bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioRxToolbox: a computational framework to streamline genetic circuit design in molecular data communications
Authors: Durmaz Merve Gorkem , Tulluk Neval , Aksoy Recep Deniz , Yilmaz Huseyin Birkan , Yang Bill , Wipat Anil , Pusane Ali Emre , Mısırlı Göksel , Tugcu Tuna 
Published: November 2024

Abstract
Developments in bioengineering and nanotechnology have ignited the research on biological and molecular communication systems. Despite potential benefits, engineering communication systems to carry data signals using biological messenger molecules and engineered cells is challenging. Diffusing molecules may fall behind their schedule to arrive at the receiver, interfering with symbols of subsequent time slots and distorting the signal. Existing theoretical molecular communication models often focus solely on the characteristics of a communication channel and fail to provide an end-to-end system response since they assume a simple thresholding process for a receiver cell and overlook how the receiver can detect the incoming distorted molecular signal. In this paper, we present a model-based and computational framework called BioRxToolbox for designing diffusion-based and end-to-end molecular communication systems coupled with synthetic genetic circuits. We describe a novel framework to encode information as a sequence of bits, each transmitted from the sender as a burst of molecules, control cellular behavior at the receiver, and minimize cellular signal interference by employing equalization techniques from communication theory. This approach allows the encoding and decoding of data bits efficiently using two different types of molecules that act as the data carrier and the antagonist to cancel out the heavy tail of the former. Here, BioRxToolbox is demonstrated using a biological design and computational simulations for various communication scenarios. This toolbox facilitates automating the choice of communication parameters and identifying the best communication scenarios that can produce efficient cellular signals.
LC3B-regulated autophagy mitigates zinc oxide nanoparticle-induced epithelial cell dysfunction and acute lung injury
Authors: Chen Ruonan , Luo Sen , Zhang Yunxiao , Mao Lejiao , Diao Jun , Cheng Shuqun , Zou Zhen , Chen Chengzhi , Qin Xia , Jiang Xuejun , Zhang Jun 
Published: November 2024

Abstract
Zinc oxide nanoparticles (ZnONPs) are widely utilized across various industries, raising concerns about their potential toxicity, especially in the respiratory system. This study explores the role of autophagy, regulated by microtubule-associated protein 1A/1B-light chain 3B (LC3B), in ZnONPs-induced toxicity using both in vivo (LC3B knockout mice) and in vitro (BEAS-2B cells) models. Our findings demonstrate that LC3B-regulated autophagy mitigates ZnONPs-induced epithelial cell dysfunction and acute lung injury. In the absence of LC3B, oxidative stress, inflammation, and intracellular zinc accumulation are exacerbated, resulting in mitochondrial dysfunction and epithelial cell death. In vitro, LC3B knockdown disrupted zinc ion transporter expression and impaired mitophagic flux in BEAS-2B cells. Treatment with zinc ion chelators alleviated these toxic effects, confirming that free zinc ions play a critical role in driving ZnONPs toxicity. These findings highlight that targeting autophagy and maintaining zinc homeostasis could offer therapeutic strategies to reduce ZnONPs-induced lung damage.
Impact of Knee Osteoarthritis and Arthroplasty on Full Body Sagittal Alignment in Adult Spinal Deformity Patients
Authors: Daher Mohammad , Daniels Alan H , Knebel Ashley , Balmaceno-Criss Mariah , Lafage Renaud , Lenke Lawrence G , Ames Chrisotpher P , Burton Douglas , Lewis Stephen M , Klineberg Eric O , Eastlack Robert K , Gupta Munish C. , Mundis Gregory M. , Gum Jeffrey L. , Hamilton Kojo D. , Hostin Richard , Passias Peter G. , Protopsaltis Themistocles S. , Kebaish Khaled M. , Kim Han Jo , Schwab Frank , Shaffrey Christopher I. , Smith Justin S. , Line Breton , Bess Shay , Lafage Virginie , Diebo Bassel G ,   on behalf of the International Spine Study Group (ISSG)
Published: November 2024

Study Design.
Retrospective analysis of prospectively collected data

Objective.
This study evaluates the impact of knee osteoarthritis (OA) and knee arthroplasty on alignments and patient-reported outcomes measures (PROMS) of patients undergoing adult spinal deformity (ASD) corrective surgery.

