tbuckley/cabot-search huggingface dataset:
Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs
Authors: Ming Zhang, Yanbo Song, Caihui Wang, Guoping Sun, Lina Zhuang, Mingjian Guo, Lele Ren, Shargan Wangdue, Guanghui Dong, Qingyan Dai, Peng Cao, Ruowei Yang, Feng Liu, Xiaotian Feng, E Andrew Bennett, Xiaoling Zhang, Xi Chen, Fen Wang, Fengshi Luan, Wenbin Dong, Guoquan Lu, Daohua Hao, Hongwei Hou, Hui Wang, Hong Qiao, Zhongxin Wang, Xiaojun Hu, Wei He, Lin Xi, Weilin Wang, Jing Shao, Zhouyong Sun, Lianjian Yue, Yan Ding, Norbu Tashi, Yang Tsho, Yan Tong, Yangheshan Yang, Shilun Zhu, Bo Miao, Wenjun Wang, Lizhao Zhang, Songmei Hu, Xijun Ni, Qiaomei Fu
Journal: Molecular Biology and Evolution (2024)

Abstract Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.
Correlated Allele Frequency Changes Reveal Clonal Structure and Selection in Temporal Genetic Data
Authors: Yunxiao Li, John P Barton
Journal: Molecular Biology and Evolution (2024)

Abstract In evolving populations where the rate of beneficial mutations is large, subpopulations of individuals with competing beneficial mutations can be maintained over long times. Evolution with this kind of clonal structure is commonly observed in a wide range of microbial and viral populations. However, it can be difficult to completely resolve clonal dynamics in data. This is due to limited read lengths in high-throughput sequencing methods, which are often insufficient to directly measure linkage disequilibrium or determine clonal structure. Here, we develop a method to infer clonal structure using correlated allele frequency changes in time-series sequence data. Simulations show that our method recovers true, underlying clonal structures when they are known and accurately estimate linkage disequilibrium. This information can then be combined with other inference methods to improve estimates of the fitness effects of individual mutations. Applications to data suggest novel clonal structures in an E. coli long-term evolution experiment, and yield improved predictions of the effects of mutations on bacterial fitness and antibiotic resistance. Moreover, our method is computationally efficient, requiring orders of magnitude less run time for large data sets than existing methods. Overall, our method provides a powerful tool to infer clonal structures from data sets where only allele frequencies are available, which can also improve downstream analyses.
Updated Analysis of Comparative Toxicity of Proton and Photon Radiation for Prostate Cancer
Authors: James B. Yu, David M. DeStephano, Brian Jeffers, David P. Horowitz, Pamela R. Soulos, Cary P. Gross, Simon K. Cheng
Journal: Journal of Clinical Oncology (2024)

Previous comparative effectiveness studies have not demonstrated a benefit of proton beam therapy (PBT) compared with intensity-modulated radiation therapy (IMRT) for prostate cancer. An updated comparison of GI and genitourinary (GU) toxicity is needed.
Reduced-Volume Irradiation of Uninvolved Neck in Patients With Nasopharyngeal Cancer: Updated Results From an Open-Label, Noninferiority, Multicenter, Randomized Phase III Trial
Authors: Cheng-Long Huang, Ning Zhang, Wei Jiang, Fang-Yun Xie, Xiao-Qing Pei, Shao Hui Huang, Xue-Yan Wang, Yan-Ping Mao, Kun-Peng Li, Qing Liu, Ji-Bin Li, Shao-Qiang Liang, Guan-Jie Qin, Wei-Han Hu, Guan-Qun Zhou, Jun Ma, Ying Sun, Lei Chen, Ling-Long Tang
Journal: Journal of Clinical Oncology (2024)

JCO
Germline cancer susceptibility in individuals with melanoma
Authors: Pauline Funchain, Ying Ni, Brandie Heald, Brandon Bungo, Michelle Arbesman, Tapas R. Behera, Shelley McCormick, Jung Min Song, Lucy Boyce Kennedy, Sarah M. Nielsen, Edward D. Esplin, Emily Nizialek, Jennifer Ko, Claudia M. Diaz-Montero, Brian Gastman, Alexander J. Stratigos, Mykyta Artomov, Hensin Tsao, Joshua Arbesman
Journal: Journal of the American Academy of Dermatology (2024)
Correction: Effectiveness of a monthly schedule of follow-up for the treatment of uncomplicated severe acute malnutrition in Sokoto, Nigeria: A cluster randomized crossover trial
Authors: Matt D. T. Hitchings, Fatou Berthé, Philip Aruna, Ibrahim Shehu, Muhammed Ali Hamza, Siméon Nanama, Chizoba Steve-Edemba, Rebecca F. Grais, Sheila Isanaka
Journal: PLoS Medicine (2024)

