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Article ; Online: Fixed Cell Immunofluorescence for Quantification of Hypoxia-Induced Changes in Histone Methylation.

Shakir, Dilem / Batie, Michael / Rocha, Sonia

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2675, Page(s) 261–269

Abstract: Hypoxia and its signalling pathway play a key role in human physiology and a variety of diseases. Alterations in histone methylation coordinate transcriptional responses to hypoxia. Here, we detail a fixed cell immunofluorescence method for quantifying ... ...

Abstract	Hypoxia and its signalling pathway play a key role in human physiology and a variety of diseases. Alterations in histone methylation coordinate transcriptional responses to hypoxia. Here, we detail a fixed cell immunofluorescence method for quantifying hypoxia-induced changes in histone methylation, exemplified by the measurement of H3K27me3.
MeSH term(s)	Humans ; Methylation ; Histones/metabolism ; Hypoxia/metabolism ; Protein Processing, Post-Translational ; Fluorescent Antibody Technique ; DNA Methylation
Chemical Substances	Histones
Language	English
Publishing date	2023-05-31
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3247-5_19
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Article ; Online: Discussion: Surgical Timing and Neurocognitive Development among Patients with Craniosynostosis: Analysis of Confounders.

Shakir, Sameer / Birgfeld, Craig B / Susarla, Srinivas M

Plastic and reconstructive surgery

2023 Volume 151, Issue 4, Page(s) 830–831

MeSH term(s)	Humans ; Craniosynostoses/complications ; Craniosynostoses/surgery ; Plastic Surgery Procedures
Language	English
Publishing date	2023-03-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	208012-6
ISSN	1529-4242 ; 0032-1052 ; 0096-8501
ISSN (online)	1529-4242
ISSN	0032-1052 ; 0096-8501
DOI	10.1097/PRS.0000000000010005
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Article ; Online: Effect of Epididymal Spermatozoa of Local Iraqi Goat on <i>in vitro</i> Fertilization and Evolution of Embryos.

Shakir Hammoud, S / Adil Jebur, M

Archives of Razi Institute

2022 Volume 77, Issue 2, Page(s) 641–646

Abstract: ... In vitro ... fertilization (IVF) has been considered one of the greatest improvements in livestock science and production. Epididymal spermatozoon is a valuable gamete source obtained from slaughtered animals, and it has great importance in livestock ... ...

Abstract	In vitro fertilization (IVF) has been considered one of the greatest improvements in livestock science and production. Epididymal spermatozoon is a valuable gamete source obtained from slaughtered animals, and it has great importance in livestock IVF. This study aimed to create caprine embryos in Baghdad using local Iraqi goats. Ovaries were obtained from 50 female local goats at the Al-shu'alah abattoir. The ovaries were transported to the laboratory in physiological saline solution at 38°C. After oocyte recovery from the mature antral follicle, the oocytes with grades A or B were used for in vitro maturation (IVM). Moreover, 10 testicles were obtained from slaughtered adult goats, and the sperm was recovered from the caudal epididymis. All the stage-specific culture mediums were incubated at 39°C with 5% CO<sub>2</sub> and 90% relative humidity. In this study, embryonic development on a 24-h basis was evaluated and in vitro culture media was replaced 50% of the volume every day for nine days with fresh media until an enlarged or hatched blastocyst appeared. The recorded data showed that the mean size of the large follicles was 6.23±1.34 mm, while the small follicles were in the mean size of 3.10±0.62. On the other hand, the results showed a significant increase in the oocyte recovery rate from the large size follicle (81.22%), compared to the small size follicle (62.67%). The recorded data showed that the total number of retrieved oocytes with grades A and B was 290 (79.5%) . The recorded data showed that 50.1% of these oocyte cohorts had reached metaphase II (145/290). Furthermore, 45.45% of the recovered oocytes by aspiration from large follicles were developed to the blastocyst stage, compared to 25% of recovered oocytes from the small follicles reaching the same developmental stage (blastocyst). On the other hand, the recorded data showed that the oocyte recovery method had a great influence on the oocyte competence regardless of the follicle size. The results revealed that the number of recovered oocytes by aspiration was greater than slicing. In conclusion, the results approved that the slicing method could be considered a safe and more efficient method in oocyte recovery from the slaughtered animals, compared to the aspiration method. On the other hand, according to the findings, the epididymal spermatozoa from local Iraqi goats are a reliable source of oocytes for IVF and in vitro conversion.
MeSH term(s)	Pregnancy ; Male ; Female ; Animals ; Goats ; Epididymis ; Saline Solution ; Carbon Dioxide ; Iraq ; Semen ; Fertilization in Vitro/veterinary ; Spermatozoa ; Culture Media
Chemical Substances	Saline Solution ; Carbon Dioxide (142M471B3J) ; Culture Media
Language	English
Publishing date	2022-04-30
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2555498-0
ISSN	2008-9872 ; 0365-3439
ISSN (online)	2008-9872
ISSN	0365-3439
DOI	10.22092/ARI.2022.357269.2008
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Article ; Online: Schistosoma mansoni excretory-secretory products induce protein kinase signalling, hyperkinesia, and stem cell proliferation in the opposite sex.