Background.
The relationship between knee OA and spinal alignment in patients with ASD is incompletely understood. It is also unknown how patients with knee arthroplasty and ASD compare to ASD patients with native knees.

Methods.
Baseline full-body radiographs were used, and hip and knee OA were graded by two independent reviewers using the KL classification. Spinopelvic parameters and PROMs were compared across the different knee OA groups and compared between patients with knee replacement and native knees.

Results.
199 patients with bilateral non severe OA (G1), 31 patients with unilateral severe knee OA (G2), and 60 patients with bilateral severe knee OA (G3). Patients with severe knee OA presented with worse spinopelvic parameters. However, after multivariable regression analysis controlling for age, frailty, PI, T1PA, knee OA was an independent predictor of knee flexion (G1:-0.02±7.3, G2: 7.8±9.4, G3: 4.5±8.7, P<0.001), and ankle dorsiflexion (G1: 2.3±4.0, G2: 6.6±4.5, G3: 5.1±4.1, P<0.001). There was no difference in PROMs (P>0.05). Secondary analysis included 96 patients: 48 patients (50%) with non-severe knee OA, and 48 patients (50%) with knee replacement. There was no difference in radiographic parameters or PROMs between the groups.

Conclusion.
In this study of complex ASD patients, patients with worse spinal deformity were more likely to have concomitant knee OA. Knee OA was shown to be a predictor of knee flexion and ankle dorsiflexion angles, but was not associated with worse PROMs in this study population. Patients with knee arthroplasty, however, had comparable spinal alignment and PROMs relative to those with mild OA.
Perioperative Considerations in Patients with Rett Syndrome as Compared to Those with Cerebral Palsy
Authors: Sarwahi Vishal , Rahman Effat , Eigo Katherine , Galina Jesse , Hasan Sayyida , Ko Andrew , Lo Yungtai , Amaral Terry , Djukic Aleksandra , Santiago Maria , Schneider James 
Published: November 2024

Study Design.
Retrospective cohort study

Objective.
This study aimed to compare perioperative outcomes of Rett syndrome and Cerebral palsy patients undergoing posterior spinal fusion for neuromuscular scoliosis.

Summary of Background Data.
Surgical correction in the treatment of scoliosis for patients with Rett syndrome (RS) has been shown to increase survival rate. Cerebral palsy (CP) patients, like RS patients, are often nonverbal, nonambulatory, with frequent surgical complications.

Methods.
Retrospective review of 36 RS and 80 CP patients undergoing PSF from 2005-2023. Data and x-ray measurements were collected pre- and post-operatively. Sub-analysis was performed comparing non-ambulatory patients (GMFCS IV-V). Wilcoxon-Rank Sum, Fisher’s Exact, and Chi-square tests were utilized.

Results.
The primary outcome measure, complication rates, was similar between the groups (P=0.09). Preoperative Cobb angle, levels fused, fixation points, and LOS were similar (P>0.05). EBL was significantly higher in CP patients as was rate of transfusion (P=0.001) and surgical time (P=0.001). Postoperative Cobb angle (P=0.002) was significantly higher for CP patients. There was no significant difference between CP and RS patients in both preoperative (P=0.383) and postoperative (P=0.051) coronal decompensation. Nonambulatory status was associated with increased odds of having a postoperative complication (OR=6.17, 95% C.I. 1.36 – 28.04). Sub-analysis of non-ambulatory RS and CP patients revealed significantly higher postoperative Cobb (P=0.008), EBL (P=0.019) and surgical time (P=0.017) in CP patients compared to RS patients. There were no significant differences in preoperative Cobb, levels fused, fixation points, hospital stay, or complication rate (P>0.05).