[This corrects the article DOI: 10.1371/journal.pmed.1003923.].
Real-time Trajectory Planning and Tracking Control of Bionic Underwater Robot in Dynamic Environment
Authors: Feng Ding, Rui Wang, Tiandong Zhang, Gang Zheng, Zhengxing Wu, Shuo Wang
Journal: Cyborg and Bionic Systems (2024)

In this article, we study the trajectory planning and tracking control of a bionic underwater robot under multiple dynamic obstacles. We first introduce the design of the bionic leopard cabinet underwater robot developed in our lab. Then, we model the trajectory planning problem of the bionic underwater robot by combining its dynamics and physical constraints. Furthermore, we conduct global trajectory planning for bionic underwater robots based on the temporal-spatial Bezier curves. In addition, based on the improved proximal policy optimization, local dynamic obstacle avoidance trajectory replanning is carried out. In addition, we design the fuzzy proportional-integral-derivative controller for tracking control of the planned trajectory. Finally, the effectiveness of the real-time trajectory planning and tracking control method is verified by comparative simulation in dynamic environment and semiphysical simulation of UWSim. Among them, the real-time trajectory planning method has advantages in trajectory length, trajectory smoothness, and planning time. The error of trajectory tracking control method is controlled around 0.2 m.
A Wrist-Inspired Magneto-Pneumatic Hybrid-Driven Soft Actuator with Bidirectional Torsion
Authors: Yan Xu, Kaiwen Ju, Chao Zhang
Journal: Cyborg and Bionic Systems (2024)

A novel wrist-inspired soft actuator, which is driven by a magneto-pneumatic hybrid system and based on a Kresling origami unit, is proposed. The geometric model, kinematic analysis model, and quasistatic analysis model of the Kresling origami unit are presented. A key focus is on the formulation and investigation of the variation in rotation angle using the kinematic analysis model. A wrist-inspired soft actuator is designed, and its quasistatic characteristics are validated through various experiments. The paper proposes an innovative magneto-pneumatic hybrid actuation method, capable of achieving bidirectional torsion. This actuation method is experimentally validated, demonstrating the actuator's ability to maintain 3 steady states and its capability for bidirectional torsion deformation. Furthermore, the paper highlights the potential of the Kresling origami unit in designing soft actuators capable of achieving large rotation angles. For instance, an actuator with 6 sides ( n = 6) is shown to achieve a rotation angle of 239.5°, and its rotation ratio exceeds 277°, about twice the largest one reported in other literature. The actuator offers a practical and effective solution for bidirectional torsion deformation in soft robotic applications.
An Operating Stiffness Controller for the Medical Continuum Robot Based on Impedance Control
Authors: Jinyu Duan, Kai Zhang, Kun Qian, Jianxiong Hao, Zhiqiang Zhang, Chaoyang Shi
Journal: Cyborg and Bionic Systems (2024)

Continuum manipulators can conform to curvilinear paths and manipulate objects in complex environments, which makes it emerging to be applied in minimally invasive surgery (MIS). However, different and controllable operating stiffness of the continuum manipulator is required during different stages of surgery to achieve safe access or stable and precise operation. This work proposes an operating stiffness controller (OSC) for the typical tendon-driven continuum manipulator based on the variable impedance control method with Lagrangian dynamic modeling. This controller can adjust the operating stiffness by modifying the driving forces along the driving tendons of the continuum manipulator without changing its material or structure. The proposed OSC converts the damping and stiffness matrices of the impedance control into variable parameters. This merit allows it to dynamically adjust the operating stiffness of the continuum manipulator according to the desired constant or time-varying stiffness. Furthermore, the OSC stability can be proven based on a Lyapunov function, and its stiffness control performances have been analyzed and evaluated in both simulations and experiments. The OSC controller generated average relevant error values of 7.82% and 3.09% for the operating stiffness control experiments with constant and time-varying desired stiffness, respectively. These experimental results indicate that the OSC has high accuracy, stability, and strong robustness in the operating stiffness control tasks.
Stem cell factor and cKIT modulate endothelial glycolysis in hypoxia
Authors: Hayoung Jeong, Ryul-I Kim, Hyunwoo Koo, Yang Hee Choi, Minju Kim, Hyejin Roh, Sang Gyu Park, Jong-Hyuk Sung, Koung Li Kim, Wonhee Suh
Journal: Cardiovascular Research (2024)

