bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Early-Phase Clinical Trial Participants at Risk for Experiencing Worse Clinical Outcomes
Authors: Lundquist Debra M. , Jimenez Rachel , Durbin Sienna , Horick Nora , Healy Megan , Johnson Andrew , Bame Viola , Capasso Virginia , McIntyre Casandra , Cashavelly Barbara , Juric Dejan , Nipp Ryan D. 
Published: February 2023

PURPOSE: To identify early-phase clinical trial (EP-CT) participants at risk for experiencing worse clinical outcomes and describe receipt of supportive care services. METHODS: A retrospective review of the electronic health records of consecutive patients enrolled in EP-CTs from 2017 to 2019 examined baseline characteristics, clinical outcomes, and receipt of supportive care services. The validated Royal Marsden Hospital (RMH) prognosis score was calculated using data at the time of EP-CT enrollment (scores range from 0 to 3; scores ≥ 2 indicate poor prognosis). Differences in patient characteristics, clinical outcomes, and receipt of supportive care services were compared on the basis of RMH scores. RESULTS: Among 350 patients (median age = 63.2 years [range, 23.0-84.3 years], 57.1% female, 98.0% metastatic cancer), 31.7% had an RMH score indicating a poor prognosis. Those with poor prognosis RMH scores had worse overall survival (hazard ratio [HR], 2.00; P < .001), shorter time on trial (HR, 1.53; P < .001), and lower likelihood of completing the dose-limiting toxicity period (odds ratio, 0.42; P = .006) versus those with good prognosis scores. Patients with poor prognosis scores had greater risk of emergency room visits (HR, 1.66; P = .037) and hospitalizations (HR, 1.69; P = .016) while on trial, and earlier hospice enrollment (HR, 2.22; P = .006). Patients with poor prognosis scores were significantly more likely to receive palliative care consultation (46.8% v 27.6%; P < .001), but not other supportive care services. CONCLUSION: This study found that RMH prognosis score could identify patients at risk for decreased survival, shorter time on trial, and greater use of health care services. The findings underscore the need to develop supportive care interventions targeting EP-CT participants' distinct needs.
Single Cell Analysis of Human Thyroid Reveals the Transcriptional Signatures of Aging
Authors: Hong Yourae , Kim Hyun Jung , Park Seongyeol , Yi Shinae , Lim Mi Ae , Lee Seong Eun , Chang Jae Won , Won Ho-Ryun , Kim Je-Ryong , Ko Hyemi , Kim Seon-Young , Kim Seon-Kyu , Park Jong-Lyul , Chu In-Sun , Kim Jin Man , Kim Kun Ho , Lee Jeong Ho , Ju Young Seok , Shong Minho , Koo Bon Seok , Park Woong-Yang , Kang Yea Eun 
Published: February 2023

Abstract
The thyroid gland plays a critical role in the maintenance of whole-body metabolism. However, aging frequently impairs homeostatic maintenance by thyroid hormones due to increased prevalence of subclinical hypothyroidism associated with mitochondrial dysfunction, inflammation, and fibrosis. To understand the specific aging-related changes of endocrine function in thyroid epithelial cells, we performed single-cell RNA sequencing (RNA-seq) of 54 726 cells derived from pathologically normal thyroid tissues from 7 patients who underwent thyroidectomy. Thyroid endocrine epithelial cells were clustered into 5 distinct subpopulations, and a subset of cells was found to be particularly vulnerable with aging, showing functional deterioration associated with the expression of metallothionein (MT) and major histocompatibility complex class II genes. We further validated that increased expression of MT family genes are highly correlated with thyroid gland aging in bulk RNAseq datasets. This study provides evidence that aging induces specific transcriptomic changes across multiple cell populations in the human thyroid gland.
Successful therapeutic intervention in new mouse models of frizzled 2-associated congenital malformations
Authors: Liegel Ryan P. , Michalski Megan N. , Vaidya Sanika , Bittermann Elizabeth , Finnerty Erin , Menke Chelsea A. , Diegel Cassandra R. , Zhong Zhendong A. , Williams Bart O. , Stottmann Rolf W. 
Published: February 2023