Conclusion.
RS patients are shown to have better outcomes to CP patients in terms of surgical, perioperative, and radiographic variables. Ambulatory status was identified as an independent risk factor for complications.
Quantitative Validation of Hematocrit Percentage Drop Cutoff Points in Postpartum Hemorrhage: An Automated Gravimetric Approach
Authors: Kway Venance Basil , Rojas José Enrique Calacuayo , Cuevas Josué Sidonio Rodríguez , Moreno Ursula Medina , Juárez José Sergio Camacho , González Jorge Francisco Ayala , Larraga Karla Krebs , Martinez Ilse Veronica Castro , Reyther Roberto Arturo Castillo , Moscoso Antonio Gordillo 
Published: November 2024

Abstract

Objective:
To validate the hematocrit percentage drop cutoff points for blood loss in patients with postpartum hemorrhage (PPH) using the automated gravimetric method.

Methods:
A prospective cohort study was conducted from January 2023 to July 2023, in which 107 patients 18 years of age and above were scheduled for elective cesarean with obstetrical indications. We excluded cases with difficulty quantifying blood loss, those with incomplete data, and those of patients who did not consent to participate. Blood loss was measured by an automated gravimetric system integrated into a suction blood collector and surgical gauze weighing systems to automatically sum up blood loss immediately after hysterectomy and fetal delivery. The percentage drop in hematocrit was determined by subtracting the 8-hour postsurgical from presurgical hematocrit, divided by presurgical hematocrit. We performed the Pearson correlation test, and the receiver operating characteristic curve was used to determine cutoff points, their sensitivity, and their specificity. The κ index was used to determine the diagnostic agreement between the two methods.

Results:
A positive correlation was observed between the volume of blood loss and the percentage drop in hematocrit, with a Pearson correlation index of 0.70 and P < 0.0001. A 14% decrease in hematocrit had an 81.7% agreement rate, with a good κ index of 0.602, a sensitivity of 82.5%, and a specificity of 80.0%. A 10% drop in hemoglobin was sensitive (93.0%) but not very specific (56.0%) for blood loss greater than 1000 mL.

Conclusion:
The automated gravimetric method strongly correlates with hematocrit changes, providing an accurate real-time diagnosis of PPH. Additionally, a hematocrit percentage drop can retrospectively indicate significant blood loss, aiding in managing patients at risk for long-term PPH complications.
Platelet-derived mitochondria regulate lipid metabolism in nonalcoholic steatohepatitis through extracellular vesicles
Authors: Liao Tsai-Ling , Chen Der-Yuan , Hsieh Shie-Liang , Yang Ying-Ying , Chen Yi-Ming , Tang Kuo-Tung , Chang Chung-Hsin , Yang Sheng-Shun 
Published: November 2024

Background and Aims:
Immune system activation, along with lipotoxicity due to excessive lipid droplet (LD) accumulation in the liver, are key drivers of NASH. Extracellular vesicles (EVs) released by cells that carry biological signals contribute to intercellular communication. However, the roles of immune cell–derived EVs in the pathogenesis of NASH are unclear.

Approach and Results:
Platelets are abundant in blood. We explored the role of platelet-derived EVs (pEVs) in LD accumulation from 30 patients with nonalcoholic fatty liver disease of different severity as well as 20 healthy subjects, a rat model, and an in vitro cell-based assay. There was increased platelet activation, accompanied by pEVs release, in NASH patients/rat model, and palmitate-treated cells. The mitochondria in the platelets and pEVs from NASH patients/rats were increased but dysfunctional, including a reduction in fatty acid β-oxidation, inactivated acetyl-CoA carboxylase 2, and suppressed oxidative phosphorylation system complex II/III/IV activity. These damaged mitochondria could be transferred to hepatocytes through pEVs to increase the number of lipid droplet–bound mitochondria. An increase in dysfunctional lipid droplet–bound mitochondria in hepatocytes affects lipid metabolism, resulting in excessive LD accumulation, elevated mitochondrial reactive oxygen species production, and apoptosis.

Conclusions:
We offer a novel molecular mechanism that connects platelets, pEVs, and excessive LD accumulation to the development of NASH. Our results suggest that NASH progression may be alleviated by specifically inhibiting the production and release of pEVs, or by targeting pEV components and inhibiting their uptake. Additional experiments are required to confirm this potentiality.
Human amniotic membrane overlay grafting for large retinal breaks in eyes with recurrent retinal detachment
Authors: Singh Deependra V , Reddy Raja R , Sharma Yog R 
Published: November 2024

Purpose:
To describe a new technique for placing large epiretinal human amniotic membrane grafts in 2 eyes with high myopia and recurrent retinal detachment resulting from large breaks over staphyloma not amenable to laser or cryo retinopexy.