In hypoxia, endothelial cells (ECs) proliferate, migrate, and form new vasculature in a process called angiogenesis. Recent studies have suggested that ECs rely on glycolysis to meet metabolic needs for angiogenesis in ischaemic tissues, and several studies have investigated the molecular mechanisms integrating angiogenesis and endothelial metabolism. Here, we investigated the role of stem cell factor (SCF) and its receptor, cKIT, in regulating endothelial glycolysis during hypoxia-driven angiogenesis.
The Effect of Chronic Altitude Exposure on COPD Outcomes in the SPIROMICS Cohort
Authors: Rajat Suri, Daniela Markovic, Han Woo, Mehrdad Arjomandi, R. Graham Barr, Russell P. Bowler, Gerard Criner, Jeffrey L. Curtis, Mark T. Dransfield, M. Bradley Drummond, Spyridon Fortis, MeiLan K. Han, Eric A. Hoffman, Robert J. Kaner, Joel D. Kaufman, Jerry A. Krishnan, Fernando J. Martinez, Jill Ohar, Victor E. Ortega, Robert Paine, Xavier Soler, Prescott G. Woodruff, Nadia N. Hansel, Christopher B. Cooper, Donald P. Tashkin, Russell G. Buhr, Igor Z. Barjaktarevic
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

Rationale: Individuals with COPD have airflow obstruction and maldistribution of ventilation. For those living at high altitude, any gas exchange abnormality is compounded by reduced partial pressures of inspired oxygen. Objectives: Does residence at higher-altitude exposure affect COPD outcomes, including lung function, imaging characteristics, symptoms, health status, functional exercise capacity, exacerbations, or mortality? Methods: From the SPIROMICS cohort, we identified individuals with COPD living below 1,000 ft (305 m) elevation (n= 1,367) versus above 4,000 ft (1,219 m) elevation (n= 288). Multivariable regression models were used to evaluate associations of exposure to high altitude with COPD-related outcomes. Measurements and Main Results: Living at higher altitude was associated with reduced functional exercise capacity as defined by 6MWD (-32.3 m, (-55.7 to -28.6)). There were no differences in patient-reported outcomes as defined by symptoms (CAT, mMRC), or health status (SGRQ). Higher altitude was not associated with a different rate of FEV1 decline. Higher altitude was associated with lower odds of severe exacerbations (IRR 0.65, (0.46 to 0.90)). There were no differences in small airway disease, air trapping, or emphysema. In longitudinal analyses, higher altitude was associated with increased mortality (HR 1.25, (1.0 to 1.55)); however, this association was no longer significant when accounting for air pollution. Conclusions: Chronic altitude exposure is associated with reduced functional exercise capacity in individuals with COPD, but this did not translate into differences in symptoms or health status. Additionally, chronic high-altitude exposure did not affect progression of disease as defined by longitudinal changes in spirometry.
Light emitting diode (LED) irradiation of liposomes enhances drug encapsulation and delivery for improved cancer eradication
Authors: Sujeong Lee, Hye Jin Kim, Jin-Ho Choi, Hye Jung Jang, Hui Bang Cho, Hye-Ryoung Kim, Ji-in Park, Kyung-soon Park, Keun-Hong Park
Journal: Journal of Controlled Release (2024)