ABSTRACT
Frizzled 2 (FZD2) is a transmembrane Wnt receptor. We previously identified a pathogenic human FZD2 variant in individuals with FZD2-associated autosomal dominant Robinow syndrome. The variant encoded a protein with a premature stop and loss of 17 amino acids, including a region of the consensus dishevelled-binding sequence. To model this variant, we used zygote microinjection and i-GONAD-based CRISPR/Cas9-mediated genome editing to generate a mouse allelic series. Embryos mosaic for humanized Fzd2W553* knock-in exhibited cleft palate and shortened limbs, consistent with patient phenotypes. We also generated two germline mouse alleles with small deletions: Fzd2D3 and Fzd2D4. Homozygotes for each allele exhibit a highly penetrant cleft palate phenotype, shortened limbs compared with wild type and perinatal lethality. Fzd2D4 craniofacial tissues indicated decreased canonical Wnt signaling. In utero treatment with IIIC3a (a DKK inhibitor) normalized the limb lengths in Fzd2D4 homozygotes. The in vivo replication represents an approach for further investigating the mechanism of FZD2 phenotypes and demonstrates the utility of CRISPR knock-in mice as a tool for investigating the pathogenicity of human genetic variants. We also present evidence for a potential therapeutic intervention.
The X chromosome still has a lot to reveal – revisiting Hermann Henking's work on firebugs
Authors: Paliulis Leocadia , Fabig Gunar , Müller-Reichert Thomas 
Published: February 2023

ABSTRACT
In 1891, the existence of an X chromosome was noted for the first time. Hermann Henking was studying spermatocyte divisions of the firebug Pyrrhocoris apterus and observed that one chromosome behaved differently than all of the rest of the chromosomes. Henking called this chromosome ‘Element x’. Henking's discovery of the X element (later called X chromosome) initiated more than a century of fascinating genetics and cell biology, forming the foundation of several avenues of research in biology. His work led to exploration of a number of questions in a wide range of model systems and very soon to the abandonment of the firebug as a model for studies on the behavior of chromosomes in meiosis. Here, we argue that studies on both bivalent and univalent chromosome behavior in general, and work on how to solve chromosome lagging to prevent aneuploidy in particular, should lead us back to using the firebug as a model for error correction during cell division.
Evolutionary trade-offs in osmotic and ionic regulation and expression of gill ion transporter genes in high latitude, cold clime Neotropical crabs from the ‘end of the world’
Authors: McNamara John Campbell , Maraschi Anieli Cristina , Tapella Federico , Romero Maria Carolina 
Published: February 2023

ABSTRACTOsmoregulatory findings on crabs from high Neotropical latitudes are entirely lacking. Seeking to identify the consequences of evolution at low temperature, we examined hyperosmotic/hypo-osmotic and ionic regulation and gill ion transporter gene expression in two sub-Antarctic Eubrachyura from the Beagle Channel, Tierra del Fuego. Despite sharing the same osmotic niche, Acanthocyclus albatrossis tolerates a wider salinity range (2–65‰ S) than Halicarcinus planatus (5–60‰ S); their respective lower and upper critical salinities are 4‰ and 12‰ S, and 63‰ and 50‰ S. Acanthocyclus albatrossis is a weak hyperosmotic regulator, while H. planatus hyperosmoconforms; isosmotic points are 1380 and ∼1340 mOsm kg−1 H2O, respectively. Both crabs hyper/hypo-regulate [Cl−] well with iso-chloride points at 452 and 316 mmol l−1 Cl−, respectively. [Na+] is hyper-regulated at all salinities. mRNA expression of gill Na+/K+-ATPase is salinity sensitive in A. albatrossis, increasing ∼1.9-fold at 5‰ compared with 30‰ S, decreasing at 40–60‰ S. Expression in H. planatus is very low salinity sensitive, increasing ∼4.7-fold over 30‰ S, but decreasing at 50‰ S. V-ATPase expression decreases in A. albatrossis at low and high salinities as in H. planatus. Na+/K+/2Cl− symporter expression in A. albatrossis increases 2.6-fold at 5‰ S, but decreases at 60‰ S versus 30‰ S. Chloride uptake may be mediated by increased Na+/K+/2Cl− expression but Cl− secretion is independent of symporter expression. These unrelated eubrachyurans exhibit similar systemic osmoregulatory characteristics and are better adapted to dilute media; however, the expression of genes underlying ion uptake and secretion shows marked interspecific divergence. Cold clime crabs may limit osmoregulatory energy expenditure by hyper/hypo-regulating hemolymph [Cl−] alone, apportioning resources for other energy-demanding processes.
Multiscale flow between the branches and polyps of gorgonians
Authors: Hamlet Christina L. , Strickland W. Christopher , Battista Nicholas , Miller Laura A. 
Published: February 2023