Shakir, Eman M N / Rinaldi, Gabriel / Kirk, Ruth S / Walker, Anthony J

Communications biology

2023 Volume 6, Issue 1, Page(s) 985

Abstract: Adult male and female schistosomes in copula dwell within human blood vessels and lay eggs that cause the major Neglected Tropical Disease human schistosomiasis. How males and females communicate to each other is poorly understood; however, male-female ... ...

Abstract	Adult male and female schistosomes in copula dwell within human blood vessels and lay eggs that cause the major Neglected Tropical Disease human schistosomiasis. How males and females communicate to each other is poorly understood; however, male-female physical interaction is known to be important. Here, we investigate whether excretory-secretory products (ESPs), released into the external milieu by mature Schistosoma mansoni, might induce responses in the opposite sex. We demonstrate that ESPs adhere to the surface of opposite sex worms inducing the activation of extracellular signal-regulated kinase (ERK) and p38 mitogen-activated protein kinase (p38 MAPK) pathways, particularly in the parasite tegument. Furthermore, we show that mature worms stimulated signalling in juvenile worms. Strikingly, we demonstrate that ESPs from the opposite sex promote stem cell proliferation, in an ERK- and p38 MAPK-dependent manner, in the tegument and within the testes of males, and the ovaries and vitellaria of females. Hyperkinesia also occurs following opposite sex ESP exposure. Our findings support the hypothesis that male and female schistosomes may communicate over distance to modulate key processes underlying worm development and disease progression, opening unique avenues for schistosomiasis control.
MeSH term(s)	Adult ; Humans ; Animals ; Female ; Male ; Schistosoma mansoni ; Hyperkinesis ; Signal Transduction ; Biological Transport ; Extracellular Signal-Regulated MAP Kinases ; Cell Proliferation
Chemical Substances	Extracellular Signal-Regulated MAP Kinases (EC 2.7.11.24)
Language	English
Publishing date	2023-09-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05333-9
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Article ; Online: Seize the Opportunity: Increasing the HIV Screening Rate in Adolescents Presenting to a Community Pediatric Emergency Department.

Shakir, Rashida M / Doshi, Samir / Blakeslee, Samantha / Jessee, Morgan

Pediatric emergency care

2023 Volume 39, Issue 10, Page(s) 801–806

Abstract: Objectives: Our objective was to increase human immunodeficiency virus (HIV) screening in adolescents presenting to our community pediatric emergency department with symptoms suggestive of a sexually transmitted infection (STI) and who were being tested ...

Abstract	Objectives: Our objective was to increase human immunodeficiency virus (HIV) screening in adolescents presenting to our community pediatric emergency department with symptoms suggestive of a sexually transmitted infection (STI) and who were being tested for gonorrhea and chlamydia. Specifically, we aimed to increase the monthly average proportion of adolescents concurrently screened for HIV in this target group from 11% to 50% in 6 months. Methods: We identified barriers to HIV screening, focusing on physician-related challenges and adolescents' concerns about confidentiality. We designed interventions targeting these barriers and implemented them in plan-do-study-act cycles beginning in February 2020. We educated physicians and nurses about screening recommendations, emphasized a physician-conducted private interview during which confidential contact information could be obtained, and assured confidentiality on after visit summaries by removing STI results. We also provided regular feedback to physicians on the screening rate. In addition, we implemented an electronic health record quick order set and a documentation tool. Using a statistical process control chart, we measured the average monthly proportion of adolescents in the target group who were offered HIV screening or tested for HIV before and after interventions. Results: A total of 140 adolescents in the target group presented to our pediatric emergency department from February 2020 through December 2021. After plan-do-study-act cycles, the average monthly screening rate increased to 80%. Conclusions: Raising physician awareness of HIV screening recommendations and the importance of conducting a private interview improved screening rates. Assuring adolescent minors of confidentiality in a private interview, removing STI results from the after visit summary, and obtaining confidential contact information were important measures to overcome confidentiality barriers.
MeSH term(s)	Child ; Humans ; Adolescent ; Mass Screening/methods ; Sexually Transmitted Diseases/diagnosis ; Sexually Transmitted Diseases/epidemiology ; Gonorrhea/diagnosis ; Emergency Service, Hospital ; HIV Infections/diagnosis ; HIV Infections/epidemiology ; Chlamydia Infections/diagnosis
Language	English
Publishing date	2023-09-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	632588-9
ISSN	1535-1815 ; 0749-5161
ISSN (online)	1535-1815
ISSN	0749-5161
DOI	10.1097/PEC.0000000000003044
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Article: Multiple intussusceptions secondary to Peutz-Jegher's syndrome in an adult male: a case report from Pakistan.