Liposomes are widely used as drug delivery nanoplatforms because of their versatility and biocompatibility; however, their ability to load certain drugs may be suboptimal. In this study, we generated liposomes using a combination of DSPE and DSPE-PEG-2 k lipids and loaded them with doxorubicin (DOX) and paclitaxel (PTX), to investigate the effects of light emitting diode (LED) irradiation on liposome structure and drug loading efficiency. Scanning and transmission electron microscopy revealed that the surface of liposomes irradiated with blue or near-infrared LEDs (LsLipo) was rougher and more irregular than that of non-LED-irradiated liposomes (NsLipo). Nuclear magnetic resonance analysis showed that the hydrogen peak originating from the lipid head groups was lower in LsLipo than in NsLipo preparations, indicating that LED irradiation changed the chemical and physical properties of the liposome. Structural changes, such as reduced rigidity, induced by LED irradiation, increased the loading efficiency of DOX and PTX. In vitro and in vivo experiments showed that LsLipo were more effective at inhibiting the growth of cancer cells than NsLipo. Our findings suggest that LED irradiation enhances the drug delivery efficacy of liposomes and offer new possibilities for improving drug delivery systems.
FAK, vinculin, and talin control mechanosensitive YAP nuclear localization
Authors: Elijah N. Holland, Marc A. Fernández-Yagüe, Dennis W. Zhou, Eric B. O'Neill, Ayanna U. Woodfolk, Ana Mora-Boza, Jianping Fu, David D. Schlaepfer, Andrés J. García
Journal: Biomaterials (2024)
An unusual complication of arteriovenous fistula
Authors: Marc-Antoine Béland, Nicolas A.D. Bergeron, Mathieu Béland, Ludwig Haydock, Paul Isenring
Journal: Kidney International (2024)

A 73-year-old woman undergoing hemodialysis began to develop small skin crusts over a 1.5-cm area in her left forearm, where repeated punctures had been performed to access a native radiocephalic fistula. Over several weeks, these crusts expanded progressively and merged into a single scab. Subsequently, the scab detached from the skin to reveal a large 0.5 by 1.0 cm ulcer that extended onto the surface of a venous stent (Figure 1a and b). There were no apparent signs of local infection, and wound cultures were negative. Antibiotics were administered for a duration of 4 weeks. A computed tomography angiogram of the left arm showed that the vein was patent and contained the stent at the site of exposure (Figure 1c). The forearm portion of the cephalic vein containing the stent was ultimately excised. The structure seen at the base of the ulcer was a Supera stent (Figure 1d) that had been deployed in the cephalic vein 2 years before to address an intractable stenotic lesion (Figure 1e). The complication of an exposed venous stent does not appear to have been reported in the literature. The ulcer likely occurred from repeated punctures, and the adjacent adventitial/medial wall also appeared to be affected by the degenerative process. As such, vascular integrity at this location was essentially secured by a thick intimal layer of hyperplastic and fibrotic tissue (Figure 1e). This complication should serve as a warning against overusing the same confined site to cannulate native hemodialysis accesses. All the authors declared no competing interests. This work was supported by the Canadian Institutes of Health and Research.
A toolkit for ISN’s registry initiative, SharE-RR
Authors: Maria Pippias, Rajitha A. Abeysekera, Silvia Arruebo, M. Razeen Davids, Sandrine Damster, Maria C. Gonzales-Bedat, Norio Hanafusa, Junichi Hoshino, Anne Hradsky, Georgina L. Irish, Kitty J. Jager, Sabine Karam, Vivek Kumar, Stephen P. McDonald, Guillermo J. Rosa-Diez, Elliot K. Tannor, James B. Wetmore, Fergus J. Caskey
Journal: Kidney International (2024)
Apelin stimulation of the vascular skeletal muscle stem cell niche enhances endogenous repair in dystrophic mice
Authors: Emmeran Le Moal, Yuguo Liu, Jasmin Collerette-Tremblay, Simon Dumontier, Paul Fabre, Thomas Molina, Junio Dort, Zakaria Orfi, Nicolas Denault, Joël Boutin, Joris Michaud, Hugo Giguère, Alexandre Desroches, Kien Trân, Benjamin Ellezam, François Vézina, Sonia Bedard, Catherine Raynaud, Frederic Balg, Philippe Sarret, Pierre-Luc Boudreault, Michelle S. Scott, Jean-Bernard Denault, Eric Marsault, Jerome N. Feige, Mannix Auger-Messier, Nicolas A. Dumont, C. Florian Bentzinger
Journal: Science Translational Medicine (2024)