ABSTRACT
Gorgonians, including sea fans, are soft corals well known for their elaborate branching structure and how they sway in the ocean. This branching structure can modify environmental flows to be beneficial for feeding in a particular range of velocities and, presumably, for a particular size of prey. As water moves through the elaborate branches, it is slowed, and recirculation zones can form downstream of the colony. At the smaller scale, individual polyps that emerge from the branches expand their tentacles, further slowing the flow. At the smallest scale, the tentacles are covered in tiny pinnules where exchange occurs. In this paper, we quantified the gap to diameter ratios for various gorgonians at the scale of the branches, the polyp tentacles and the pinnules. We then used computational fluid dynamics to determine the flow patterns at all three levels of branching. We quantified the leakiness between the branches, tentacles and pinnules over the biologically relevant range of Reynolds numbers and gap-to-diameter ratios, and found that the branches and tentacles can act as either leaky rakes or solid plates depending upon these dimensionless parameters. The pinnules, in contrast, mostly impede the flow. Using an agent-based modeling framework, we quantified plankton capture as a function of the gap-to-diameter ratio of the branches and the Reynolds number. We found that the capture rate depends critically on both morphology and Reynolds number. The results of the study have implications for how gorgonians modify ambient flows for efficient feeding and exchange.
Virtual biopsy in abdominal pathology: where do we stand?
Authors: Defeudis Arianna , Panic Jovana , Nicoletti Giulia , Mazzetti Simone , Giannini Valentina , Regge Daniele 
Published: February 2023

Abstract
In recent years, researchers have explored new ways to obtain information from pathological tissues, also exploring non-invasive techniques, such as virtual biopsy (VB). VB can be defined as a test that provides promising outcomes compared to traditional biopsy by extracting quantitative information from radiological images not accessible through traditional visual inspection. Data are processed in such a way that they can be correlated with the patient’s phenotypic expression, or with molecular patterns and mutations, creating a bridge between traditional radiology, pathology, genomics, and artificial intelligence (AI). Radiomics is the backbone of VB, since it allows the extraction and selection of features from radiological images, feeding them into AI models in order to derive lesions' pathological characteristics and molecular status. Presently, the output of VB provides only a gross approximation of the findings of tissue biopsy. However, in the future, with the improvement of imaging resolution and processing techniques, VB could partially substitute the classical surgical or percutaneous biopsy, with the advantage of being non-invasive, comprehensive, accounting for lesion heterogeneity, and low cost. In this review, we investigate the concept of VB in abdominal pathology, focusing on its pipeline development and potential benefits.
Effect of the annealing temperature on structural, morphological, and nonlinear optical properties of TeO2 thin films used for efficient THz generation
Authors: Mahendar M. , Krishna R. N. Vamsi , Chaudhary A. K. 
Published: February 2023