Methods:
Surgical technique demonstration with video and images. We examined 2 high myopic eyes with large retinal breaks and recurrent rhegmatogenous retinal detachment (RRD) who had undergone RRD repair with silicon oil tamponade. Break was seen over nasal staphyloma in first case and over an atrophic area along with retinoschisis at posterior pole in the second. 25G vitrectomy with silicon oil removal was done and a large multilayered hAM graft was placed over large retinal breaks. Both eyes receive Gas tamponade. The patients were positioned face down for the first week after surgery. Optical coherence tomography (OCT) scans were performed in the follow-up visits.

Results:
Retinal breaks could be successfully closed in both eyes at 2 weeks and 3 months follow up. Large hAM grafts were stable and nicely visualized on post operative OCT scans and fundus photographs. These grafts were well tolerated with no displacement even at 12 months follow up. There was no recurrence of RRD noted in either eye.

Conclusion:
The large overlay hAM grafting is an effective and safe technique for closing large retinal breaks over staphyloma or atrophic retina in high myopes.
Corneal Refractive Surgery Considerations in Patients With History of Orthokeratology
Authors: Wang Victoria M. , Moin Kayvon A. , Hoopes Phillip C. , Moshirfar Majid 
Published: November 2024

Objective:
To review the current literature describing corneal changes observed with orthokeratology (ortho-k) use and to formulate preliminary recommendations for these patients seeking corneal refractive surgery.

Methods:
The literature search was conducted through the PubMed, Scopus, and Ovid databases through June 4, 2024, for articles regarding corneal physiological, tomographic, and biomechanical changes secondary to ortho-k use.

Results:
Forty-one articles were found describing several changes associated with ortho-k use, including higher corneal staining, central corneal epithelial thinning and midperipheral thickening, increased higher-order aberrations, decreased contrast sensitivity, reduced corneal hysteresis and corneal resistance factor, and alterations in the tear proteome. The majority of these parameters returned to baseline after ortho-k lens discontinuation, with timing potentially dependent on the amount of myopic correction, duration of ortho-k use, and age of lens fitting.

Conclusions:
Despite the paucity of articles describing prior ortho-k patients undergoing corneal refractive surgery, it is evident that ortho-k use may potentially cause various corneal physiological, tomographic, and biomechanical changes in patients. Therefore, clinicians are advised to serially monitor ortho-k patients' refraction, tomography, pachymetry, and corneal biomechanics until stability is achieved before considering surgery.
Enhancing Ex Vivo Limbal Epithelial Cell Expansion on Amniotic Membrane: A Comparative Study of Monolayer (2D) Versus Sandwich (3D) Culture Configurations
Authors: Kamachi Kobashigawa Karina , Franchi de Barros Sobrinho Alexandre Augusto , Espírito Santo Silva Paloma , Siqueira Vasconcelos Caio Rafael , Cardoso Cristovam Priscila , Pereira Gomes José Álvaro , Laus José Luiz , Aldrovani Rodrigues Marcela 
Published: November 2024

Purpose:This study compared two-dimensional (monolayer) and three-dimensional (sandwich) systems for expanding ex vivo limbal epithelial cells on amniotic membrane and evaluated the outcomes after transplantation into rabbits with experimentally induced limbal stem cell deficiency.Methods:Evaluations included markers for progenitor cells, proliferation, apoptosis, and clinical monitoring for up to 63 days. In the monolayer culture, epithelial cells derived from limbal explants were expanded on amniotic membrane as the substrate. In the sandwich culture, the cells were cultured between 2 layers of amniotic membrane. Evaluations included markers for progenitor cells, proliferation, and apoptosis, along with clinical monitoring for up to 63 days.Results:Sandwich cultures demonstrated increased cellular proliferation and fewer progenitor cells compared with monolayer cultures. In treating limbal stem cell deficiency, the group receiving transplantation from sandwich cultures exhibited reduced neovascularization and decreased corneal ulceration compared with those treated with monolayer cultures, with similar clinical outcomes in corneal opacity. The configuration of the culture system did not affect the presence of apoptotic cells. Corneas treated with sandwich cultures showed a higher presence of progenitor cells compared with the monolayer group, suggesting a potential long-term viability advantage for these transplants.Conclusions:In conclusion, although the sandwich culture system enhanced cellular proliferation, it also resulted in a decrease in progenitor cells within the cultures. Nevertheless, both systems demonstrated comparable therapeutic efficacy in treating limbal stem cell deficiency, with the sandwich approach potentially offering long-term benefits because of the increased presence of progenitor cells in the transplanted cornea.
Overlap syndrome: a case series and literature review of concurrent pigment dispersion and pseudoexfoliation syndromes
Authors: Shah Pooja , Soundararajan Srinath , Fleischman David 
Published: November 2024

