clinically and radiologically post burosumab treatment. We present a narrative review of FGF23-mediated hypophosphatemic osteomalacia and propose a roadmap for investigating the etiology of hypophosphatemia to guide therapy.
A 29-year-old female with FGF23-mediated hypophosphatemic osteomalacia experienced multiple insufficiency fractures, including bilateral femoral diaphyseal fractures and delayed healing. This occurred on a background of juvenile enthesitis-related arthritis, narcolepsy and brittle dentition since her early teens. Whole-body magnetic resonance imaging and Gallium-68 DOTATATE positron emission tomography scans were unremarkable, making tumor-induced osteomalacia highly unlikely. No hypophosphatemic PVs were found using massively parallel sequencing. Despite phosphate and calcitriol therapy, mild hypophosphatemia persisted with minimal improvement in fracture healing or pain. One dose of 60 mg burosumab, an anti-FGF23 antibody, led to hyperphosphatemia requiring dose titration and three doses of burosumab normalized renal tubular maximum reabsorption rate of phosphate relative to glomerular filtration rate. Burosumab led to fracture healing with callus formation corresponding with improved pain at fracture sites.
Hypophosphatemic osteomalacia manifests with varus deformity of the lower limbs, gait disturbance, muscle weakness, enthesopathy, and dental necrosis. Evaluation of the etiology is crucial and requires an algorithmic approach to determine whether hypophosphatemia is renally-mediated, FGF23-mediated, acquired or inherited. The most common inherited cause of FGF23-mediated hypophosphatemic osteomalacia is X-linked hypophosphatemia (XLH) secondary to a PV of the PHEX gene. However, the absence of a PHEX PVs does not exclude a diagnosis of hereditary FGF23-mediated hypophosphatemic osteomalacia. Other inherited causes of this disorder include autosomal dominant and autosomal recessive hypophosphatemic rickets, fibrous dysplasia-McCune-Albright syndrome, cutaneous skeletal hypophosphatemia syndrome and osteoglophonic dysplasia. Burosumab significantly improves serum phosphate and fracture healing in XLH and may effectively treat other forms of FGF23-mediated hypophosphatemia.
Six-month rehabilitation following surgical hip dislocation for femoroacetabular impingement restores the preoperative strength of most hip muscles, except for external rotators
Authors: Servant Guillaume , Bothorel Hugo , Pernoud Anthony , Mayes Susan , Fourchet François , Christofilopoulos Panayiotis 
Published: December 2024

Abstract
The aim of this study was to evaluate the bilateral changes in hip muscle strength after a 6-month rehabilitation period for patients undergoing surgical hip dislocation (SHD) to treat femoroacetabular impingement syndrome (FAIS). We conducted a retrospective analysis on a cohort of 22 patients (mean ± SD age: 26 ± 7, 68% male) who underwent SHD for FAIS between March 2020 and January 2023 at La Tour Hospital. Bilateral isometric strength of eight hip muscle groups (abductors, adductors, hamstrings, quadriceps, extensors, flexors, internal, and external rotators) was assessed using a handheld dynamometer before surgery, and at 3 and 6 months postoperatively. After 6 months of rehabilitation, only the external rotators were weaker compared to preoperative levels (−13% ± 23%, P = .021). Strength levels were similar to preoperative levelsfor adductors (−2% ± 21%, P = .309), internal rotators (0% ± 25%, P = .444), quadriceps (0%± 23%, P = .501), hamstrings (7%± 20%, P = .232), extensors (7%± 19%, P = .336), flexors (8%± 34%, P = .781), and abductors (8% ± 25%, P = .266). At 6 months, 59% (abductors) to 82% (adductors) of patients did not achieve a clinically relevant strength improvement (&gt;15%) compared to their preoperative status for aforementioned muscles. Additionally, 50% of the cohort experienced a clinically relevant loss of strength in the external rotators at 6 months post-surgery. To conclude, after SHD, most FAIS patients regained their preoperative strength for all muscle groups except the external rotators with a 6-month rehabilitation program. However, the effectiveness of the rehabilitation protocol varies on an individual level.
Genome-wide identification of bacterial genes contributing to nucleus-forming jumbo phage infection
Authors: Harding Kate R , Malone Lucia M , Kyte Natalie A P , Jackson Simon A , Smith Leah M , Fineran Peter C 
Published: December 2024