This paper reports the effect of annealing on TeO2 films deposited using the thermal evaporation technique. TeO2 films of 120 nm thickness were grown on a glass substrate at room temperature (RT) and annealed at 400°C and 450°C. The structure of the film and the influence of the annealing temperature on the crystalline phase change were examined using the X-ray diffraction method. Optical properties such as transmittance, absorbance, complex refractive index, and energy bandgap were determined between ultraviolet-visible to terahertz (THz) range. These films have a direct allowed transition with the optical energy bandgap of 3.66, 3.64, and 3.54 eV at as-deposited temperatures (RTs) of 400°C and 450°C. The effect of the annealing temperature on the morphology and surface roughness of the films was investigated using atomic force microscopy. The nonlinear optical parameters, which are the refractive index and absorption coefficients, were calculated using THz time domain spectroscopy. The microstructure variation of the TeO2 films in terms of surface orientation plays an important role in understanding the change in the nonlinear optical properties of the films. Finally, these films were subjected to 800 nm wavelength of 50 fs pulse duration obtained from a Ti:sapphire amplifier at a 1 kHz repetition rate for efficient THz generation. The power of incidence of the laser beam was tuned at a range between 75 and 105 mW; the highest power of the generated THz signal was of the order of 210 nW for 450°C annealed film with respect to the incident power of 105 mW. The conversion efficiency was found to be ∼0.22×10−5%, which is 2.025 times more than the film annealed at 400°C.
Highly efficient and tunable polarization rotator based on lithium niobate on an insulator
Authors: He Xiangyu , Xu Yin , Zhang Bo , Dong Yue , Ni Yi 
Published: February 2023

The lithium niobate on an insulator (LNOI) platform has greatly advanced the development of integrated photonics recently, where efficient polarization management components are indispensable. In this work, we propose a highly efficient and tunable polarization rotator based on the LNOI platform and the low-loss optical phase change material antimony triselenide (Sb2Se3). The key polarization rotation region is formed by a LNOI waveguide with a cross section of the double trapezoidal shape and a Sb2Se3 layer deposited atop the LNOI waveguide in an asymmetrical way, where an isolating layer of silicon dioxide is sandwiched between them to reduce the material absorption loss. Based on such a structure, we have achieved the efficient polarization rotation in a length of only 17.7 µm, where the polarization conversion efficiency and insertion loss are 99.6% (99.2%) and 0.38 dB (0.4 dB) for the trans-electric (TE)-to-trans-magnetic (TM) rotation. If we further change the phase state of the Sb2Se3 layer, other polarization rotation angles besides 90° can also be obtained for the same device, revealing a tunable function. We believe that the proposed device and design scheme could offer an efficient method for realizing the polarization management on the LNOI platform.
Implementation of miniaturized modular-array fluorescence microscopy for long-term live-cell imaging
Authors: Chen Qingyu , Son Jeonghwan , Jia Shu 
Published: February 2023

Fluorescence microscopy imaging of live cells has provided consistent monitoring of dynamic cellular activities and interactions. However, because current live-cell imaging systems are limited in their adaptability, portable cell imaging systems have been adapted by a variety of strategies, including miniaturized fluorescence microscopy. Here, we provide a protocol for the construction and operational process of miniaturized modular-array fluorescence microscopy (MAM). The MAM system is built in a portable size (15cm×15cm×3cm) and provides in situ cell imaging inside an incubator with a subcellular lateral resolution (∼3µm). We demonstrated the improved stability of the MAM system with fluorescent targets and live HeLa cells, enabling long-term imaging for 12 h without the need for external support or post-processing. We believe the protocol could guide scientists to construct a compact portable fluorescence imaging system and perform time-lapse in situ single-cell imaging and analysis.
A Wedge Made in an Artificial Dielectric
Authors: Giaconia C. , Torrini R. , Murad S. , Wilkinson C.D.W. 
Published: February 2023

Conventional diffractive optical components require fabrication of an approximation to a surface shape and to achieve high efficiency, it is necessary to use multiple levels to build up the desired shape. For say 16 steps, four masking steps are required and each has to be accurately aligned. The overall process is time-consuming and does not have good yield. However the phase of the light can be controlled locally by using a series of slots of different widths provided these slots are narrow enough to avoid diffraction - thus forming an artificial dielectric. The key point is that the slots all have same depth and so only a single lithographic step is required.
We have designed artificial dielectric components using a hybrid technique that combines Rigorous Coupled Wave Theory (RCWA) and Effective Medium Theory (EMT). The model allows for the constraints imposed by fabrication (minimum linewidth and maximum aspect ratio of features) to be included automatically in the optimisation of the design. The first design is for a wedge, to be built in Gallium Arsenide for operation at a wavelength of 1.15 μm. The design has a theoretically diffraction efficiency greater than 90%.
The designed pattern is written in electron beam resist (PMMA) using a Leica Beamwriter. After development the pattern is transferred into an 100 nm thick layer of silicon oxide deposited by plasma enhanced chemical vapour deposition. This is then used as the masking layer in the transfer of the pattern into an epitaxial GaAs film on a GaAs substrate. The oxide layer is removed by wet etching prior to testing.
The wedge has an overall period of 2.3 μm and is divided into seven slots with a minimum linewidth of 70 nm. The etch depth is 740 nm. Initial devices gave a diffraction efficiency of greater than 80% - further details of the device performance will be given.
Optical body fat measurement might contribute to the search for a predictor of type-2 diabetes mellitus
Authors: Tafeit Erwin , Horejs Renate , Sudi Karl , Berg Aloys , Reibnegger Gilbert , Möller Reinhard 
Published: February 2023