Masood, Waniyah / Ahmed, Raheel / Fazlani, Faizan Ahmed / Shakir, Shaheryar / Al Hasibuzzaman, Md

Journal of surgical case reports

2024 Volume 2024, Issue 1, Page(s) rjae008

Abstract: Intussusception is a medical condition characterized by invagination of the intestinal segment, causing obstruction and leading to potential complications such as ischemia, necrosis and perforation. While paediatric intussusception is well documented ... ...

Abstract	Intussusception is a medical condition characterized by invagination of the intestinal segment, causing obstruction and leading to potential complications such as ischemia, necrosis and perforation. While paediatric intussusception is well documented with a peak in ages between 4 and 36 months, adult intussusception is a rare condition usually involving a lead point. In this article, we present an uncommon case of an adult male with worsening of his long-standing lower abdominal pain for the last 2 months. Radiological test reports revealed target-like lesions demonstrating two intestinal intussusceptions, for which he underwent a small bowel anastomosis, exploratory laprotomy and resection. On receiving the histopathology report, hamartomatous polyps with features favouring Peutz-Jegher's syndrome were identified as a possible lead point.
Language	English
Publishing date	2024-01-30
Publishing country	England
Document type	Case Reports
ZDB-ID	2580919-2
ISSN	2042-8812
ISSN	2042-8812
DOI	10.1093/jscr/rjae008
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Article ; Online: Does gender disparity exist in neurosurgery training? Evidence from a nationwide survey from Pakistan.

Shakir, Muhammad / Irshad, Hammad Atif / Altaf, Ahmed / Ladak, Shamila / Aziz, Hafiza Fatima / Enam, Syed Ather

Medical education online

2024 Volume 29, Issue 1, Page(s) 2310385

Abstract: Gender disparities are prevalent in the neurosurgical field, particularly for female trainees, despite the growing demand for neurosurgeons. The situation is bleaker in low-and middle-income countries, where gender disparities among neurosurgical ... ...

Abstract	Gender disparities are prevalent in the neurosurgical field, particularly for female trainees, despite the growing demand for neurosurgeons. The situation is bleaker in low-and middle-income countries, where gender disparities among neurosurgical trainees have not been evaluated. We aimed to gauge the gender differences in opportunities and perceptions of neurosurgery training in Pakistan by comparing responses between males and females. A nationwide web-based survey was conducted in Pakistan, covering 22 College of Physicians and Surgeons of Pakistan (CPSP) accredited neurosurgery training programs. Convenience sampling was used with a pilot-tested questionnaire. Data analysis was performed using SPSS version 26. A total of 120 trainees participated in our survey. The mean age of the participants was 30.4 ± 4.1 years, with 29.2% females and 70.8% males. Concerns about gender equity were more among females (34.3%) than males (27.1%). Poor work-life balance was reported by more females (34.3%) than males (30.6%). Burnout due to working hours was strongly agreed by more females (54.3%) than males (35.3%). More females (40%) acknowledged sufficient mentorship opportunities versus males (25%). Female respondents (65.7%) worked 50-100 hours per week, less than males (69.4%). Satisfaction with surgical exposure was lower among females (2.9%) compared to males (18.8%). More females reported access to teaching courses (82.9% vs. 77.6% males) and neurosurgical conferences (85.7% vs. 80.0% males), cadaver workshops (17.1% vs. 12.9% males), morbidity and mortality meetings (88.6% vs. 82.4% males), case-based sessions (82.9% vs. 75.3% males), and radiology discussions (82.9% vs. 74.1% males). Our study highlights substantial gender gaps in neurosurgical training, concerns over working hours, burnout, mentorship, work-life balance, and gender equity. These findings underscore the necessity for interventions to rectify these disparities and foster gender equity in neurosurgical training.
MeSH term(s)	Male ; Humans ; Female ; Adult ; Neurosurgery/education ; Pakistan ; Neurosurgeons ; Surveys and Questionnaires ; Burnout, Professional
Language	English
Publishing date	2024-01-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2052877-2
ISSN	1087-2981 ; 1087-2981
ISSN (online)	1087-2981
ISSN	1087-2981
DOI	10.1080/10872981.2024.2310385
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Article ; Online: Pediatric Panfacial Fractures.