Abstract
The Chimalliviridae family of bacteriophages (phages) form a proteinaceous nucleus-like structure during infection of their bacterial hosts. This phage ‘nucleus’ compartmentalises phage DNA replication and transcription, and shields the phage genome from DNA-targeting defence systems such as CRISPR-Cas and restriction-modification. Their insensitivity to DNA-targeting defences makes nucleus-forming jumbo phages attractive for phage therapy. However, little is known about the bacterial gene requirements during the infectious cycle of nucleus-forming phages or how phage resistance may emerge. To address this, we used the Serratia nucleus-forming jumbo phage PCH45 and exploited a combination of high-throughput transposon mutagenesis and deep sequencing (Tn-seq), and CRISPR interference (CRISPRi). We identified over 90 host genes involved in nucleus-forming phage infection, the majority of which were either involved in the biosynthesis of the primary receptor, flagella, or influenced swimming motility. In addition, the bacterial outer membrane lipopolysaccharide contributed to PCH45 adsorption. Other unrelated Serratia-flagellotropic phages used similar host genes as the nucleus-forming phage, indicating that phage resistance can lead to cross-resistance against diverse phages. Our findings demonstrate that resistance to nucleus-forming jumbo phages can readily emerge via bacterial surface receptor mutation and this should be a major factor when designing strategies for their use in phage therapy.
R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning
Authors: Brenes-Álvarez Manuel , Ropp Halie R , Papagiannidis Dimitrios , Potel Clement M , Stein Frank , Scholz Ingeborg , Steglich Claudia , Savitski Mikhail M , Vioque Agustín , Muro-Pastor Alicia M , Hess Wolfgang R 
Published: December 2024

Abstract
RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation of heterocysts in filamentous cyanobacteria is an example of cell differentiation in prokaryotes. Although multiple non-coding transcripts are involved in this process, no RBPs have been implicated thus far. Here we used quantitative mass spectrometry to analyze the differential fractionation of RNA–protein complexes after RNase treatment in density gradients yielding 333 RNA-associated proteins, while a bioinformatic prediction yielded 311 RBP candidates in Nostoc sp. PCC 7120. We validated in vivo the RNA-binding capacity of six RBP candidates. Some participate in essential physiological aspects, such as photosynthesis (Alr2890), thylakoid biogenesis (Vipp1) or heterocyst differentiation (PrpA, PatU3), but their association with RNA was unknown. Validated RBPs Asl3888 and Alr1700 were not previously characterized. Alr1700 is an RBP with two oligonucleotide/oligosaccharide-binding (OB)-fold-like domains that is differentially expressed in heterocysts and interacts with non-coding regulatory RNAs. Deletion of alr1700 led to complete deregulation of the cell differentiation process, a striking increase in the number of heterocyst-like cells, and was ultimately lethal in the absence of combined nitrogen. These observations characterize this RBP as a master regulator of the heterocyst patterning and differentiation process, leading us to rename Alr1700 to PatR.
Spatial transcriptomics in breast cancer reveals tumour microenvironment-driven drug responses and clonal therapeutic heterogeneity
Authors: Jiménez-Santos María José , García-Martín Santiago , Rubio-Fernández Marcos , Gómez-López Gonzalo , Al-Shahrour Fátima 
Published: December 2024