Impaired skeletal muscle stem cell (MuSC) function has long been suspected to contribute to the pathogenesis of muscular dystrophy (MD). Here, we showed that defects in the endothelial cell (EC) compartment of the vascular stem cell niche in mouse models of Duchenne MD, laminin α2–related MD, and collagen VI–related myopathy were associated with inefficient mobilization of MuSCs after tissue damage. Using chemoinformatic analysis, we identified the 13–amino acid form of the peptide hormone apelin (AP-13) as a candidate for systemic stimulation of skeletal muscle ECs. Systemic administration of AP-13 using osmotic pumps generated a pro-proliferative EC-rich niche that supported MuSC function through angiocrine factors and markedly improved tissue regeneration and muscle strength in all three dystrophic mouse models. Moreover, EC-specific knockout of the apelin receptor led to regenerative defects that phenocopied key pathological features of MD, including vascular defects, fibrosis, muscle fiber necrosis, impaired MuSC function, and reduced force generation. Together, these studies provide in vivo proof of concept that enhancing endogenous skeletal muscle repair by targeting the vascular niche is a viable therapeutic avenue for MD and characterized AP-13 as a candidate for further study for the systemic treatment of MuSC dysfunction.
A tough bioadhesive hydrogel supports sutureless sealing of the dural membrane in porcine and ex vivo human tissue
Authors: Kyle C. Wu, Benjamin R. Freedman, Phoebe S. Kwon, Matthew Torre, Daniel O. Kent, Wenya Linda Bi, David J. Mooney
Journal: Science Translational Medicine (2024)

Complete sequestration of central nervous system tissue and cerebrospinal fluid by the dural membrane is fundamental to maintaining homeostasis and proper organ function, making reconstruction of this layer an essential step during neurosurgery. Primary closure of the dura by suture repair is the current standard, despite facing technical, microenvironmental, and anatomic challenges. Here, we apply a mechanically tough hydrogel paired with a bioadhesive for intraoperative sealing of the dural membrane in rodent, porcine, and human central nervous system tissue. Tensile testing demonstrated that this dural tough adhesive (DTA) exhibited greater toughness with higher maximum stress and stretch compared with commercial sealants in aqueous environments. To evaluate the performance of DTA in the range of intracranial pressure typical of healthy and disease states, ex vivo burst pressure testing was conducted until failure after DTA or commercial sealant application on ex vivo porcine dura with a punch biopsy injury. In contrast to commercial sealants, DTA remained adhered to the porcine dura through increasing pressure up to 300 millimeters of mercury and achieved a greater maximum burst pressure. Feasibility of DTA to repair cerebrospinal fluid leak in a simulated surgical context was evaluated in postmortem human dural tissue. DTA supported effective sutureless repair of the porcine thecal sac in vivo. Biocompatibility and adhesion of DTA was maintained for up to 4 weeks in rodents after implantation. The findings suggest the potential of DTA to augment or perhaps even supplant suture repair and warrant further exploration.
Reactivating PTEN to impair glioma stem cells by inhibiting cytosolic iron-sulfur assembly
Authors: Jianxing Yin, Xin Ge, Fangshu Ding, Liuguijie He, Keying Song, Zhumei Shi, Zehe Ge, Junxia Zhang, Jing Ji, Xiefeng Wang, Ningwei Zhao, Chuanjun Shu, Fan Lin, Qianghu Wang, Qigang Zhou, Yuandong Cao, Wentao Liu, Dan Ye, Jeremy N. Rich, Xiuxing Wang, Yongping You, Xu Qian
Journal: Science Translational Medicine (2024)

Glioblastoma, the most lethal primary brain tumor, harbors glioma stem cells (GSCs) that not only initiate and maintain malignant phenotypes but also enhance therapeutic resistance. Although frequently mutated in glioblastomas, the function and regulation of PTEN in PTEN-intact GSCs are unknown. Here, we found that PTEN directly interacted with MMS19 and competitively disrupted MMS19-based cytosolic iron-sulfur (Fe-S) cluster assembly (CIA) machinery in differentiated glioma cells. PTEN was specifically succinated at cysteine (C) 211 in GSCs compared with matched differentiated glioma cells. Isotope tracing coupled with mass spectrometry analysis confirmed that fumarate, generated by adenylosuccinate lyase (ADSL) in the de novo purine synthesis pathway that is highly activated in GSCs, promoted PTEN C211 succination. This modification abrogated the interaction between PTEN and MMS19, reactivating the CIA machinery pathway in GSCs. Functionally, inhibiting PTEN C211 succination by reexpressing a PTEN C211S mutant, depleting ADSL by shRNAs, or consuming fumarate by the US Food and Drug Administration–approved prescription drug N -acetylcysteine (NAC) impaired GSC maintenance. Reexpressing PTEN C211S or treating with NAC sensitized GSC-derived brain tumors to temozolomide and irradiation, the standard-of-care treatments for patients with glioblastoma, by slowing CIA machinery–mediated DNA damage repair. These findings reveal an immediately practicable strategy to target GSCs to treat glioblastoma by combination therapy with repurposed NAC.