The optical device LIPOMETER allows for non-invasive, quick, precise and safe determination of subcutaneous fat distribution, so-called subcutaneous adipose tissue topography (SAT-Top).
Previously we showed how the high-dimensional SAT-Top information of women with type-2 diabetes mellitus (NIDDM) and a healthy control group can be analysed and represented in low-dimensional plots by applying special artificial neural networks (ANNs). Three top-down sorted subcutaneous adipose tissue compartments were determined (upper trunk, lower trunk, legs). NIDDM women provided significantly higher upper trunk obesity and significantly lower leg obesity ('apple' type), as compared with their healthy control group.
Now we apply these ANN results on SAT-Top measurements of young and healthy women, comparing their individual subcutaneous fat pattern to the body fat distribution of NIDDM women and to the „normal fat development" of healthy women. Some of these young and healthy women provide a subcutaneous fat distribution very similar to the SAT-Top results of NIDDM women, which might increase their risk for this disease later in life.
Testing of efficacy of photodynamic therapy with a new photosensitizer - a of chlorin e6 derivative (BLC 1010)
Authors: Stranadko E. Ph. , Riabov M.V. , N.VoIkova N. , Spaniol S. , Rauschning W. , Nifantiev N.E. 
Published: February 2023

Efficacy of PDT with new chlorin e6 photosensitizer (BLC 1010) has been tested in 72 cancer patients. 44 patients (61 %) achieved a complete response and 39 % of the patients a partial response (28 patients, including 15 patients treated for palliation).
Rapid elimination of BLC 1010 from the organism solves the problem of skin phototoxicity encountered in PDT up to now. This property together with its high tumor to normal ratio makes it a promising photosensitizer for PDT. Further advantage is that portable diode lasers with proper wavelength are available.
Defects in Coatings Deposited by Planar Magnetron Sputtering: Measurements with a Tencor Surfscan 6200
Authors: Nguyen Khanh B. , Resnick Paul , Draper Bruce , Mahl Paul , Underwood James H. , Chen Daniel , Denham Paul 
Published: February 2023

Defect densities in coatings deposited by planar magnetron sputtering were measured with a Tencor
Surfscan 6200 laser particle detector. The measurements were performed on two sets of coatings - one
deposited in a research chamber at the Center for X-ray Optics (CXRO) at Lawrence Berkeley
Laboratories, the other deposited in a MTI Sypherline used for metal deposition in a class 1
cleanroom at the Microelectronics Development Laboratory (MDL) at Sandia National Laboratories.
For coatings deposited in the research chamber, as much as 90% of the defects counted were
particulates deposited during venting of the chamber. As a result, these defects were located on the
surface of the coatings and were removable by ultrasonic clean in de-ionized water. Of the remaining
defects on these coatings, as much as 75% of them were generated from inside the chamber during the
coating process. The average number of defects in 30 bilayers of Mo/Si was 20 cm-2 for
defects of sizes ≥ 0.5 µm latex-sphere-equivalent (LSE) diameter.
For coatings deposited in a clean chamber located in a class 1 cleanroom, the density of ≥ 0.5 µm LSE
diameter defects in a 1000 Å thick Si film was 0.2 cm-2. This is two orders of magnitude
fewer defects compared with coatings deposited in a research chamber. For ≥ 0.14 µm LSE diameter
defects, defect density was 7 cm-2. Defect density also increased with increased film
thickness.