Purpose of review
The purpose of this review is to present two cases of overlap syndrome, or concurrent pigment dispersion syndrome and pseudoexfoliation syndrome. The summary of existing literature highlights the importance of accurate diagnosis and potential treatment options of overlap syndrome.

Recent findings
The cases describe two patients with overlap syndrome and resulting progressive glaucoma. The condition tends to present after age 50 years old, with presence of both pseudoexfoliative material and pigment dispersion signs. The pigment dispersion syndrome may be quiescent at the time of pseudoexfoliation onset and may have gone undiagnosed. This form of glaucoma poses challenges in controlling intraocular pressure and may progress rapidly, often requiring surgical intervention.

Summary
This paper reviews the common examination findings of pigment dispersion syndrome and pseudoexfoliation, which may aid clinicians in the diagnosis of the rare condition, overlap syndrome. The connection between the two conditions remains unclear, though studies of possible genetic associations are underway. The two-hit theory, or initial damage to the trabecular meshwork increasing susceptibility to future damage, is plausible given the severe nature of the condition. Though definitive conclusions regarding treatment strategies and outcomes of overlap syndrome are lacking, increased awareness, diagnosis, and study of the condition may help guide the management of overlap syndrome.
Prevention of cardiometabolic diseases through dietary modifications
Authors: Chávez-Alfaro Lourdes , Silveira-Sanguino Víctor , Piernas Carmen 
Published: November 2024

Purpose of review
Cardiometabolic diseases (CMDs) increasingly contribute to the cumulative burden of morbidity and mortality worldwide. Here, we reviewed intervention studies using a randomized controlled trial (RCT) design as well as meta-analyses of RCTs aimed at testing the effectiveness of different dietary approaches for CMD prevention.

Recent findings
Recent studies testing dietary approaches for CMD prevention were summarized narratively, with a focus on interventions based on caloric restriction and fasting, healthy dietary patterns and food-based dietary modifications. Evidence supports intermittent fasting, Mediterranean, Nordic, DASH, low-carbohydrate/ketogenic and plant-based diets as effective strategies for improving cardiometabolic health. However, the benefits observed with some of these dietary patterns are linked to energy restriction, and the independent effects beyond weight loss remain unclear. The effectiveness of some strategies may also depend on the overall dietary quality and adherence to the programme.

Summary
Recent findings highlight the importance of focusing on overall dietary patterns, rather than isolated nutrients, for preventing CMD. Future research should prioritize long-term intervention studies to assess the sustained effects of these dietary patterns on CMD outcomes.
Treatment of spinal muscular atrophy
Authors: Pera Maria Carmela , Mercuri Eugenio 
Published: November 2024

Purpose of review
The aim of the review was to provide an overview of safety and efficacy of the available treatments including information from both clinical trials and real-world data. Additional information form ongoing studies using other approaches than increasing SMN protein are also reported.

Recent findings
In the last 3 years, there have been over 24 studies reporting safety and the impact of the available drugs on different aspects of function, including respiratory and bulbar function. These findings, obtained in a real-world setting, are extremely important to define the spectrum of responses in individuals with different age, weight, SMN2 copies, and other variables and will be of help to the families and the clinicians to set up the right expectations at the time of starting a new treatment.

Summary
The large number of studies that became available in the last few years support and expand the information on safety and efficacy provided by the clinical trials.