Abstract
Breast cancer patients are categorized into three subtypes with distinct treatment approaches. Precision oncology has increased patient outcomes by targeting the specific molecular alterations of tumours, yet challenges remain. Treatment failure persists due to the coexistence of several malignant subpopulations with different drug sensitivities within the same tumour, a phenomenon known as intratumour heterogeneity (ITH). This heterogeneity has been extensively studied from a tumour-centric view, but recent insights underscore the role of the tumour microenvironment in treatment response. Our research utilizes spatial transcriptomics data from breast cancer patients to predict drug sensitivity. We observe diverse response patterns across tumour, interphase and microenvironment regions, unveiling a sensitivity and functional gradient from the tumour core to the periphery. Moreover, we find tumour therapeutic clusters with different drug responses associated with distinct biological functions driven by unique ligand-receptor interactions. Importantly, we identify genetically identical subclones with different responses depending on their location within the tumour ducts. This research underscores the significance of considering the distance from the tumour core and microenvironment composition when identifying suitable treatments to target ITH. Our findings provide critical insights into optimizing therapeutic strategies, highlighting the necessity of a comprehensive understanding of tumour biology for effective cancer treatment.
PyNetCor: a high-performance Python package for large-scale correlation analysis
Authors: Long Shibin , Xia Yan , Liang Lifeng , Yang Ying , Xie Hailiang , Wang Xiaokai 
Published: December 2024

Abstract
The development of multi-omics technologies has generated an abundance of biological datasets, providing valuable resources for investigating potential relationships within complex biological systems. However, most correlation analysis tools face computational challenges when dealing with these high-dimensional datasets containing millions of features. Here, we introduce pyNetCor, a fast and scalable tool for constructing correlation networks on large-scale and high-dimensional data. PyNetCor features optimized algorithms for both full correlation coefficient matrix computation and top-k correlation search, outperforming other tools in the field in terms of runtime and memory consumption. It utilizes a linear interpolation strategy to rapidly estimate P-values and achieve false discovery rate control, demonstrating a speedup of over 110 times compared to existing methods. Overall, pyNetCor supports large-scale correlation analysis, a crucial foundational step for various bioinformatics workflows, and can be easily integrated into downstream applications to accelerate the process of extracting biological insights from data.
Exploring transcription modalities from bimodal, single-cell RNA sequencing data
Authors: Regényi Enikő , Mashreghi Mir-Farzin , Schütte Christof , Sunkara Vikram 
Published: December 2024

Abstract
There is a growing interest in generating bimodal, single-cell RNA sequencing (RNA-seq) data for studying biological pathways. These data are predominantly utilized in understanding phenotypic trajectories using RNA velocities; however, the shape information encoded in the two-dimensional resolution of such data is not yet exploited. In this paper, we present an elliptical parametrization of two-dimensional RNA-seq data, from which we derived statistics that reveal four different modalities. These modalities can be interpreted as manifestations of the changes in the rates of splicing, transcription or degradation. We performed our analysis on a cell cycle and a colorectal cancer dataset. In both datasets, we found genes that are not picked up by differential gene expression analysis (DGEA), and are consequently unnoticed, yet visibly delineate phenotypes. This indicates that, in addition to DGEA, searching for genes that exhibit the discovered modalities could aid recovering genes that set phenotypes apart. For communities studying biomarkers and cellular phenotyping, the modalities present in bimodal RNA-seq data broaden the search space of genes, and furthermore, allow for incorporating cellular RNA processing into regulatory analyses.
Osteomyelitis and Septic Arthritis in the Darwin Prospective Melioidosis Study
Authors: Campbell Stuart , Hicks Dane , Shetty Rajendra P , Currie Bart J 
Published: December 2024

Abstract

Background
Melioidosis is a multisystem infectious disease caused by the environmental bacterium Burkholderia pseudomallei. Osteomyelitis (OM) and septic arthritis (SA) are uncommon primary presentations for melioidosis but important secondary foci, often requiring prolonged therapy and multiple surgeries. We characterized the epidemiology, presentation, treatment, and outcomes of patients from 24 years of the Darwin Prospective Melioidosis Study (DPMS).