Shakir, Sameer / Ettinger, Russell E / Susarla, Srinivas M / Birgfeld, Craig B

Oral and maxillofacial surgery clinics of North America

2023 Volume 35, Issue 4, Page(s) 607–617

Abstract: Pediatric panfacial trauma is a rare occurrence with poorly understood implications for the growing child. Treatment algorithms largely mirror adult panfacial protocols with notable exceptions including augmented healing and remodeling capacities that ... ...

Abstract	Pediatric panfacial trauma is a rare occurrence with poorly understood implications for the growing child. Treatment algorithms largely mirror adult panfacial protocols with notable exceptions including augmented healing and remodeling capacities that favor nonoperative management, limited exposure to avoid disruption of osseous suture and synchondroses growth centers, and creative fracture fixation techniques in the setting of an immature craniomaxillofacial skeleton. The following article provides a review of our institutional philosophy in the management of these challenges injuries with important anatomic, epidemiologic, examination, sequencing, and postoperative considerations.
MeSH term(s)	Adult ; Child ; Humans ; Facial Bones/surgery ; Facial Bones/injuries ; Fracture Fixation/methods ; Skull Fractures/diagnosis ; Skull Fractures/surgery
Language	English
Publishing date	2023-06-05
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1316546-x
ISSN	1558-1365 ; 1042-3699
ISSN (online)	1558-1365
ISSN	1042-3699
DOI	10.1016/j.coms.2023.04.006
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Article ; Online: Atypical Femur Fracture Unmasking Follicular Thyroid Cancer in a 54-year-old Woman.

Hatfield, Jennifer S / Bonneau, Peter N / Shakir, Mohamed K M / Hoang, Thanh D

AACE clinical case reports

2023 Volume 9, Issue 6, Page(s) 213–215

Language	English
Publishing date	2023-08-03
Publishing country	United States
Document type	Journal Article
ISSN	2376-0605
ISSN (online)	2376-0605
DOI	10.1016/j.aace.2023.07.005
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Article ; Online: Regulation of chromatin accessibility by hypoxia and HIF.

Batie, Michael / Frost, Julianty / Shakir, Dilem / Rocha, Sonia

The Biochemical journal

2022 Volume 479, Issue 6, Page(s) 767–786

Abstract: Reduced oxygen availability (hypoxia) can act as a signalling cue in physiological processes such as development, but also in pathological conditions such as cancer or ischaemic disease. As such, understanding how cells and organisms respond to hypoxia ... ...

Abstract	Reduced oxygen availability (hypoxia) can act as a signalling cue in physiological processes such as development, but also in pathological conditions such as cancer or ischaemic disease. As such, understanding how cells and organisms respond to hypoxia is of great importance. The family of transcription factors called Hypoxia Inducible Factors (HIFs) co-ordinate a transcriptional programme required for survival and adaptation to hypoxia. However, the effects of HIF on chromatin accessibility are currently unclear. Here, using genome wide mapping of chromatin accessibility via ATAC-seq, we find hypoxia induces loci specific changes in chromatin accessibility are enriched at a subset hypoxia transcriptionally responsive genes, agreeing with previous data using other models. We show for the first time that hypoxia inducible changes in chromatin accessibility across the genome are predominantly HIF dependent, rapidly reversible upon reoxygenation and partially mimicked by HIF-α stabilisation independent of molecular dioxygenase inhibition. This work demonstrates that HIF is central to chromatin accessibility alterations in hypoxia, and has implications for our understanding of gene expression regulation by hypoxia and HIF.
MeSH term(s)	Cell Hypoxia/genetics ; Chromatin/genetics ; Gene Expression Regulation ; Humans ; Hypoxia/genetics ; Hypoxia/metabolism ; Hypoxia-Inducible Factor 1, alpha Subunit/genetics ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; Oxygen/metabolism
Chemical Substances	Chromatin ; Hypoxia-Inducible Factor 1, alpha Subunit ; Oxygen (S88TT14065)
Language	English
Publishing date	2022-03-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BCJ20220008
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