Methods
DPMS patients from October 1, 1999, until September 30, 2023, were included if they had a primary or secondary diagnosis of OM or SA. Epidemiological, risk factor, clinical, and outcome data were retrieved from the DPMS database. Antibiotic and surgical data were collated from patient records.

Results
From 1129 consecutive patients with culture-confirmed melioidosis, 122 (10.8%) had OM and/or SA, with 115 evaluable. Ninety-four of 1129 (8.3%) had OM, and 62/1129 (5.5%) had SA, with 41/115 (35.7%) of these having both OM and SA. Many combined infections involved contiguous bone and joints or soft tissue. Fifty-nine (51.3%) were male, and only 4.3% were ≤16 years old. Diabetes mellitus was present in 69.6%, and only 12.2% had no identifiable clinical risk factor. There were 8 deaths (7.0%) and 20 (17.4%) recurrent infections. Seventy-one (61.7%) had operative management, with combined infection associated with more procedures and longer length of stay.

Conclusions
The current paradigm of care for osteoarticular melioidosis involves prolonged intravenous antibiotics in conjunction with timely and complete operative management, and in our setting where these are available, outcomes are good. In many melioidosis-endemic regions these resources are limited, and mortality remains high.
Symmetry Relationships between Crystal Structures
Authors: Müller Ulrich , de la Flor Gemma 
Published: December 2024

Abstract
In crystal chemistry and crystal physics, the relations between the symmetry groups (space groups) of crystalline solids are of special importance. Part 1 of this book presents the necessary mathematical foundations and tools: the fundamentals of crystallography with special emphasis on symmetry, the theory of the crystallographic groups, and the formalisms of the needed crystallographic computations. Part 2 gives an insight into applications to problems in crystal chemistry. With the aid of numerous examples, it is shown how crystallographic group theory can be used to make evident relationships between crystal structures, to set up a systematic order in the huge amount of known crystal structures, to predict crystal structures, to analyse phase transitions and topotactic reactions in the solid state, to understand the formation of domains and twins in crystals, and to avoid errors in crystal structure determinations. Part 3 goes more deeply into some special topics, namely the isomorphic subgroups of space groups, the theory of phase transitions, and computer programs dedicated to crystallographic group theory.
Basics of crystallography, part 1
Authors: Müller Ulrich , de la Flor Gemma 
Published: December 2024

Abstract
Crystals are described by a vector lattice that is periodical in three dimensions. Three non-coplanar basis vectors span a crystallographic basis (unit cell) and define a coordinate system. The lengths of the basis vectors and the angles between them are the lattice parameters. Planes across the vector lattice are designated by integral Miller indices hkl. The metric tensor serves to calculate distances and angles.
Equivalent descriptions of crystal structures and chirality
Authors: Müller Ulrich , de la Flor Gemma 
Published: December 2024

Abstract
By application of certain rules a standardized description of crystal structures is achieved. Frequently, often for good reasons, these rules are not observed, and for the consideration of symmetry relations they may even be inconvenient. Usually there are several different sets of coordinates to describe the very same crystal structure. The different sets of coordinates can be determined with the aid of the Euclidean normalizer. A chiral crystal structure can only adopt one of the 65 Sohncke space-group types. These have no reflections, glide reflections, rotoinversions or inversions. If these symmetry operations are also excluded for the Euclidean normalizer, the space group itself belongs to one of the 11 pairs of chiral (enantiomorphic) pairs of space-group types. The crystal structures of two compounds are isotypic it their atoms are distributed in a like manner and if they have the same space groups.
Derivation of crystal structures from closest packings of spheres
Authors: Müller Ulrich , de la Flor Gemma 
Published: December 2024

Abstract
A large number of crystal structures can be derived by partial occupation of interstices in closest packings of spheres. Examples are the rhombohedral, hexagonal and trigonal hettotypes that result from the partial occupation of octahedral voids in the hexagonal-closest packing of spheres. Other examplers are the hettotypes of the NaCl structure with a doubled unit cell and partial occupation of the octahedral voids, and the hetttotypes of the CaF2 type with a doubled unit cell and partial occupation of the tetrahedral voids.
Topotactic reactions
Authors: Müller Ulrich , de la Flor Gemma 
Published: December 2024

Abstract
A topotactic chemical reaction takes place in the solid state such that the orientation of the product crystal depends on the orientation of the initial material. Sometimes there is a group—subgroup relation between the involved space groups. When lanthanoid subhalides LnnCl2n+1 crystallize from a melt, they form topotactic mixtures such as DyCl2 + Dy7Cl15 whose structures can be derived from the fluorite type.
Facets of the Soviet
Authors: Titus Joan 
Published: December 2024

Abstract
Chapter 3 (“Facets of the Soviet”) provides an examination of Shostakovich’s scores to three disparate films representing three different film types of the late 1930s–early 1940s: Great Citizen (Velikiy grazhdanin, dir. Fridrikh Ermler, Parts 1 and 2, 1937 and 1938–1939), Man with a Gun (Chelovek s ruzh’yom, dir. Sergey Yutkevich, 1938), and Adventures of Korzinkina (Priklyucheniya Korzinkinoy, dir. Klimentiy Mints, 1940–1941). Each film and its score represent an approach to particular genres—the speech-focused propaganda film, a feature film, and a short comedy. Analyses of each film score demonstrate Shostakovich’s ability to negotiate multiple styles and genres in scores for diverse film types during the prewar period.
The Long Walk: Spring 1569
Authors: Snow Dean 
Published: December 2024

Abstract
At the northern tip of Chesapeake Bay, the three men left Eastern Algonquian territory to visit a large Northern Iroquoian town on the lower Susquehanna River. Ingram called the town “Balma,” and they remained there for a week, longer than any other place they rested. Balma was a town having large multifamily Iroquoian longhouses. Here Ingram saw fields of maize, beans, and squash. He was invited to witness masked curing ceremonies and was offered trade goods in exchange for the shell beads and other southern goods he carried. Here the travelers learned of the feared Mohawks who lived northward in the interior, their source for valued quartz crystals. Ingram returned to Eastern Algonquian country, following trails closer to the coast from eastern Pennsylvania to southern New England. There they passed through villages that had been visited described by Verrazzano in 1524.
Ingram’s Legacy
Authors: Snow Dean 
Published: December 2024

Abstract
It is unavoidable that David Ingram was a participant in English race-based slavery. However, although he was probably illiterate, the evidence shows that he was a sympathetic and accurate reporter of the environments and cultures of Africa, the Caribbean, and North America. Most important, the evidence also shows that Ingram was not a travel liar. Historians have dismissed his observations for four centuries because they have depended upon Richard Hakluyt’s poorly edited published version of Ingram’s 1582 testimony. A curious postscript is that William Shakespeare apparently used some of Ingram’s testimony as a source for his play The Tempest, which he published in 1623.
Land Concentration
Authors: Berry Albert 
Published: December 2024

Abstract
Land concentration has been a central feature of the history of all empires, regions, and countries, and has underpinned the creation of the state and of inegalitarian and elitist societies. It is the key part of a “monopolization model” whereby a small group has access to the bulk of the available land and as much labor as it needs to achieve a high level of wealth. Access to that labor can occur either through slavery or through a sufficiently large supply of labor to keep its market price very low; this latter condition is fostered by the core group having nearly all the land such that little is left for the rest of the population. The degree of land concentration and elite control of labor have varied across cultures and over time, as have the means of concentration, including physical violence. The main early manifestation of the monopolization model was feudalism, in which both lord and serf had some rights and some obligations. It later morphed into market-based capitalism. When an economy “develops” beyond the phase in which the great majority of output and employment is found in agriculture to a more industrial and service-oriented system, the level of inequality characterizing it at the beginning of this transition tends to persist long after the country is no longer mainly agricultural.